SLC7A1
Chr 13solute carrier family 7 member 1
Also known as: ATRC1, CAT-1, ERR, HCAT1, REC1L
The protein functions as a high-affinity transporter for cationic amino acids including arginine, lysine, and ornithine across cell membranes in non-hepatic tissues. Mutations cause lysinuric protein intolerance, an autosomal recessive disorder affecting amino acid transport that typically presents in infancy with failure to thrive, protein aversion, and can involve multiple organ systems including lungs, kidneys, and immune system. The gene is highly constrained against loss-of-function mutations, indicating that such variants are likely to be pathogenic.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly LoF-intolerant (top ~10% of genes)
Highly missense-constrained (top ~0.1%)
This gene has evidence for multiple mechanisms of pathogenicity (loss-of-function and gain-of-function). The Badonyi & Marsh model scores gain-of-function highest among its predictions, but genomic evidence (constraint, ClinVar variant spectrum, and literature) most strongly supports loss-of-function (haploinsufficiency). Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.
ClinVar Variant Classifications
112 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 32 | 0 | 32 |
Likely Pathogenic | 0 | 0 | 3 | 0 | 3 |
VUS | 0 | 53 | 4 | 0 | 57 |
Likely Benign | 0 | 3 | 0 | 2 | 5 |
Benign | 0 | 1 | 0 | 5 | 6 |
| Total | 0 | 57 | 39 | 7 | 103 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
SLC7A1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools