SLC7A1

Chr 13

solute carrier family 7 member 1

Also known as: ATRC1, CAT-1, ERR, HCAT1, REC1L

NCBI Gene: 6541 ENSG00000139514 UniProt: P30825

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.

ResearchSummary from RefSeq, UniProt

Enables L-arginine transmembrane transporter activity; L-histidine transmembrane transporter activity; and L-lysine transmembrane transporter activity. Involved in carboxylic acid transport. Located in apical plasma membrane and basolateral plasma membrane. Part of protein-containing complex. Is active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.27

LOEUF· LoF intol.

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Dual constrained — LoF & missense intolerant

LoF Constraint?

0.27LOEUF

pLI 0.993

Z-score 4.12

OE 0.08 (0.03–0.27)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

3.30Z-score

OE missense 0.53 (0.47–0.59)

206 obs / 388.9 exp

Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?

LoF OE?0.08 (0.03–0.27)

0≤0.351.4

Missense OE?0.53 (0.47–0.59)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 2 / 23.6Missense obs/exp: 206 / 388.9Syn Z: 0.19

Background carrier burden — how many people carry a rare variant somewhere in SLC7A1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 150

554 rare PASS variants

Rare truncating (LoF)

1 in 21,000

19 rare PASS variants

Rare synonymous (reference)

1 in 84

361 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SLC7A1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 160	1 in 26,000
South Asian	~43k	1 in 110	1 in 2,200
Remaining (unassigned)	~30k	1 in 160	none seen
European (Finnish)	~27k	1 in 340	none seen
Admixed American	~22k	1 in 120	≈ 1 in 22,000
African / African American	~21k	1 in 140	≈ 1 in 17,000
East Asian	~20k	1 in 120	none seen
Ashkenazi Jewish	~13k	1 in 930	none seen
Middle Eastern	~2,884	1 in 160	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 11 coding exons well covered in gnomAD exomes and genomes.? see exons ↓