SLC38A7

Chr 16

solute carrier family 38 member 7

Also known as: SNAT7

NCBI Gene: 55238ENSG00000103042UniProt: Q9NVC3

The protein functions as a lysosomal membrane symporter that cotransports sodium ions with L-glutamine and L-asparagine from the lysosome into the cytoplasm, requiring an acidic lysosomal lumen and potentially participating in mTORC1 activation. Based on the provided data, the gene appears tolerant to loss-of-function variants with predicted gain-of-function mechanism of pathogenicity, though no specific associated diseases are documented in the provided information.

Summary from RefSeq, UniProt, Mechanism
0
Active trials
4
Pubs (1 yr)
23
P/LP submissions
0%
P/LP missense
0.82
LOEUF
GOF
Mechanism· predicted
Clinical Summary— SLC38A7
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
22 unique Pathogenic / Likely Pathogenic· 56 VUS of 89 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.82LOEUF
pLI 0.000
Z-score 2.20
OE 0.50 (0.31–0.82)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.00Z-score
OE missense 0.83 (0.74–0.93)
228 obs / 274.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.50 (0.31–0.82)
0≤0.351.4
Missense OE0.83 (0.74–0.93)
0≤0.61.4
Synonymous OE0.95
0≤1.21.6
LoF obs/exp: 11 / 22.2Missense obs/exp: 228 / 274.7Syn Z: 0.40
DN
0.7130th %ile
GOF
0.82top 10%
LOF
0.1994th %ile

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.

GOFprediction above median
DNprediction above median

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

89 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic19
Likely Pathogenic3
VUS56
Benign3
19
Pathogenic
3
Likely Pathogenic
56
VUS
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
19
0
19
Likely Pathogenic
0
0
3
0
3
VUS
0
49
7
0
56
Likely Benign
0
0
0
0
0
Benign
0
2
0
1
3
Total05129181

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

View in ClinVar →

Protein Context — Lollipop Plot

SLC38A7 · 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
Open Research Assistant →
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 2 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