SLC3A1

Chr 2ADAR

solute carrier family 3 member 1

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

NCBI Gene: 6519ENSG00000138079UniProt: Q07837

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]

Primary Disease Associations & Inheritance

CystinuriaMIM #220100
ADAR
UniProtHypotonia-cystinuria syndrome
0
Active trials
153
Pathogenic / LP
575
ClinVar variants
19
Pubs (1 yr)
-3.1
Missense Z
1.62
LOEUF
Clinical Summary— SLC3A1
🧬
Gene-Disease Validity (ClinGen)
cystinuria · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
153 Pathogenic / Likely Pathogenic· 290 VUS of 575 total submissions
📖
GeneReview available — SLC3A1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

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 OE1.23 (0.94–1.62)
0≤0.351.4
Missense OE1.45 (1.35–1.56)
0≤0.61.4
Synonymous OE1.25
0≤1.21.6
LoF obs/exp: 36 / 29.3Missense obs/exp: 559 / 385.4Syn Z: -2.34

ClinVar Variant Classifications

575 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic91
Likely Pathogenic62
VUS290
Likely Benign68
Benign31
Conflicting33
91
Pathogenic
62
Likely Pathogenic
290
VUS
68
Likely Benign
31
Benign
33
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
17
6
68
0
91
Likely Pathogenic
17
30
15
0
62
VUS
2
242
36
10
290
Likely Benign
0
4
30
34
68
Benign
1
0
27
3
31
Conflicting
—33
Total3728217647575

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

View in ClinVar →

SLC3A1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients