SLC3A1

Chr 2ADAR

solute carrier family 3 member 1

Also known as: ATR1, CSNU1, D2H, NBAT, RBAT

NCBI Gene: 6519 ENSG00000138079 UniProt: Q07837 OMIM: 104614

This protein serves as a chaperone that facilitates the formation and trafficking of amino acid transporter complexes, particularly mediating renal reabsorption of cystine and dibasic amino acids in the proximal tubules. Mutations cause cystinuria, a disorder of amino acid transport that leads to kidney stone formation due to impaired cystine reabsorption. The condition shows both autosomal dominant and autosomal recessive inheritance patterns depending on the specific mutation.

GeneReviews OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a type II membrane glycoprotein which is one of the components of the renal amino acid transporter which transports neutral and basic amino acids in the renal tubule and intestinal tract. Mutations and deletions in this gene are associated with cystinuria. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

GeneReviews OMIM ResearchGenerating clinical summary…

AD/ARLOEUF 1.621 OMIM phenotype

Clinical Summary— SLC3A1

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Gene-Disease Validity (ClinGen)

cystinuria · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

166 unique Pathogenic / Likely Pathogenic· 361 VUS of 730 total submissions

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GeneReview available — SLC3A1

Authoritative clinical overview · Recommended first read

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.62LOEUF

pLI 0.000

Z-score -1.16

OE 1.23 (0.94–1.62)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-3.14Z-score

OE missense 1.45 (1.35–1.56)

559 obs / 385.4 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.23 (0.94–1.62)

0≤0.351.4

Missense OE?1.45 (1.35–1.56)

0≤0.61.4

Synonymous OE?1.25

0≤1.21.6

LoF obs/exp: 36 / 29.3Missense obs/exp: 559 / 385.4Syn Z: -2.34

ClinVar Variant Classifications

730 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic85

Likely Pathogenic81

VUS361

Likely Benign120

Benign35

Conflicting38

Pathogenic

Likely Pathogenic

361

VUS

120

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	45	8	31	1	85
Likely Pathogenic	39	36	6	0	81
VUS	3	319	29	10	361
Likely Benign	0	5	49	66	120
Benign	1	0	30	4	35
Conflicting	—				38
Total	88	368	145	81	720

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

38 pathogenic / likely-pathogenic (of 61) ClinVar copy-number / structural variants overlap SLC3A1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →