SLC38A5
protein-codingsolute carrier family 38 member 5, the group of Solute carrier family 38
Gene summary
The protein encoded by this gene is a system N sodium-coupled amino acid transporter. The encoded protein transports glutamine, asparagine, histidine, serine, alanine, and glycine across the cell membrane, but does not transport charged amino acids, imino acids, or N-alkylated amino acids. Alternative splicing results in multiple transcript variants, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Aug 2013]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.7 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 SLC38A5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_033518.4. 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 | 4 | 2 | 6 | |||
| missense | 41 | 8 | 49 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 12 | 12 | ||||
| Total | 0 | 0 | 58 | 10 | 0 | 68 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_277053.2 | 15 | MANE Select | |
| Ensembl | ENSP00000481291.1 | 15 | MANE Select | |
| Ensembl | ENSP00000403976.1 | 9 | Standard | |
| Ensembl | ENSP00000389644.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- GABAergic synapse - Homo sapiens (human)
- Glutaminolysis and Cancer
- miR-targeted genes in muscle cell - TarBase
- Amino acid transport across the plasma membrane
- Amino acid and oligopeptide SLC transporters
Biological Process
- amino acid transmembrane transport
- amino acid transport
- glycine transport
Molecular Function
- amino acid transmembrane transporter activity
- glycine transmembrane transporter activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000376876
- Coding exons
- 15
- Length
- 11725
- Individuals with no LoFs
- 124370
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 0
- Defined
- 124371
- p
- 0.00000402
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.44 | 91 | 184 | 0.494 | 0.0000147 | 3054 |
| Missense (PolyPhen) | 21 | 62.617 | 0.33537 | 1177 | ||
| Synonymous | 0.295 | 73 | 76.3 | 0.957 | 0.00000651 | 962 |
| Loss of Function | 3.47 | 1 | 16.0 | 0.0627 | 0.00000116 | 286 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000012 | 0.0000089 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Functions as a sodium-dependent amino acid transporter which countertransport protons. Mediates the saturable, pH- sensitive, and electrogenic cotransport of several neutral amino acids including glycine, asparagine, alanine, serine, glutamine and histidine with sodium. {ECO:0000269|PubMed:11243884}.;
Recessive Scores
- pRec
- 0.242
Intolerance Scores
- RVIS EVS
- -0.36
- RVIS percentile EVS
- 28.93
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.266
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |