SLC36A1
protein-codingsolute carrier family 36 member 1, the group of Solute carrier family 36
Gene summary
This gene encodes a member of the eukaryote-specific amino acid/auxin permease (AAAP) 1 transporter family. The encoded protein functions as a proton-dependent, small amino acid transporter. This gene is clustered with related family members on chromosome 5q33.1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~55.3 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 SLC36A1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_078483.4. 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 | 1 | 1 | ||||
| missense | 60 | 5 | 1 | 66 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 61 | 5 | 2 | 68 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_510968.2 | 10 | MANE Select | |
| Ensembl | ENSP00000243389.3 | 10 | MANE Select | |
| RefSeq | NP_001295079.1 | 10 | Standard | |
| RefSeq | NP_001295080.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Protein digestion and absorption - Homo sapiens (human)
- Amino acid transport across the plasma membrane
- Amino acid and oligopeptide SLC transporters
- Transport of inorganic cations/anions and amino acids/oligopeptides
- SLC-mediated transmembrane transport
Biological Process
- amino acid transmembrane transport
- ion transport
- amino acid transport
- L-alanine transport
- glycine transport
Molecular Function
- amino acid:proton symporter activity
- proton transmembrane transporter activity
- amino acid transmembrane transporter activity
- L-alanine transmembrane transporter activity
- glycine transmembrane transporter activity
Cellular Component
- lysosomal membrane
- endoplasmic reticulum
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000243389
- Coding exons
- 10
- Length
- 55336
- Individuals with no LoFs
- 125672
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 76
- Defined
- 125748
- p
- 0.000302
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.38 | 220 | 286 | 0.770 | 0.0000164 | 3099 |
| Missense (PolyPhen) | 49 | 81.966 | 0.59781 | 988 | ||
| Synonymous | 0.0328 | 123 | 123 | 0.996 | 0.00000764 | 989 |
| Loss of Function | 1.92 | 13 | 22.9 | 0.567 | 0.00000133 | 230 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00056 | 0.00055 | rare |
| Latino/Admixed American | 0.00098 | 0.00098 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00060 | 0.00060 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00016 | 0.00016 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Neutral amino acid/proton symporter. Has a pH-dependent electrogenic transport activity for small amino acids such as glycine, alanine and proline. Besides small apolar L-amino acids, it also recognizes their D-enantiomers and selected amino acid derivatives such as gamma-aminobutyric acid (By similarity). {ECO:0000250, ECO:0000269|PubMed:12809675}.;
Recessive Scores
- pRec
- 0.149
Intolerance Scores
- LoFtool
- 0.656
- RVIS EVS
- -0.62
- RVIS percentile EVS
- 17.36
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.858
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |