SLC7A2
Chr 8solute carrier family 7 member 2
Also known as: ATRC2, CAT-2A, CAT-2B, CAT2, HCAT2, SLC7A2A, SLC7A2B
The protein functions as a cationic amino acid transporter responsible for cellular uptake of arginine, lysine, ornithine, and homoarginine across cell membranes. Mutations cause lysinuric protein intolerance, an autosomal recessive disorder characterized by defective transport of these amino acids leading to failure to thrive, hepatosplenomegaly, osteoporosis, and potential pulmonary complications. The gene is extremely intolerant to loss-of-function variants and has a GeneReviews entry reflecting its established clinical significance.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly tolerant — LoF variants common in population
Tolerant to missense variation
This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. 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.
ClinVar Variant Classifications
236 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 | 76 | 0 | 76 |
Likely Pathogenic | 0 | 0 | 4 | 0 | 4 |
VUS | 0 | 109 | 6 | 0 | 115 |
Likely Benign | 0 | 6 | 1 | 0 | 7 |
Benign | 0 | 5 | 3 | 5 | 13 |
| Total | 0 | 120 | 90 | 5 | 215 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
SLC7A2 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
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