SLC15A1
protein-codingsolute carrier family 15 member 1, the group of Solute carrier family 15
Gene summary
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]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~68.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLC15A1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005073.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 3 | ||||
| missense | 92 | 9 | 1 | 102 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 96 | 9 | 4 | 109 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005064.1 | 23 | MANE Select | |
| Ensembl | ENSP00000365686.4 | 23 | MANE Select | |
| Ensembl | ENSP00000526834.1 | 21 | Standard | |
| Ensembl | ENSP00000526834.1 | 21 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Protein digestion and absorption - Homo sapiens (human)
- Statin Pathway - Generalized, Pharmacokinetics
- Fluvastatin Pathway, Pharmacokinetics
- Ibuprofen Pathway, Pharmacokinetics
- Proton/oligopeptide cotransporters
Biological Process
- ion transport
- protein transport
- dipeptide transmembrane transport
- proton transmembrane transport
Molecular Function
- proton-dependent oligopeptide secondary active transmembrane transporter activity
- peptide:proton symporter activity
- oligopeptide transmembrane transporter activity
- dipeptide transmembrane transporter activity
- peptide transmembrane transporter activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
- brush border
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000376503
- Coding exons
- 23
- Length
- 68854
- Individuals with no LoFs
- 125636
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 112
- Defined
- 125748
- p
- 0.000445
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0404 | 401 | 399 | 1.01 | 0.0000212 | 4682 |
| Missense (PolyPhen) | 91 | 95.895 | 0.94895 | 1143 | ||
| Synonymous | 0.634 | 145 | 155 | 0.935 | 0.00000976 | 1328 |
| Loss of Function | 2.13 | 26 | 40.6 | 0.640 | 0.00000203 | 462 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00053 | 0.00052 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.0020 | 0.0020 | notable |
| Finnish | 0.00028 | 0.00028 | rare |
| European (Non-Finnish) | 0.00031 | 0.00031 | rare |
| South Asian | 0.00036 | 0.00036 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Proton-coupled intake of oligopeptides of 2 to 4 amino acids with a preference for dipeptides. May constitute a major route for the absorption of protein digestion end-products.;
Recessive Scores
- pRec
- 0.196
Intolerance Scores
- LoFtool
- 0.883
- RVIS EVS
- 0.03
- RVIS percentile EVS
- 55.81
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.119
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |