IEMbase 0048: SLC3A1-related cystinuria type A
Scope
| Field | Value |
|---|---|
| IEMbase ID | 48 |
| Nosology | 1.11.04.01 |
| Gene | SLC3A1 |
| External IDs | OMIM:220100 |
| Generated mapping | MAPPED by identifier:OMIM:220100 |
| Candidate DisMech targets | Cystinuria.yaml |
| Review date | 2026-07-07 |
IEMbase phenotype signal
IEMbase represents this as autosomal recessive SLC3A1-related cystinuria type A. The listed prevalence is 1:7,000 and treatability is marked yes, although no specific treatment rows are present in the cached record.
The biochemical pattern is the expected COLA transporter profile: markedly increased urinary arginine, cystine, lysine, and ornithine from infancy onward, with low-to-normal plasma arginine, cystine, lysine, and ornithine. The characteristic clinical feature is cystine urolithiasis, strongest in adulthood. Additional clinical features include hematuria, obstructive uropathy, chronic renal failure, and urinary infections.
DisMech phenotype coverage
The generated mapping to Cystinuria.yaml is correct. The local entry models
cystinuria as an SLC3A1 or SLC7A9 proximal tubular cystine/dibasic amino acid
transport disorder and explicitly includes cystinuria type A as the SLC3A1/rBAT
subtype.
DisMech covers the SLC3A1 and SLC7A9 genetic causes, impaired b(0,+) cystine and dibasic amino acid transport, increased urinary cystine, arginine, lysine, and ornithine, cystine supersaturation, crystalluria, recurrent cystine nephrolithiasis, hematuria, recurrent urinary tract infections, renal insufficiency, hypertension, flank pain, nausea/vomiting, abnormal urinary odor, hypocitraturia, hypercalciuria, hyperuricosuria, stone composition and urinary cystine evaluation, and SLC3A1/SLC7A9 genetic testing.
DisMech is also much richer therapeutically: high fluid intake and dietary sodium/protein moderation, urinary alkalinization with potassium citrate, cystine-binding thiol drugs such as tiopronin or D-penicillamine, calculi removal for symptomatic or large stones, and investigational alpha-lipoic acid.
Concordance and completeness
Judgement: correct mapping and high concordance. If a subtype-level target is
available in downstream tooling, the best target is Cystinuria.yaml#Cystinuria
type A; otherwise the file-level mapping is acceptable because type A is
already represented inside the file.
IEMbase adds useful subtype-specific framing and plasma low-to-normal COLA amino acid values. DisMech adds the broader type A/type B structure, stone chemistry modifiers, diagnostic detail, chronic complication modeling, and treatment coverage.
Curation actions
- Keep the generated mapping to
Cystinuria.yaml. - Prefer subtype placement at
Cystinuria.yaml#Cystinuria type Aif the crosswalk later supports entity-level subtype anchors. - Consider adding IEMbase's plasma low-to-normal arginine/cystine/lysine/ ornithine detail if supported by citable evidence.
- Do not import an empty IEMbase treatment block over the richer DisMech management content.