Dyskeratosis Congenita, Autosomal Recessive 2 (DKCB2) — Research Report

MONDO:0013519 | OMIM #613987 | Gene: NHP2 (HGNC:14377, NCBI Gene 55651, chr5q35.3, NM_017838) | Also known as: NOLA2-related dyskeratosis congenita; DKCB2

Given your background, I'm skipping the general explanation of AR inheritance mechanics, penetrance/expressivity concepts, and mosaicism, and leading with the disease-specific claims and their sources. This is an ultra-rare entity — worldwide, published cases number in the single digits to low teens — so several template sections below have thin or no NHP2-specific literature; I've flagged those rather than padding with generic dyskeratosis congenita (DC) content that isn't gene-specific.

1. Disease Identity

DKCB2 is the biallelic-NHP2 subtype of dyskeratosis congenita / telomere biology disorder (DC/TBD). It was defined by Vulliamy et al. (PMID:18523010, PNAS 2008), who found compound-heterozygous or homozygous NHP2 variants in 2 of 117 DC patients screened, both Turkish [OMIM #613987]. It sits within the broader DC/TBD nosology alongside the AD forms (TERC, TERT, TINF2, RTEL1, PARN, ACD) and the other AR/XL forms (DKC1 X-linked; NOP10/DKCB1; WRAP53/TCAB1/DKCB3; biallelic RTEL1, PARN, ACD). GeneReviews treats DC and related TBDs as a single clinical spectrum ("Dyskeratosis Congenita and Related Telomere Biology Disorders," Savage & Niewisch, NBK22301) rather than splitting management guidance by causal gene — worth flagging for lump/split purposes: OMIM assigns NHP2 its own phenotypic MIM (613987/DKCB2), but clinical practice does not distinguish it from other AR-TBD forms except by molecular diagnosis.

• ICD-10: Q82.8 (Other specified congenital malformations of skin) — not gene-specific; DC/TBD as a class has no dedicated ICD-10/11 code.
• Orphanet: ORPHA:1775 covers dyskeratosis congenita generically; I did not find an NHP2-specific ORPHA subtype code in this pass — worth verifying directly against Orphadata XML before binding mappings.mondo_mappings/ORPHA in a KB entry.
• ClinGen gene-disease validity: NHP2–dyskeratosis congenita is classified Limited by the ClinGen Syndromic Disorders GCEP, "at the higher end of the Limited classification point range, likely to change classification with one or two additional studies" (ClinGen Syndromic Disorders GCEP curation, cf. PMC11601709/PMC12151239, 2024). This is a materially weaker validity tier than DKC1, TERT, or TINF2, and reflects the very small published case count — worth surfacing explicitly if this goes into a KB entry rather than treating gene-disease validity as settled.

Source basis: the disease-level facts above come from a structured database (OMIM, ClinGen) plus the two primary case-series/functional papers below (PMID:18523010; the 2023 HMG functional paper) — I have not independently verified every detail against the primary PDFs (PNAS and PMC fetches were blocked by 403/CAPTCHA in this session; abstracts below are reconstructed from search-engine snippets, not read in full), so treat quoted fragments as leads to re-verify against the primary text before using them as curation snippets.

2. Etiology

Causal factor: Biallelic (homozygous or compound-heterozygous) loss-of-function or hypomorphic missense variants in NHP2 (NOLA2). No environmental, infectious, or multifactorial contribution is described for this subtype — DC/TBD as a class is a monogenic telomere-maintenance disorder.

Reported variants (all missense to date, consistent with an essential gene where complete loss is likely non-viable or embryonic-lethal, by analogy to the core-complex partner genes):

Functional mechanism of the variants: V126M and Y139H "impaired association with NOP10, leading to major pre-RNP assembly defects with all H/ACA RNAs tested, including the H/ACA domain of hTR [TERC]" (search-derived summary of PMID:20008900, Trahan & Dragon, Hum Mol Genet 2010 — re-verify wording against primary text). A39T and T44M destabilize the NHP2 N-terminal domain via molecular-dynamics-demonstrated distortion of residues 33–41 (A39T) and residues 1–24 (T44M), driving proteasomal degradation of the mutant protein when competing with wild-type NHP2 for RNP incorporation, with consequent reduction in hTR levels and telomerase activity (2023 HMG paper, PMC10508036).

Risk/protective/gene-environment factors: No NHP2-specific modifier genes, environmental risk factors, or protective variants have been reported in the literature I could locate — this is a gap, not a documented absence, given how few cases exist to study. General TBD literature (not NHP2-specific) notes that even within families carrying an identical variant, disease severity varies considerably (per GeneReviews) — consistent with genetic-anticipation-type telomere-length inheritance effects seen across DC/TBD broadly, but this has not been specifically demonstrated for NHP2 pedigrees in the sources I found.

3. Phenotypes

The classic DC mucocutaneous triad plus multisystem stem-cell-exhaustion features, as reported for the ~4 published NHP2 patients (2 Vulliamy 2008; 1 index case in the 2023 HMG functional paper; a sibling pair in a 2025 case report, PMID:40352450, PMC12065628 — full text not retrievable in this session, only stub metadata confirmed).

Frequencies: with only ~4 published patients, no meaningful phenotype-frequency percentages can be derived for the NHP2 subtype specifically. The Y139H patient's phenotype (testicular atrophy, growth/intellectual impairment, intracranial calcification, opportunistic infection) is notably severe for an adult-diagnosed case (age 22) and approaches the Hoyeraal-Hreidarsson-syndrome end of the DC severity spectrum, though I did not find an explicit HH designation applied to this patient in the sources retrieved — flag rather than assert if curating.

QoL data: none specific to NHP2 located; general DC/TBD QoL literature was not pursued given the gene-level focus requested.

4. Genetic/Molecular Information

• Gene: NHP2 ribonucleoprotein (HGNC:14377; NCBI Gene 55651; chr5q35.3; aliases NOLA2, NHP2P, SPAG12, DKCB2).
• Variant classification: All reported variants are missense; ClinVar lists p.Val126Met (NM_017838.4:c.376G>A) as pathogenic for "Dyskeratosis congenita, autosomal recessive 2" (RCV000004502).
• Functional impact category: loss-of-function via protein destabilization/misfolding and impaired complex incorporation (not classic catalytic-site LOF) — PARTIAL_LOSS_OF_FUNCTION is likely the most accurate FunctionalImpactEnum value pending confirmation against the primary functional papers, since residual telomerase activity is reduced but not abolished in the biochemical assays described.
• Population frequency: no NHP2 pathogenic-variant carrier frequency or gnomAD allele-frequency data specific to these variants was retrieved in this pass — check gnomAD directly for p.Tyr139His/p.Val126Met/p.Ala39Thr/p.Thr44Met before citing a number.
• Somatic vs. germline: exclusively germline; DC/TBD is a constitutional disorder. (The secondary MDS/AML and squamous carcinomas that DC patients are predisposed to are separate somatic events arising in the germline-predisposed marrow/epithelium — keep these as distinct pathophysiology nodes/entries rather than folding them into the germline syndrome, consistent with design-decisions §3a.)
• Epigenetics/structural variation: none reported for this gene/subtype in the sources retrieved.

5. Environmental Information

No NHP2-specific environmental, lifestyle, or infectious contributory factors are reported. General DC/TBD clinical guidance (not NHP2-specific) advises avoiding additional telomere/marrow stressors (e.g., excess sun exposure given SCC risk, hepatotoxic exposures given fibrosis risk) but I did not find this stated as NHP2-specific literature — would need to be sourced from GeneReviews management sections rather than asserted as disease-specific etiology.

6. Mechanism / Pathophysiology

Causal chain (numbered), noting where each step is directly demonstrated vs. inferred:

1. Biallelic NHP2 missense variants (p.Tyr139His, p.Val126Met — PMID:18523010; p.Ala39Thr, p.Thr44Met — PMC10508036) destabilize the NHP2 protein or impair its N-terminal domain conformation. Demonstrated by molecular-dynamics simulation and cell-based degradation assays for A39T/T44M.
2. This leads to impaired NHP2–NOP10 association and reduced/defective incorporation of NHP2 into the core H/ACA ribonucleoprotein complex (dyskerin–NOP10–NHP2–GAR1), with mutant protein undergoing proteasome-dependent degradation when competing against wild-type. Demonstrated (PMID:20008900; PMC10508036).
3. This results in defective assembly of H/ACA snoRNPs generally and, specifically, of the H/ACA domain of TERC (the telomerase RNA component), which depends on this same core complex for stability. Demonstrated for V126M/Y139H (PMID:20008900).
4. This leads to reduced steady-state TERC (hTR) levels — "patients with NHP2 mutations, in common with patients bearing dyskerin and NOP10 mutations, had short telomeres and low TERC levels" (PMID:18523010, paraphrased from search snippet — re-verify exact wording against primary text before quoting as a KB snippet).
5. Reduced TERC availability results in diminished assembly and activity of the telomerase holoenzyme (telomerase reverse transcriptase + TERC + accessory H/ACA proteins). Demonstrated directly for A39T/T44M via reduced telomerase activity assays (PMC10508036).
6. Insufficient telomerase activity leads to progressive, division-coupled telomere shortening, most consequential in high-turnover stem/progenitor compartments (hematopoietic stem cells, epidermal/mucosal basal keratinocytes, germ cells, alveolar and hepatic progenitor populations). Inferred by extension from the general DC/TBD mechanism — telomere length was not independently measured in the NHP2 cohort beyond "short" per the cited source.
7. Critically short telomeres trigger a persistent DNA-damage response, replicative senescence, and apoptosis in affected stem/progenitor pools, causing tissue-specific stem-cell exhaustion. Inferred, extrapolated from the general DC/TBD literature rather than NHP2-specific data.
8. Stem-cell exhaustion manifests as: (a) hematopoietic stem cell attrition → progressive trilineage bone marrow failure (thrombocytopenia documented in the index case); (b) epithelial stem-cell attrition → nail dystrophy, mucosal leukoplakia, skin pigmentation changes; (c) hepatic/pulmonary progenitor attrition → organ fibrosis (liver cirrhosis documented in the Y139H patient); (d) germline stem-cell attrition → testicular atrophy (documented).
9. Branch — malignant transformation (distinct somatic process, not part of the germline mechanism above): chronic replicative stress and genomic instability in the exhausted, telomere-crisis-prone marrow and epithelium predisposes to acquisition of somatic driver mutations, manifesting as myelodysplastic syndrome (documented in the 2023 index case) and, by extension from general DC biology, squamous cell carcinoma and AML. This should be modeled as a separate somatic pathophysiology branch downstream of the germline telomere-maintenance defect, per the germline/somatic separation convention.

Second, less-established mechanistic thread — ribosome biogenesis: because NHP2/dyskerin/NOP10/GAR1 form the core machinery for essentially all box H/ACA snoRNPs (not only the telomerase-associated one), and box H/ACA snoRNPs guide pseudouridylation of ribosomal RNA, some literature frames DC as having a partial ribosomopathy component alongside the telomere defect. I did not find this explicitly demonstrated for the NHP2 subtype specifically in this pass (it is more thoroughly documented for DKC1-associated X-linked DC); flag as a plausible but unconfirmed-for-NHP2 mechanistic branch rather than asserting it.

Suggested GO terms: telomerase activity (GO:0003720), telomere maintenance via telomerase (GO:0007004), box H/ACA snoRNP assembly (GO:0031120), pseudouridine synthesis (GO:0001522), telomerase RNA stabilization (no precise GO term confirmed — verify via OAK before binding).

Suggested cell types (CL): hematopoietic stem cell (CL:0000037), epidermal keratinocyte (CL:0000312), basal cell of epidermis, hepatocyte/hepatic stellate cell (fibrosis), spermatogonial stem cell.

7. Anatomical Structures Affected

• Primary organs: bone marrow (UBERON:0002371), skin/nail unit (UBERON:0001003 epidermis; nail plate), oral mucosa (UBERON:0003729).
• Secondary/complication organs: liver (UBERON:0002107 — fibrosis/cirrhosis documented), lung (UBERON:0002048 — fibrosis reported generally for DC/TBD, not confirmed NHP2-specific here), testis (UBERON:0000473 — atrophy documented), CNS (intracranial calcification documented in one patient).
• Body systems: hematologic, integumentary, hepatic, reproductive (male), and — per general DC/TBD biology rather than NHP2-specific confirmation — respiratory and skeletal (osteoporosis).
• Subcellular: nucleolus (site of H/ACA snoRNP assembly), Cajal bodies (TCAB1/WRAP53-mediated telomerase trafficking — relevant to the pathway family though not NHP2 itself specifically), telomeres (chromosome ends).

8. Temporal Development

The Y139H patient presented at age 22 (Vulliamy 2008); the 2023 HMG index case presented in adulthood (age 38) with MDS and gastric cancer as the presenting/index features rather than classic pediatric mucocutaneous triad. This is notable: unlike the more common AD (TERT, TINF2) and X-linked (DKC1) forms, which often present in childhood, the published NHP2 cases skew toward later-childhood/adult presentation, though the n is far too small (~4 patients) to generalize a typical age-of-onset or progression pattern. No formal staging system exists for DC/TBD; general GeneReviews guidance frames it as a progressive, generally non-remitting stem-cell-exhaustion disorder with bone marrow failure as the dominant driver of mortality across the DC/TBD class as a whole.

9. Inheritance and Population

• Inheritance: autosomal recessive (biallelic NHP2 variants required); HP:0000007.
• Prevalence: DC/TBD overall is estimated at roughly 1:1,000,000; NHP2 pathogenic variants account for less than 1% of all dyskeratosis congenita cases (GeneReviews, NBK22301) — making DKCB2 one of the rarest molecularly defined DC subtypes. No NHP2-specific incidence/prevalence figure exists; prevalence_class: ULTRA_RARE / NOT_YET_DOCUMENTED with measure_type: CASES_IN_LITERATURE would be the honest framing for a KB entry given only ~4 published cases.
• Population/ancestry: the two founding cases were Turkish (Vulliamy 2008); no founder-effect or specific-population enrichment has been established from this small case count — a shared ancestry between the two original probands raises consanguinity as a plausible but unconfirmed factor (not stated explicitly as consanguineous in the retrieved abstract fragments — verify against full text).
• Sex ratio, geographic distribution: insufficient case count to characterize.
• Penetrance/expressivity: general DC/TBD literature (GeneReviews) states penetrance "varies considerably, even within families with identical variants" — this is a class-level statement, not one independently demonstrated for NHP2 pedigrees specifically in the sources found.

10. Diagnostics

• Primary diagnostic test (class-level, per GeneReviews, applies to NHP2 as to other DC/TBD genes): lymphocyte telomere length by flow-FISH, showing values below the 1st percentile for age, combined with either clinical diagnostic criteria or biallelic pathogenic NHP2 variants on molecular testing.
• Molecular testing: multigene DC/TBD panel or exome sequencing; "sequence analysis has detected pathogenic variants in all studied NHP2 families" (GeneReviews) — i.e., no large structural variants have been reported for this gene in the DC context.
• Laboratory: low TERC levels have been demonstrated biochemically in NHP2 patients specifically (PMID:18523010), which is a distinguishing molecular signature shared with DKC1- and NOP10-associated disease (all three encode core H/ACA RNP components) but not with TERT/TINF2/RTEL1-associated disease (where TERC itself is not depleted).
• Differential diagnosis: the other 8+ molecularly defined DC/TBD genes; Fanconi anemia (bone marrow failure + some overlapping congenital features — distinguish via chromosome breakage/DEB testing and telomere length, which is normal in FA); Hoyeraal-Hreidarsson syndrome (severe end of the DC/TBD spectrum — the Y139H patient's phenotype approaches this).
• Screening: no population or newborn screening program exists for DC/TBD; family cascade testing is appropriate once a proband's biallelic NHP2 variants are identified, given AR inheritance and the implied ~25% recurrence risk in future sibs of carrier parents.

11. Outcome/Prognosis

Insufficient NHP2-specific cohort data exists for survival statistics. Class-level DC/TBD data (GeneReviews) states bone marrow failure is the principal cause of mortality; solid-organ (pulmonary fibrosis, hepatic disease) and secondary-malignancy (MDS/AML, SCC) complications are the other major drivers of morbidity/mortality across DC/TBD broadly. Within the NHP2 case reports specifically: the 2023 index patient developed both MDS and gastric adenocarcinoma by age 38 — a data point consistent with, but not proof of, the general DC malignancy-predisposition pattern extending to this subtype.

12. Treatment

No NHP2-specific treatment trial or outcome data exists; management follows general DC/TBD guidance (GeneReviews):

• Hematopoietic cell transplantation (NCIT:C15431) — the only curative approach for bone marrow failure; DC/TBD patients require reduced-intensity/fludarabine-based conditioning given radiosensitivity and organ fragility (class-level guidance, not NHP2-specific confirmation found).
• Androgens (e.g., danazol, oxymetholone; NCIT:C15986 Pharmacotherapy + CHEBI therapeutic_agent) — used off-label to stimulate hematopoiesis when transplant is not immediately available/suitable, per class-level DC/TBD guidance.
• Supportive/surveillance care: per GeneReviews — annual CBC and marrow evaluation, monthly self skin/mucosal exams plus annual dermatology and otolaryngology exams (SCC surveillance), pulmonary function testing from ~age 8, semi-annual dental evaluation.
• Genetic counseling (NCIT:C15240) — appropriate given AR inheritance and availability of molecular carrier/prenatal testing once the familial variants are known.
• No gene therapy, RNA-based therapy, or targeted molecular therapy specific to NHP2/telomerase restoration has reached clinical trials for this subtype; I found no registered NCT trial specific to NHP2-DC in this pass (would need a direct ClinicalTrials.gov search restricted to "NHP2" or "dyskeratosis congenita" to confirm absence rather than asserting it from a general search).

13. Prevention

No primary prevention exists (germline monogenic disorder). Secondary prevention is carrier/prenatal testing and preimplantation genetic diagnosis once familial variants are identified, per standard AR-disorder genetic counseling practice — not NHP2-specific literature. Tertiary prevention is the surveillance program under Diagnostics/Treatment above (cancer screening, pulmonary monitoring) aimed at early detection of DC/TBD complications.

14. Other Species / Natural Disease

No naturally occurring NHP2-associated disease in non-human species was located in this search pass (no OMIA entry found for NHP2/DKCB2-equivalent veterinary disease). NHP2 is broadly conserved (ortholog present across vertebrates given its essential role in H/ACA snoRNP biology and ribosome synthesis), but disease-causing biallelic variants have only been reported in humans.

15. Model Organisms

• Mouse: Nhp2 (MGI:1098547), chromosome 11 (syntenic band 11B1.3), human ortholog confirmed. I did not find a published disease-modeling Nhp2 knockout/knock-in mouse paper specific to DC phenotype recapitulation in this search pass — this is a notable gap relative to the Terc−/−, Dkc1 hypomorphic, and Tinf2 mouse models that are well-characterized in the DC/TBD literature. Given Nhp2's essential role in ribosome biogenesis generally (not just telomerase), a complete knockout is plausibly embryonic lethal, which may explain why disease-modeling has favored patient-variant knock-in approaches or has simply not yet been published for this gene — this is my inference, not a sourced claim, and should be verified directly (e.g., via MGI phenotype records or IMPC) before use.
• Cellular models: patient-derived and engineered cell lines expressing mutant NHP2 (A39T, T44M) were used directly in the 2023 functional study (PMC10508036) to demonstrate reduced telomerase activity and hTR levels — this is the strongest "model system" evidence available for this subtype, though it is a cellular/in-vitro model rather than an organismal one, and fidelity to the whole-organism human phenotype (marrow failure, organ fibrosis) is not established by this data alone.

Summary of Confidence and Gaps

This is a genuinely thin literature — roughly 4 published patients across 3 papers spanning 2008–2025, and a ClinGen validity classification of only Limited. The strongest, most directly sourced claims are the gene identity, the specific variants, and the H/ACA RNP-assembly/TERC-depletion mechanism (PMID:18523010; PMID:20008900; PMC10508036). The weakest are anything requiring cohort-level statistics (prevalence, penetrance, age-of-onset distribution, treatment response rates) and the model-organism section, where I found no NHP2-specific animal model. Several PubMed/PMC/PNAS full-text fetches were blocked (403/CAPTCHA) in this session, so quoted fragments above are reconstructed from search-engine result snippets rather than read directly from primary text — before using any of these as a KB snippet:, re-fetch the primary source (just fetch-reference PMID:18523010 etc.) and re-verify the exact quoted substring.

Sources consulted: - OMIM #613987 — Dyskeratosis Congenita, Autosomal Recessive 2 - OMIM *606470 — NHP2 Ribonucleoprotein - PubMed 18523010 — Vulliamy et al., "Mutations in the telomerase component NHP2 cause the premature ageing syndrome dyskeratosis congenita," PNAS 2008 - PNAS full text (fetch blocked, HTTP 403) - PubMed 20008900 — Trahan & Dragon, "Effects of dyskeratosis congenita mutations in dyskerin, NHP2 and NOP10 on assembly of H/ACA pre-RNPs," Hum Mol Genet 2010 - PMC10508036 — "Novel pathological variants of NHP2 affect N-terminal domain flexibility, protein stability, H/ACA RNP complex formation and telomerase activity," Hum Mol Genet 2023 - PubMed 40352450 / PMC12065628 — "Siblings with a Homozygous Variant in the NHP2 Gene: A Case Report and Review of Literature," 2025 - GeneReviews NBK22301 — Savage & Niewisch, "Dyskeratosis Congenita and Related Telomere Biology Disorders" - ClinGen — NHP2 curation results (MONDO:0013519) - ClinGen Syndromic Disorders GCEP — 111 gene-disease relationships (PMC11601709/PMC12151239, 2024) - ClinVar RCV000004502 — NHP2 c.376G>A (p.Val126Met) - NIH GTR — Dyskeratosis congenita, autosomal recessive 2 - MGI — Nhp2 mouse gene detail (MGI:1098547) - GeneCards — NHP2 - Orphanet — Dyskeratosis congenita (ORPHA:1775)

Reference Validation

Checked with linkml-reference-validator 0.3.0rc1.

Quotes not found in the cited source

Searched the abstract, any retrieved full text, and the title. A quote drawn from a part of the paper that was not retrieved will appear here too, so check before treating one as invented:

Every one of these was searched against an abstract alone, with no full text retrieved - marked abstract only below. Where full text can be fetched, re-running with it will settle them; where the source publishes only a summary to PubMed, as GeneReviews chapters do, it will not, and the quote has to be checked by hand against the chapter itself.

• PMC:PMC11601709 (abstract only): "at the higher end of the Limited classification point range, likely to change classification with one or two additional studies"
• closest text in source: "A full review of 111 GDRs for 100 genes followed, with 78 classified as Definitive, 9 as Strong, 15 as Moderate, and 9 as Limited highlighting where further data are needed"
• PMC:PMC12151239 (abstract only): "at the higher end of the Limited classification point range, likely to change classification with one or two additional studies"
• closest text in source: "A full review of 111 GDRs for 100 genes followed, with 78 classified as Definitive, 9 as Strong, 15 as Moderate, and 9 as Limited, highlighting cases in which further data are needed"

Term Validation

Checked with linkml-term-validator 0.4.5, through the ols: adapter.

Terms the report names something else

These identifiers resolve, so nothing about them looks wrong, and the ontology calls them something unrelated to what the report calls them. That usually means the identifier is not the one the sentence needs:

• HP:0007441 (1 mention) - the report calls it "Reticulated/lacy skin hyperpigmentation"; HP calls it Hyperpigmented/hypopigmented macules
• HP:0012126 (1 mention) - the report calls it "neoplasm of stomach, approximate"; HP calls it Stomach cancer
• UBERON:0002107 (1 mention) - the report calls it "fibrosis/cirrhosis documented"; UBERON calls it liver
• UBERON:0002048 (1 mention) - the report calls it "fibrosis reported generally for DC/TBD, not confirmed NHP2-specific here"; UBERON calls it lung
• UBERON:0000473 (1 mention) - the report calls it "atrophy documented"; UBERON calls it testis

Terms whose name is worth a second look

The report's name for these is recognisably related to the term's own name without being one of them. A loose paraphrase reads the same way as a citation of the wrong sibling term - and so does a related synonym, which the ontology records precisely because it names something adjacent rather than the same thing - so these are listed rather than judged:

• HP:0005528 (1 mention) - the report calls it "Progressive bone marrow failure / aplastic anemia"; HP calls it Bone marrow hypocellularity, and lists "Bone marrow failure" among its other names
• HP:0002863 (1 mention) - the report calls it "Myelodysplastic syndrome"; HP calls it Myelodysplasia, and lists "Myelodysplastic syndrome" among its other names
• HP:0001394 (1 mention) - the report calls it "Hepatic fibrosis / cirrhosis"; HP calls it Cirrhosis, and lists "Hepatic cirrhosis" among its other names
• HP:0002514 (1 mention) - the report calls it "Intracranial calcification"; HP calls it Cerebral calcification
• HP:0002719 (1 mention) - the report calls it "Recurrent/opportunistic infection"; HP calls it Recurrent infections
• UBERON:0002371 (1 mention) - the report calls it "Primary organs: bone marrow"; UBERON calls it bone marrow**

Terms named inconsistently

The report gives these identifiers more than one name of its own:

• MGI:1098547 - called "Nhp2", "Mouse:* Nhp2"

Prefixes with no resolver

Terms carrying these prefixes were not checked either way, because no configured ontology covers them. An unrecognised prefix may name an ontology this run could not reach as easily as one that does not exist, so nothing here is evidence of fabrication: ORPHA, MGI.