S-Adenosylhomocysteine Hydrolase Deficiency: Disease Characteristics Report
Executive summary
S-adenosylhomocysteine hydrolase deficiency (SAHHD; AHCY deficiency) is an ultra-rare autosomal-recessive disorder of the methionine/transmethylation cycle caused by biallelic pathogenic variants in AHCY. Deficient enzyme activity impairs conversion of S-adenosylhomocysteine (SAH) to adenosine and homocysteine, producing marked SAH and S-adenosylmethionine (SAM) accumulation, hypermethioninemia, and widespread disturbance of methylation-dependent biology. The major affected systems are liver, skeletal muscle, and central nervous system. Severity ranges from fetal hydrops and fatal neonatal encephalomyopathy/liver failure to minimally symptomatic childhood disease and adult-onset myopathy, cirrhosis, and hepatocellular carcinoma (HCC). Only 16 affected individuals had been reported by September 2024, so frequencies, penetrance, prognosis, and treatment effects remain imprecise (pinto2024asymptomaticpediatricpresentation pages 1-2, pinto2024asymptomaticpediatricpresentation pages 7-7, pinto2024asymptomaticpediatricpresentation pages 2-2).
The most important recent development is recognition of a mild, probably underdiagnosed p.Arg49His phenotype in children of Pakistani/South Asian ancestry. In two 2024 cases, methionine restriction corrected hypermethioninemia and reversed mild white-matter abnormalities but did not normalize SAH, SAM, liver enzymes, or muscle biomarkers (pinto2024asymptomaticpediatricpresentation pages 1-2, pinto2024asymptomaticpediatricpresentation pages 9-10, pinto2024asymptomaticpediatricpresentation pages 2-3).
The following table provides a compact knowledge-base summary; the narrative below supplies qualifications and additional ontology annotations.
Table (click to expand)
| Knowledge-base field | Concise finding | Ontology / identifier suggestions | Key sources (year, DOI URL) | Evidence |
|---|---|---|---|---|
| Definition / inheritance | Ultra-rare autosomal recessive inborn error of methionine-cycle / transmethylation metabolism caused by biallelic AHCY variants, producing multisystem disease ranging from lethal neonatal encephalomyopathy/liver failure to mild or asymptomatic childhood presentations with later liver/muscle complications. | MONDO: not confidently confirmed here; OMIM AHCY gene/protein record reported as 180960 in literature, but disease-specific mapping uncertain; HPO disease grouping could include hypermethioninemia / myopathy / liver disease terms. | Pinto et al. 2024, https://doi.org/10.1002/jmd2.12449; Barić et al. 2017, https://doi.org/10.1007/s10545-016-9972-7 | (pinto2024asymptomaticpediatricpresentation pages 1-2, pinto2024asymptomaticpediatricpresentation pages 2-2) |
| Gene / protein | AHCY encodes S-adenosylhomocysteine hydrolase (also SAHH; adenosylhomocysteinase), the key mammalian enzyme clearing SAH. | HGNC symbol: AHCY; protein name: S-adenosylhomocysteine hydrolase / adenosylhomocysteinase. | Stender et al. 2015, https://doi.org/10.1016/j.ymgme.2015.10.009; Vizán et al. 2021, https://doi.org/10.3389/fcell.2021.654344 | (stender2015adultonsetliverdisease pages 5-6, vizan2021functionalandpathological pages 4-5) |
| Enzyme reaction | Catalyzes hydrolysis of S-adenosylhomocysteine (SAH) to adenosine + homocysteine; reduced activity causes SAH accumulation, impaired methyltransferase flux, and disturbed SAM/SAH balance. Residual activity reported around 3%–20% of normal in affected individuals. | GO suggestion: adenosylhomocysteinase activity; CHEBI suggestions: SAH, adenosine, homocysteine, SAM, methionine. | Stender et al. 2015, https://doi.org/10.1016/j.ymgme.2015.10.009; Motzek et al. 2016, https://doi.org/10.1371/journal.pone.0151261 | (stender2015adultonsetliverdisease pages 6-8, motzek2016abnormalhypermethylationat pages 8-9) |
| Hallmark biomarkers | Core biochemical pattern: hypermethioninemia, markedly elevated SAH and SAM, mild hyperhomocysteinemia in some patients, elevated CK, elevated aminotransferases, and low enzyme activity. Example mild pediatric case: SAM 2426 nmol/L (ref 55–116), SAH 1408 nmol/L (ref 9–45). Example homozygous adult family data: SAH 3260 nmol/L, SAM 1930 nmol/L, methionine 528 μmol/L. | HPO suggestions: Hypermethioninemia, Elevated circulating S-adenosylhomocysteine, Elevated circulating S-adenosylmethionine, Elevated creatine kinase, Elevated hepatic transaminases. | Pinto et al. 2024, https://doi.org/10.1002/jmd2.12449; Stender et al. 2015, https://doi.org/10.1016/j.ymgme.2015.10.009; Barić et al. 2017, https://doi.org/10.1007/s10545-016-9972-7 | (pinto2024asymptomaticpediatricpresentation pages 4-4, stender2015adultonsetliverdisease pages 5-6) |
| Clinical spectrum | Frequent manifestations: neonatal/infantile hypotonia, developmental delay, myopathy, liver dysfunction/failure, coagulopathy, delayed myelination or leukodystrophy, absent reflexes, cognitive/language issues, and in long-term survivors cirrhosis/hepatocellular carcinoma. Severity is highly variable, including asymptomatic children with biochemical disease. | HPO suggestions: Hypotonia, Global developmental delay, Myopathy, Leukodystrophy, Delayed myelination, Hepatic failure, Coagulopathy, Hepatocellular carcinoma. | Pinto et al. 2024, https://doi.org/10.1002/jmd2.12449; Stender et al. 2015, https://doi.org/10.1016/j.ymgme.2015.10.009; Bas et al. 2020, https://doi.org/10.1002/ajmg.a.61489 | (pinto2024asymptomaticpediatricpresentation pages 1-2, stender2015adultonsetliverdisease pages 6-8) |
| Major organs / systems | Primary organ involvement: liver, skeletal muscle, central nervous system. Secondary/late complications include hepatic cirrhosis and hepatocellular carcinoma. | UBERON suggestions: liver, skeletal muscle tissue, brain, cerebral white matter; CL suggestions uncertain from current evidence. | Barić et al. 2017, https://doi.org/10.1007/s10545-016-9972-7; Ramadža et al. 2022, https://doi.org/10.3389/fped.2022.847445; Stender et al. 2015, https://doi.org/10.1016/j.ymgme.2015.10.009 | (stender2015adultonsetliverdisease pages 6-8, pinto2024asymptomaticpediatricpresentation pages 8-9) |
| Known reported variants | Reported disease-associated variants include p.Arg49His, p.Arg49Cys, p.Tyr143Cys, p.Trp112Ter, p.Asp86Gly, p.Gly71Ser, p.Tyr328Asp, p.Ala89Val, and newer presumed pathogenic variants p.Thr57Ile and p.Val217Met. Most are missense; at least one nonsense variant is reported. | Variant ontology IDs not asserted here; inheritance consistent with biallelic pathogenic / likely pathogenic germline variants. | Stender et al. 2015, https://doi.org/10.1016/j.ymgme.2015.10.009; Bas et al. 2020, https://doi.org/10.1002/ajmg.a.61489; Vugrek et al. 2009, https://doi.org/10.1002/humu.20985 | (stender2015adultonsetliverdisease pages 6-8, stender2015adultonsetliverdisease pages 16-16) |
| Epidemiology / patient count | Extremely rare; 2024 report states 16 patients reported globally. A mild South Asian / Pakistani p.Arg49His hotspot is suggested, with allele frequency cited in the report as about 1/15,300 in South Asia vs 1/83,400 globally; this should be treated as preliminary case-series/population-database interpretation rather than definitive prevalence. | Orphanet / MONDO IDs not confidently confirmed from current context; prevalence/incidence not established. | Pinto et al. 2024, https://doi.org/10.1002/jmd2.12449 | (pinto2024asymptomaticpediatricpresentation pages 7-7, pinto2024asymptomaticpediatricpresentation pages 2-2) |
| Diagnosis | Recommended workup for unexplained isolated hypermethioninemia or liver-muscle-neurologic syndrome: plasma amino acids plus SAM and SAH measurement, CK, liver enzymes, and molecular testing of AHCY (single gene, panel, exome/genome depending presentation). Differential diagnosis within inherited methylation disorders is important. Newborn screening is not currently recommended as a primary target based on consensus guidance. | HPO / lab ontology suggestions: Hypermethioninemia, Elevated SAM, Elevated SAH; ICD/MeSH not confidently confirmed. | Barić et al. 2017, https://doi.org/10.1007/s10545-016-9972-7; Pinto et al. 2024, https://doi.org/10.1002/jmd2.12449 | (pinto2024asymptomaticpediatricpresentation pages 1-2, pinto2024asymptomaticpediatricpresentation pages 2-3) |
| Treatment | Evidence is case-based. Main management: methionine-restricted diet (often with methionine-free amino acid formula). Adjuncts reported/considered: creatine, phosphatidylcholine, N-acetylcysteine. Biochemical and neurologic responses are variable; diet may lower methionine but often does not normalize SAH/SAM. Liver transplantation has been used in severe disease with reported biochemical and developmental improvement in at least one case. No approved gene/RNA/cell therapy and no disease-specific interventional trial identified from current search. | NCIT suggestions: Dietary modification, creatine supplementation, phosphatidylcholine supplementation, liver transplantation. | Barić et al. 2005, https://doi.org/10.1007/s10545-005-0192-9; Grubbs et al. 2010, https://doi.org/10.1007/s10545-010-9171-x; Barić et al. 2017, https://doi.org/10.1007/s10545-016-9972-7; Pinto et al. 2024, https://doi.org/10.1002/jmd2.12449 | (pinto2024asymptomaticpediatricpresentation pages 8-9, stender2015adultonsetliverdisease pages 6-8) |
| Prognosis | Prognosis is highly variable. Severe perinatal/infantile forms can be fatal within months; other patients survive into adulthood but remain at risk for progressive liver disease, myopathy, cognitive effects, and hepatocellular carcinoma. Long-term natural history remains poorly defined because of very small case numbers. | HPO suggestions: Early death, Liver cirrhosis, Hepatocellular carcinoma, Progressive myopathy. | Stender et al. 2015, https://doi.org/10.1016/j.ymgme.2015.10.009; Bas et al. 2020, https://doi.org/10.1002/ajmg.a.61489 | (stender2015adultonsetliverdisease pages 6-8, pinto2024asymptomaticpediatricpresentation pages 1-2) |
| Latest 2023–2024 developments | 2024: two asymptomatic Pakistani siblings expanded the mild phenotype and showed diet-reversible leukodystrophy, reinforcing concern for underdiagnosis and adult complications. 2023: AHCY knockdown RNA-seq/cell work linked deficiency to Wnt/LEF1-related transcriptional changes; C. elegans partial-deficiency model with human-corresponding variant supported altered SAM/SAH biology and longevity effects. These mechanistic findings are experimental and not yet validated clinically. | GO suggestions: Wnt signaling pathway, regulation of transcription, methylation-related processes; model-organism mappings only. | Pinto et al. 2024, https://doi.org/10.1002/jmd2.12449; Pavičić et al. 2023, https://doi.org/10.3390/ijms242216102; Thapa et al. 2023, https://doi.org/10.1038/s41514-023-00125-1 | (pinto2024asymptomaticpediatricpresentation pages 9-10, pinto2024asymptomaticpediatricpresentation pages 1-2) |
| Evidence gaps | No robust prevalence/incidence estimates; no controlled treatment trials; no validated genotype-specific management algorithm; penetrance and carrier frequency remain uncertain outside limited population-database observations; no established disease-specific QoL metrics; limited longitudinal biomarker-outcome correlation; no clearly documented natural disease in other species; disease identifiers across OMIM/Orphanet/MONDO require separate authoritative confirmation. | Flag as uncertain / absent data where noted. | Barić et al. 2017, https://doi.org/10.1007/s10545-016-9972-7; Pinto et al. 2024, https://doi.org/10.1002/jmd2.12449 | (pinto2024asymptomaticpediatricpresentation pages 1-2, pinto2024asymptomaticpediatricpresentation pages 8-9) |
Table: This table summarizes the most actionable disease-knowledge-base facts for S-adenosylhomocysteine hydrolase deficiency, including core biology, clinical features, diagnosis, treatment, and recent developments. It emphasizes evidence-backed details, ontology suggestions where confident, and explicit uncertainty where identifiers or data are not firmly established.
1. Disease information
Definition and names
Preferred name: S-adenosylhomocysteine hydrolase deficiency. Common alternatives are SAH hydrolase deficiency, SAHH deficiency, AHCY deficiency, adenosylhomocysteinase deficiency, and hypermethioninemia due to S-adenosylhomocysteine hydrolase deficiency. It is an inherited methylation disorder and Mendelian inborn error of methionine metabolism.
The 2024 clinical description states: “Its clinical spectrum spans from severe perinatal encephalomyopathy and liver failure to asymptomatic course in patients with isolated hypermethioninemia.” This is an appropriate concise disease definition (Pinto et al., published September 2024; DOI: https://doi.org/10.1002/jmd2.12449) (pinto2024asymptomaticpediatricpresentation pages 1-2).
Identifiers
- Causal gene: AHCY; the literature cites OMIM 180960 for AHCY. This appears to be the gene record rather than a confidently verified disease-entry number (stender2015adultonsetliverdisease pages 5-6).
- MONDO: a disease-specific MONDO identifier was not reliably recoverable from the evidence searched and should be verified directly in the current MONDO release before database ingestion.
- Orphanet: no identifier was reliably established from the retrieved primary literature.
- ICD-10/ICD-11: no dedicated code was identified; coding generally falls under other specified disorders of amino-acid metabolism/metabolism.
- MeSH: no disease-specific descriptor was verified; broader headings include Amino Acid Metabolism, Inborn Errors and Hypermethioninemia.
These findings are aggregated from disease-level literature and case reports, not EHR-derived individual-patient records.
2. Etiology, risk, and protective factors
The necessary cause is biallelic germline AHCY dysfunction. The inheritance pattern is autosomal recessive; heterozygous parents are typically clinically unaffected, although modest SAM/SAH elevations have been observed in carriers. Pathogenic alleles reduce enzyme abundance, stability, catalytic activity, or a combination thereof (stender2015adultonsetliverdisease pages 5-6, stender2015adultonsetliverdisease pages 6-8).
Reported alleles include p.Arg49His, p.Arg49Cys, p.Gly71Ser, p.Asp86Gly, p.Ala89Val, p.Trp112Ter, p.Tyr143Cys, p.Tyr328Asp, and the proposed disease-associated p.Thr57Ile/p.Val217Met compound-heterozygous genotype. Most are missense; p.Trp112Ter is nonsense. Published classifications predate or do not uniformly apply current ACMG/AMP criteria, so each variant should be re-evaluated in ClinVar/gnomAD using transcript-specific HGVS before clinical reporting (stender2015adultonsetliverdisease pages 6-8, stender2015adultonsetliverdisease pages 16-16).
The best-supported genotype–phenotype observation is that homozygous c.146G>A (p.Arg49His) can retain sufficient function to permit an asymptomatic or mild childhood course, although adult liver malignancy and myopathy have occurred in the same extended phenotype. Its reported frequency was approximately 1/15,300 in South Asians versus 1/83,400 globally, suggesting regional enrichment rather than a proven founder effect (pinto2024asymptomaticpediatricpresentation pages 7-7).
No environmental toxin, infection, sex, occupation, smoking, alcohol, or lifestyle exposure is known to cause the disorder. Dietary methionine is a burden modifier, not a cause: reducing intake may lower plasma methionine, while excessive restriction risks poor growth and essential-amino-acid deficiency. No validated protective allele, modifier gene, or gene–environment interaction has been demonstrated. Consanguinity and family history increase the probability of homozygosity but do not alter the biochemical mechanism.
3. Phenotypes
Because only 16 patients were known by 2024, percentages would be misleading. The following frequencies should be recorded qualitatively.
Table (click to expand)
| Phenotype | Type, onset, course, impact | Suggested HPO term |
|---|---|---|
| Hypermethioninemia | Laboratory hallmark; may be absent or less conspicuous in early infancy; chronic and diet-responsive | Hypermethioninemia |
| Elevated SAH and SAM | Most discriminating laboratory abnormality; often persists despite diet | Increased circulating SAH; increased circulating SAM |
| Hypotonia/weakness | Common in severe neonatal and infantile disease; may progress to proximal myopathy | HP:0001252 Hypotonia, muscular weakness |
| Myopathy/CK elevation | Early or subclinical childhood onset through adult progression; proximal/lower-limb predominance; impairs mobility | Myopathy; elevated serum CK |
| Developmental or cognitive impairment | Variable—severe global delay to isolated verbal-processing weakness or normal mainstream schooling | Global developmental delay; intellectual disability; language impairment |
| Delayed myelination/leukodystrophy | Infantile or subtle childhood MRI finding; at least one case was reversible after diet | Delayed myelination; leukodystrophy |
| Hepatic dysfunction | Elevated aminotransferases, synthetic dysfunction, coagulopathy, steatosis, chronic failure or cirrhosis | Elevated transaminases; hepatic failure; liver cirrhosis |
| Fetal hydrops/edema | Severe prenatal/neonatal presentations; associated with high early mortality | Hydrops fetalis; generalized edema |
| HCC | Late complication in adolescent/adult survivors; reported at ages 17 and 32 in one family | Hepatocellular carcinoma |
In the 2024 sibling report, one child had methionine 985 µmol/L (reference 10–60), ALT approximately sixfold above normal, reversible leukodystrophy, and persistently abnormal liver/muscle markers despite biochemical correction of methionine (pinto2024asymptomaticpediatricpresentation pages 2-3). Another had SAM 2,426 nmol/L (reference 55–116) and SAH 1,408 nmol/L (reference 9–45), mild white-matter disease, and low-average verbal reasoning while attending mainstream school (pinto2024asymptomaticpediatricpresentation pages 4-4).
Quality-of-life instruments such as EQ-5D, SF-36, or PROMIS have not been reported. Severe disease compromises feeding, mobility, communication, development, and survival; mild pediatric disease may have little apparent daily effect but requires burdensome diet and lifelong surveillance.
4. Genetic and molecular information
AHCY encodes the highly conserved, NAD-dependent tetrameric enzyme S-adenosylhomocysteine hydrolase. Reported patients have approximately 3–20% residual activity, consistent predominantly with partial loss of function; complete loss is probably incompatible with embryonic survival (stender2015adultonsetliverdisease pages 6-8, vizan2021functionalandpathological pages 4-5).
All established patient variants are constitutional/germline. There is no evidence that somatic AHCY variants cause SAHHD, nor is there evidence for dominant-negative or gain-of-function disease, chromosomal rearrangements, repeat expansions, mitochondrial variants, or recurrent copy-number abnormalities. No validated modifier gene is known.
Epigenetics
SAH is a potent product inhibitor of methyltransferases. Patient blood studies found global DNA hypermethylation in two of three examined patients and abnormal imprinting-control-region methylation in four of seven, but changes were neither universal nor uniform. A proposed explanation is differential methyltransferase sensitivity: under high SAH, DNMT1 activity fell approximately 30%, whereas PRMT7 activity fell approximately 90%; excess SAM may therefore sustain DNA methylation while protein/RNA methylation remains inhibited (motzek2016abnormalhypermethylationat pages 8-9).
The authors’ conclusion is appropriately cautious: DNA hypermethylation is “a frequent but not a constant feature” affecting genomic regions to different degrees (Motzek et al., March 2016; DOI: https://doi.org/10.1371/journal.pone.0151261) (motzek2016abnormalhypermethylationat pages 8-9).
No diagnostic episignature, validated transcriptomic biomarker, structural genomic signature, or clinically actionable modifier has been established.
5. Environmental, lifestyle, and infectious information
SAHHD is not infectious and has no zoonotic transmission. No causal toxin, radiation, pollution, occupational exposure, exercise pattern, smoking, or alcohol relationship has been demonstrated. Nutrition affects substrate flux: dietary protein/methionine can alter methionine concentrations but does not reliably correct the primary SAH clearance defect. Environmental “prevention” is therefore not applicable beyond medically supervised dietary management after diagnosis.
6. Mechanism and pathophysiology
Causal chain
- Upstream genetic trigger: biallelic AHCY hypomorphic/loss-of-function variants.
- Primary biochemical lesion: reduced hydrolysis of SAH to adenosine and homocysteine.
- Metabolite disturbance: profound SAH accumulation, elevated SAM, altered SAM:SAH methylation potential, and secondary hypermethioninemia. One reported homozygous case had SAH 3,260 nmol/L, SAM 1,930 nmol/L, and methionine 528 µmol/L (stender2015adultonsetliverdisease pages 5-6).
- Cellular consequences: inhibition or imbalance of DNA, RNA, histone, protein, phospholipid, and small-molecule methyltransferase reactions; altered chromatin and gene expression; probable impairment of creatine and phosphatidylcholine synthesis; and disturbed adenosine/homocysteine handling.
- Tissue injury: myocyte dysfunction and lipid replacement, abnormal myelination/white matter, hepatocellular steatosis and degeneration, synthetic liver failure, fibrosis/cirrhosis, and possibly carcinogenesis.
- Clinical manifestations: hypotonia/myopathy, CK elevation, neurodevelopmental disease, liver failure, and late HCC.
The enzyme reaction is reversible in vitro but is driven toward hydrolysis in vivo by rapid removal of adenosine and homocysteine. SAH elevation may exceed 100-fold in patients (motzek2016abnormalhypermethylationat pages 8-9).
Human mechanistic evidence
Human evidence directly supports metabolite accumulation, residual enzyme deficiency, altered methylation, delayed myelination, myopathy, and liver disease. The exact pathway from methylation disturbance to organ-selective injury remains unresolved. PRMT7 inhibition has been proposed as relevant to myelin-basic-protein methylation, but this is not proven to be the principal neurological mechanism (motzek2016abnormalhypermethylationat pages 8-9).
Recent molecular profiling
In 2023, AHCY knockdown in SW480 colorectal cells produced RNA-seq changes involving Wnt signaling, epithelial–mesenchymal transition, proliferation, and increased LEF1 RNA/protein. This establishes a cell-model link between AHCY depletion and Wnt/LEF1 regulation, not a demonstrated patient mechanism or indication that colorectal cancer is part of SAHHD (DOI: https://doi.org/10.3390/ijms242216102).
Additional experimental work suggests SAH can inhibit autophagy through an AHCYL1–PIK3C3 axis, but direct involvement in human SAHHD organ pathology remains unproven. Likewise, circadian, p53/senescence, and adenosine-depletion effects are biologically plausible but not validated clinical drivers (vizan2021functionalandpathological pages 4-5, vizan2021functionalandpathological pages 7-8).
Suggested GO annotations include S-adenosylhomocysteine hydrolase activity, methionine metabolic process, S-adenosylmethionine metabolic process, methylation, chromatin organization, regulation of Wnt signaling, myelination, skeletal-muscle development, and liver development. Candidate cell types are hepatocyte, skeletal muscle fiber/myocyte, oligodendrocyte, neuron, and glial cell; evidence is strongest for hepatocytes and muscle tissue, not for a uniquely targeted neural cell type.
7. Anatomical structures affected
- Primary: liver (UBERON: liver), skeletal muscle tissue, brain/cerebral white matter.
- Secondary: peripheral neuromuscular system and systemic coagulation through hepatic synthetic failure.
- Tissue findings: hepatic macrovesicular lipid droplets/steatosis; skeletal-muscle lipid infiltration and atrophy; delayed or abnormal cerebral myelination.
- Subcellular context: AHCY functions in cytosolic and nuclear/chromatin-associated methylation environments. Relevant GO cellular components include cytosol, nucleus, chromatin, and protein-containing complex.
- Lateralization: no characteristic unilateral or asymmetric pattern.
Skeletal-muscle MRI/MRS in three brothers aged 8, 11, and 13 years showed age-increasing lipid fraction, greatest in proximal lower-extremity muscles, supporting progressive subclinical muscle replacement and a role for MRI/MRS in longitudinal monitoring.
8. Temporal development and natural history
The disease may begin prenatally with hydrops, neonatally with hypotonia/encephalopathy/liver failure, in infancy with delayed motor development and myopathy, or remain clinically silent into childhood/adulthood. Severe infantile cases have died between approximately 3 and 12 months; intermediate cases develop chronic neuromuscular and liver disease; p.Arg49His homozygotes may remain minimally symptomatic for years before adult myopathy, cirrhosis, or HCC (stender2015adultonsetliverdisease pages 5-6, pinto2024asymptomaticpediatricpresentation pages 1-2, stender2015adultonsetliverdisease pages 6-8).
There is no validated staging system. A practical sequence is: biochemical/asymptomatic phase → neurologic, muscle, or hepatic manifestations → chronic progressive myopathy/cirrhosis → hepatic malignancy or organ failure. Course is chronic and lifelong rather than episodic. Treatment-induced biochemical improvement and white-matter reversal are possible, but spontaneous remission is not established (pinto2024asymptomaticpediatricpresentation pages 9-10).
Early childhood is probably an intervention window because myelination and muscle development are ongoing, but the evidence is a single/few cases rather than a controlled study.
9. Inheritance and population
Inheritance is autosomal recessive. For two confirmed carrier parents, recurrence risks per pregnancy are 25% affected, 50% heterozygous carrier, and 25% unaffected/non-carrier. Penetrance of severe biallelic variants appears high, but penetrance of mild alleles and age-dependent manifestations is unknown. Expressivity is markedly variable. Anticipation and germline mosaicism have not been reported.
No population prevalence or annual incidence can be calculated reliably. Sixteen published patients worldwide by 2024 indicates extreme rarity but also substantial underdiagnosis (pinto2024asymptomaticpediatricpresentation pages 7-7, pinto2024asymptomaticpediatricpresentation pages 2-2). Cases have been reported from Croatia, the United States, Czech Republic, Türkiye, and Pakistani/South Asian families. No sex predominance is established. Consanguinity has contributed to homozygous cases. Carrier frequency and a definitive founder haplotype are unknown.
10. Diagnostics
Recommended workflow
- Clinical suspicion: unexplained hypermethioninemia, hypotonia/myopathy, persistent CK elevation, liver dysfunction/coagulopathy, delayed myelination, or fetal hydrops.
- First-line chemistry: quantitative plasma amino acids, total homocysteine, liver panel, bilirubin, albumin, coagulation profile, CK, renal profile, glucose, and ammonia as clinically indicated.
- Discriminating metabolites: plasma SAH and SAM measured in an experienced biochemical-genetics laboratory. Isolated hypermethioninemia alone is nonspecific; SAM/SAH testing is central to distinguishing inherited methylation disorders (pinto2024asymptomaticpediatricpresentation pages 4-4, pinto2024asymptomaticpediatricpresentation pages 2-3).
- Confirmation: biallelic pathogenic/likely pathogenic AHCY variants plus compatible biochemistry; fibroblast, erythrocyte, or liver AHCY activity can provide functional confirmation where available.
- Baseline organ assessment: neurologic/developmental evaluation; brain MRI; CK and muscle examination, with muscle MRI/MRS if useful; liver ultrasound/elastography, synthetic function, and AFP/HCC surveillance; ECG/echocardiography when clinically indicated.
Single-gene sequencing with deletion/duplication analysis is appropriate when biochemistry is characteristic. A hypermethioninemia, liver-failure, neurometabolic, or myopathy panel is efficient for overlapping presentations. WES/WGS is useful for atypical neonatal disease or unresolved cases, as illustrated by novel-variant discovery, but biochemical confirmation remains important. CMA, karyotype, FISH, mtDNA testing, and repeat-expansion testing are not routine unless another diagnosis is suspected.
Differential diagnosis
Key alternatives are MAT1A-related methionine adenosyltransferase I/III deficiency, glycine N-methyltransferase deficiency, adenosine kinase deficiency, cystathionine beta-synthase deficiency, tyrosinemia, citrin deficiency, generalized liver failure, congenital disorders of glycosylation—especially PMM2-CDG—and primary neuromuscular/leukodystrophy disorders. SAH and SAM profiles, total homocysteine, liver phenotype, CK, and molecular testing distinguish these conditions. SAHHD can clinically resemble PMM2-CDG (pinto2024asymptomaticpediatricpresentation pages 1-2, pinto2024asymptomaticpediatricpresentation pages 2-2).
Consensus authors concluded that inherited methylation disorders did not qualify as primary biochemical newborn-screening targets, partly because hypermethioninemia may be absent early and treatment evidence is limited. Genomic newborn screening may eventually detect AHCY variants, but no disease-specific effectiveness data exist.
11. Outcomes and prognosis
No 5- or 10-year survival estimates, mortality rates, or life-expectancy tables exist. Prognosis is genotype- and severity-dependent. Severe neonatal disease may be fatal within months; a 2020 infant with compound-heterozygous p.Thr57Ile/p.Val217Met died at 3 months from cardiovascular collapse. Conversely, mild homozygous p.Arg49His patients may survive into adulthood (pinto2024asymptomaticpediatricpresentation pages 1-2, stender2015adultonsetliverdisease pages 6-8).
Major morbidity includes developmental disability, progressive proximal myopathy, chronic liver failure/cirrhosis, and HCC. HCC at ages 17 and 32 suggests that malignancy surveillance is justified in long-term survivors, although the absolute risk cannot be estimated (stender2015adultonsetliverdisease pages 6-8). Residual enzyme activity, genotype, baseline liver synthetic function, CK/muscle imaging, SAM/SAH concentrations, and response to diet are plausible prognostic markers, but none is validated.
12. Treatment and real-world implementation
Methionine restriction
A specialist metabolic diet—with natural-protein/methionine restriction and methionine-free amino-acid formula—is the principal disease-directed intervention. It may lower methionine and sometimes SAM/SAH and improve strength or brain MRI, but responses are inconsistent. In the 2024 children, intake was reduced to approximately 1.6 g protein/kg/day and 32 mg methionine/kg/day; methionine fell, while SAH/SAM and liver/muscle biomarkers remained abnormal (pinto2024asymptomaticpediatricpresentation pages 7-7, pinto2024asymptomaticpediatricpresentation pages 2-3).
Over-restriction is hazardous because methionine is essential for growth. Diet should therefore be individualized using growth, essential amino acids, methionine, SAH/SAM, liver function, CK, development, and imaging—not methionine concentration alone (pinto2024asymptomaticpediatricpresentation pages 8-9).
Supplements
Creatine and phosphatidylcholine have been used to bypass high methyl-demand biosynthetic pathways; N-acetylcysteine has been considered to support glutathione/oxidative-stress handling. Evidence consists of small uncontrolled case reports, and long-term benefit or adverse-event rates are unknown. The 2024 family declined these supplements because the children were asymptomatic and evidence was limited (pinto2024asymptomaticpediatricpresentation pages 8-9).
Liver transplantation
Transplantation replaces a major source of systemic AHCY activity. A severely affected child resistant to diet reportedly showed normalization of metabolites and improvement in growth, psychomotor, and cognitive outcomes after transplantation at approximately 40 months. It remains a high-risk, non-randomized intervention; indications in mild disease are unresolved, and extrahepatic muscle disease may not be fully corrected (stender2015adultonsetliverdisease pages 6-8, vizan2021functionalandpathological pages 7-8).
Supportive care and surveillance
Management should involve metabolic medicine, hepatology, neurology, dietetics, physiotherapy, occupational/speech therapy, developmental services, and genetic counseling. Treat coagulopathy, nutritional deficiency, seizures, feeding problems, and liver complications conventionally. Monitor growth, neurodevelopment, CK/strength, liver synthetic function, fibrosis, ultrasound and AFP; use brain and muscle MRI selectively.
Suggested NCIT intervention concepts are dietary therapy/methionine restriction, amino-acid formula, creatine supplementation, phosphatidylcholine supplementation, N-acetylcysteine, physical therapy, and liver transplantation. No approved gene replacement, CRISPR, RNA, cell, targeted small-molecule, or immunotherapy exists. The ClinicalTrials.gov search found no clearly disease-specific interventional trial; retrieved broad observational/newborn-screening records did not provide explicit AHCY-deficiency enrollment evidence.
13. Prevention
There is no lifestyle or vaccine-based primary prevention. Effective genetic prevention consists of carrier testing for relatives, reproductive counseling, partner testing, prenatal diagnosis, and preimplantation genetic testing when familial variants are known. Cascade testing can identify asymptomatic biallelic relatives before irreversible liver, muscle, or white-matter injury.
Secondary prevention is early biochemical/genetic diagnosis followed by monitored dietary intervention and organ surveillance. Tertiary prevention includes rehabilitation, avoidance of malnutrition, management of liver failure, and HCC surveillance. Population biochemical newborn screening is not currently recommended specifically for SAHHD; targeted testing is reasonable in affected families and populations in which p.Arg49His enrichment is confirmed.
14. Other species and natural disease
No naturally occurring veterinary syndrome confidently equivalent to human SAHHD was identified, and there is no zoonotic relevance. AHCY is evolutionarily conserved across eukaryotes, and complete loss is developmentally deleterious in several organisms. Suggested taxa for model annotation include Danio rerio (NCBI Taxon 7955), Mus musculus (10090), and Caenorhabditis elegans (6239). Ortholog identifiers should be retrieved directly from current NCBI Gene/Alliance releases before database ingestion.
15. Model organisms
- Zebrafish ahcy/ducttrip mutant: develops hepatic steatosis, TNF-dependent liver degeneration, and exocrine-pancreas/liver developmental abnormalities. It recapitulates liver injury and methionine-cycle disruption but not the full human neurodevelopmental/myopathy spectrum.
- Mouse Ahcy knockout: homozygous deletion is embryonic lethal before approximately E9.5, demonstrating essential developmental function but limiting its utility for postnatal disease; conditional/hypomorphic models are needed (vizan2021functionalandpathological pages 4-5).
- C. elegans partial deficiency: a 2023 knock-in AHCY-1 p.Tyr145Cys, corresponding to human p.Tyr143Cys, lowered SAM, moderately increased SAH, and extended lifespan through AMPK, VRK-1, and DAF-16. This is a useful methionine/aging model but does not reproduce human liver or muscle anatomy (DOI: https://doi.org/10.1038/s41514-023-00125-1).
- Cell models: patient-derived cells and AHCY-knockdown HEK293, HepG2, SW480, and mouse embryonic fibroblasts support studies of methylation, DNA damage, proliferation, Wnt/LEF1 signaling, and adenosine biology. Cancer-cell backgrounds and acute knockdown are important limitations (vizan2021functionalandpathological pages 4-5, vizan2021functionalandpathological pages 7-8).
No validated patient iPSC, organoid, single-cell, spatial-transcriptomic, or CRISPR therapeutic-screen platform was established in the retrieved disease-specific literature.
Current expert interpretation and evidence gaps
The authoritative consensus view is that SAHHD is a multisystem inherited methylation disorder in which SAH and SAM measurement is essential, methionine restriction is biologically rational but incompletely effective, and management must be individualized. The 2024 cases materially broaden this view: apparently well children may harbor severe biochemical abnormalities and subtle reversible brain disease, while adult relatives demonstrate potentially fatal delayed complications (pinto2024asymptomaticpediatricpresentation pages 1-2, pinto2024asymptomaticpediatricpresentation pages 9-10, pinto2024asymptomaticpediatricpresentation pages 2-2).
Principal unresolved questions are true prevalence, penetrance of p.Arg49His, complete variant-level ACMG classification, natural history, optimal methionine targets, benefit of creatine/phosphatidylcholine/N-acetylcysteine, transplantation timing, HCC risk, reliable pharmacodynamic biomarkers, quality of life, and feasibility of gene or mRNA replacement. No controlled trial, registry-scale cohort, validated clinical outcome assessment, or disease-specific multi-omics atlas is available.
Key cited publications and URLs
- Pinto PL et al. Asymptomatic pediatric presentation of S-adenosylhomocysteine hydrolase deficiency. JIMD Reports. Published September 2024. https://doi.org/10.1002/jmd2.12449 (pinto2024asymptomaticpediatricpresentation pages 1-2)
- Stender S et al. Adult-onset liver disease and hepatocellular carcinoma in S-adenosylhomocysteine hydrolase deficiency. Molecular Genetics and Metabolism. December 2015. https://doi.org/10.1016/j.ymgme.2015.10.009 (stender2015adultonsetliverdisease pages 5-6, stender2015adultonsetliverdisease pages 6-8)
- Motzek A et al. Abnormal hypermethylation at imprinting control regions in patients with AHCY deficiency. PLoS ONE. March 2016. https://doi.org/10.1371/journal.pone.0151261 (motzek2016abnormalhypermethylationat pages 8-9)
- Vizán P et al. Functional and pathological roles of AHCY. Frontiers in Cell and Developmental Biology. March 2021. https://doi.org/10.3389/fcell.2021.654344 (vizan2021functionalandpathological pages 4-5, vizan2021functionalandpathological pages 7-8)
PMIDs were not consistently present in the retrieved full-text metadata and therefore are not supplied where they could not be verified; DOI URLs are provided to avoid introducing incorrect identifiers.
References
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(pinto2024asymptomaticpediatricpresentation pages 1-2): Patrícia Lipari Pinto, Marjorie Dixon, Sniya Sudhakar, Ivo Baric, and Julien Baruteau. Asymptomatic pediatric presentation of s‐adenosylhomocysteine hydrolase deficiency. JIMD Reports, 65:371-381, Sep 2024. URL: https://doi.org/10.1002/jmd2.12449, doi:10.1002/jmd2.12449. This article has 2 citations and is from a peer-reviewed journal.
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(pinto2024asymptomaticpediatricpresentation pages 7-7): Patrícia Lipari Pinto, Marjorie Dixon, Sniya Sudhakar, Ivo Baric, and Julien Baruteau. Asymptomatic pediatric presentation of s‐adenosylhomocysteine hydrolase deficiency. JIMD Reports, 65:371-381, Sep 2024. URL: https://doi.org/10.1002/jmd2.12449, doi:10.1002/jmd2.12449. This article has 2 citations and is from a peer-reviewed journal.
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(pinto2024asymptomaticpediatricpresentation pages 2-2): Patrícia Lipari Pinto, Marjorie Dixon, Sniya Sudhakar, Ivo Baric, and Julien Baruteau. Asymptomatic pediatric presentation of s‐adenosylhomocysteine hydrolase deficiency. JIMD Reports, 65:371-381, Sep 2024. URL: https://doi.org/10.1002/jmd2.12449, doi:10.1002/jmd2.12449. This article has 2 citations and is from a peer-reviewed journal.
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(pinto2024asymptomaticpediatricpresentation pages 9-10): Patrícia Lipari Pinto, Marjorie Dixon, Sniya Sudhakar, Ivo Baric, and Julien Baruteau. Asymptomatic pediatric presentation of s‐adenosylhomocysteine hydrolase deficiency. JIMD Reports, 65:371-381, Sep 2024. URL: https://doi.org/10.1002/jmd2.12449, doi:10.1002/jmd2.12449. This article has 2 citations and is from a peer-reviewed journal.
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(pinto2024asymptomaticpediatricpresentation pages 2-3): Patrícia Lipari Pinto, Marjorie Dixon, Sniya Sudhakar, Ivo Baric, and Julien Baruteau. Asymptomatic pediatric presentation of s‐adenosylhomocysteine hydrolase deficiency. JIMD Reports, 65:371-381, Sep 2024. URL: https://doi.org/10.1002/jmd2.12449, doi:10.1002/jmd2.12449. This article has 2 citations and is from a peer-reviewed journal.
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(stender2015adultonsetliverdisease pages 5-6): Stefan Stender, Rima S. Chakrabarti, Chao Xing, Garrett Gotway, Jonathan C. Cohen, and Helen H. Hobbs. Adult-onset liver disease and hepatocellular carcinoma in s-adenosylhomocysteine hydrolase deficiency. Molecular genetics and metabolism, 116 4:269-74, Dec 2015. URL: https://doi.org/10.1016/j.ymgme.2015.10.009, doi:10.1016/j.ymgme.2015.10.009. This article has 52 citations and is from a peer-reviewed journal.
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(vizan2021functionalandpathological pages 4-5): Pedro Vizán, Luciano Di Croce, and Sergi Aranda. Functional and pathological roles of ahcy. Frontiers in Cell and Developmental Biology, Mar 2021. URL: https://doi.org/10.3389/fcell.2021.654344, doi:10.3389/fcell.2021.654344. This article has 119 citations.
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(stender2015adultonsetliverdisease pages 6-8): Stefan Stender, Rima S. Chakrabarti, Chao Xing, Garrett Gotway, Jonathan C. Cohen, and Helen H. Hobbs. Adult-onset liver disease and hepatocellular carcinoma in s-adenosylhomocysteine hydrolase deficiency. Molecular genetics and metabolism, 116 4:269-74, Dec 2015. URL: https://doi.org/10.1016/j.ymgme.2015.10.009, doi:10.1016/j.ymgme.2015.10.009. This article has 52 citations and is from a peer-reviewed journal.
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(motzek2016abnormalhypermethylationat pages 8-9): Antje Motzek, Jelena Knežević, Olivier J. Switzeny, Alexis Cooper, Ivo Barić, Robert Beluzić, Kevin A. Strauss, Erik G. Puffenberger, S. Harvey Mudd, Oliver Vugrek, and Ulrich Zechner. Abnormal hypermethylation at imprinting control regions in patients with s-adenosylhomocysteine hydrolase (ahcy) deficiency. PLoS ONE, 11:e0151261, Mar 2016. URL: https://doi.org/10.1371/journal.pone.0151261, doi:10.1371/journal.pone.0151261. This article has 19 citations and is from a peer-reviewed journal.
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(pinto2024asymptomaticpediatricpresentation pages 4-4): Patrícia Lipari Pinto, Marjorie Dixon, Sniya Sudhakar, Ivo Baric, and Julien Baruteau. Asymptomatic pediatric presentation of s‐adenosylhomocysteine hydrolase deficiency. JIMD Reports, 65:371-381, Sep 2024. URL: https://doi.org/10.1002/jmd2.12449, doi:10.1002/jmd2.12449. This article has 2 citations and is from a peer-reviewed journal.
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(pinto2024asymptomaticpediatricpresentation pages 8-9): Patrícia Lipari Pinto, Marjorie Dixon, Sniya Sudhakar, Ivo Baric, and Julien Baruteau. Asymptomatic pediatric presentation of s‐adenosylhomocysteine hydrolase deficiency. JIMD Reports, 65:371-381, Sep 2024. URL: https://doi.org/10.1002/jmd2.12449, doi:10.1002/jmd2.12449. This article has 2 citations and is from a peer-reviewed journal.
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(stender2015adultonsetliverdisease pages 16-16): Stefan Stender, Rima S. Chakrabarti, Chao Xing, Garrett Gotway, Jonathan C. Cohen, and Helen H. Hobbs. Adult-onset liver disease and hepatocellular carcinoma in s-adenosylhomocysteine hydrolase deficiency. Molecular genetics and metabolism, 116 4:269-74, Dec 2015. URL: https://doi.org/10.1016/j.ymgme.2015.10.009, doi:10.1016/j.ymgme.2015.10.009. This article has 52 citations and is from a peer-reviewed journal.
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(vizan2021functionalandpathological pages 7-8): Pedro Vizán, Luciano Di Croce, and Sergi Aranda. Functional and pathological roles of ahcy. Frontiers in Cell and Developmental Biology, Mar 2021. URL: https://doi.org/10.3389/fcell.2021.654344, doi:10.3389/fcell.2021.654344. This article has 119 citations.
Artifacts
Reference Validation
Checked with linkml-reference-validator 0.2.1.
Table (click to expand)
| Outcome | Count |
|---|---|
| References checked | 12 |
| Resolved | 12 |
| Unresolved (possible confabulation) | 0 |
| Unverifiable | 0 |
| References weighed for topical relevance | 12 |
| On topic | 5 |
| Off topic | 0 |
All extracted references resolved successfully.