SLC15A1

Chr 13

solute carrier family 15 member 1

Also known as: HPECT1, HPEPT1, PEPT1

NCBI Gene: 6564ENSG00000088386UniProt: P46059

This gene encodes an intestinal hydrogen peptide cotransporter that is a member of the solute carrier family 15. The encoded protein is localized to the brush border membrane of the intestinal epithelium and mediates the uptake of di- and tripeptides from the lumen into the enterocytes. This protein plays an important role in the uptake and digestion of dietary proteins. This protein also facilitates the absorption of numerous peptidomimetic drugs. [provided by RefSeq, Apr 2010]

Research Assistant →
0
Active trials
14
Pubs (1 yr)
89
P/LP submissions
0%
P/LP missense
0.89
LOEUF
DN
Mechanism· predicted
Clinical Summary— SLC15A1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
89 unique Pathogenic / Likely Pathogenic· 95 VUS of 213 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.89LOEUF
pLI 0.000
Z-score 2.13
OE 0.64 (0.47–0.89)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
-0.04Z-score
OE missense 1.01 (0.93–1.09)
401 obs / 398.7 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.64 (0.47–0.89)
0≤0.351.4
Missense OE1.01 (0.93–1.09)
0≤0.61.4
Synonymous OE0.94
0≤1.21.6
LoF obs/exp: 26 / 40.6Missense obs/exp: 401 / 398.7Syn Z: 0.63
DN
0.76top 25%
GOF
0.5660th %ile
LOF
0.2288th %ile

The highest-scoring mechanism for this gene is dominant-negative.

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

213 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic87
Likely Pathogenic2
VUS95
Likely Benign8
Benign5
87
Pathogenic
2
Likely Pathogenic
95
VUS
8
Likely Benign
5
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
87
0
87
Likely Pathogenic
0
0
2
0
2
VUS
0
91
4
0
95
Likely Benign
0
8
0
0
8
Benign
0
1
1
3
5
Total0100943197

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

View in ClinVar →

Protein Context — Lollipop Plot

SLC15A1 · 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.

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Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 4 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Susceptibility Loci in SLC15A1, UGT1A3, and CWC27 Genes Associated with Bladder Cancer in the Northeast Chinese Population.
Wu P et al.·Biomed Res Int
2022
Association of SLC15A1 polymorphisms with susceptibility to dyslipidaemia in a Chinese Han population.
Liu S et al.·J Clin Pharm Ther
2019
Indoxyl Sulfate Elevated Lnc-SLC15A1-1 Upregulating CXCL10/CXCL8 Expression in High-Glucose Endothelial Cells by Sponging MicroRNAs.
Huang YC et al.·Toxins (Basel)
2021
Combined inhibition of histone deacetylase and cytidine deaminase improves epigenetic potency of decitabine in colorectal adenocarcinomas.
Tang Z et al.·Clin Epigenetics
2023
Identification and validation of biomarkers related to mitochondria-associated endoplasmic reticulum membranes in type 2 diabetes mellitus using peripheral blood transcriptomics.
Li S et al.·Eur J Med Res
2025
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