SLC38A2
protein-codingsolute carrier family 38 member 2, the group of Solute carrier family 38
Gene summary
Enables neutral L-amino acid:sodium symporter activity. Involved in several processes, including cellular response to arsenite(3-); neutral amino acid transport; and positive regulation of RNA splicing. Located in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~14.6 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 SLC38A2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018976.5. 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 | 2 | |||
| missense | 46 | 5 | 51 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 49 | 6 | 1 | 56 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_061849.2 | 15 | MANE Select | |
| Ensembl | ENSP00000256689.5 | 15 | MANE Select | |
| RefSeq | NP_001294865.1 | 13 | Standard | |
| Ensembl | ENSP00000449695.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- GABAergic synapse - Homo sapiens (human)
- Glutamatergic synapse - Homo sapiens (human)
- Protein digestion and absorption - Homo sapiens (human)
- miR-targeted genes in epithelium - TarBase
- miR-targeted genes in lymphocytes - TarBase
Biological Process
- amino acid transmembrane transport
- sodium ion transport
- amino acid transport
- glutamine transport
- female pregnancy
Molecular Function
- protein binding
- amino acid transmembrane transporter activity
- L-glutamine transmembrane transporter activity
- symporter activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
- brush border
- axon
- dendrite
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000256689
- Coding exons
- 15
- Length
- 14679
- Individuals with no LoFs
- 125735
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 125748
- p
- 0.0000517
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.797 | 227 | 263 | 0.862 | 0.0000127 | 3284 |
| Missense (PolyPhen) | 65 | 92.678 | 0.70135 | 1147 | ||
| Synonymous | -0.807 | 106 | 95.9 | 1.10 | 0.00000488 | 971 |
| Loss of Function | 4.36 | 2 | 26.0 | 0.0770 | 0.00000110 | 364 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00011 | 0.000087 | rare |
| Ashkenazi Jewish | 0.00011 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.000035 | 0.000035 | rare |
| South Asian | 0.00010 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Functions as a sodium-dependent amino acid transporter. Mediates the saturable, pH-sensitive and electrogenic cotransport of neutral amino acids and sodium ions with a stoichiometry of 1:1. May function in the transport of amino acids at the blood- brain barrier and in the supply of maternal nutrients to the fetus through the placenta. {ECO:0000269|PubMed:10930503, ECO:0000269|PubMed:15922329}.;
Recessive Scores
- pRec
- 0.121
Intolerance Scores
- LoFtool
- 0.460
- RVIS EVS
- 0.13
- RVIS percentile EVS
- 63.36
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.773
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |