SLC38A1
solute carrier family 38 member 1, the group of Solute carrier family 38
Basic information
Region (hg38): 12:46183062-46270017
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC38A1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 0 | 1 |
Variants in SLC38A1
This is a list of pathogenic ClinVar variants found in the SLC38A1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-46188978-C-T | not specified | Uncertain significance (Dec 16, 2023) | ||
| 12-46188981-C-T | not specified | Uncertain significance (Feb 05, 2024) | ||
| 12-46197734-T-C | not specified | Uncertain significance (Aug 04, 2023) | ||
| 12-46197779-A-C | not specified | Uncertain significance (Jul 08, 2022) | ||
| 12-46198662-A-G | not specified | Uncertain significance (Feb 28, 2024) | ||
| 12-46201196-C-T | not specified | Uncertain significance (Dec 06, 2022) | ||
| 12-46204329-G-A | not specified | Uncertain significance (Mar 11, 2022) | ||
| 12-46204384-C-A | not specified | Uncertain significance (Jun 17, 2024) | ||
| 12-46206102-A-C | Benign (Jul 16, 2018) | |||
| 12-46206143-G-A | not specified | Uncertain significance (Jun 24, 2022) | ||
| 12-46206161-C-T | not specified | Uncertain significance (Jun 21, 2022) | ||
| 12-46207565-C-T | not specified | Uncertain significance (Jun 27, 2022) | ||
| 12-46207591-T-G | not specified | Uncertain significance (Aug 21, 2023) | ||
| 12-46229247-C-T | not specified | Uncertain significance (Apr 19, 2023) | ||
| 12-46229623-G-A | not specified | Uncertain significance (May 22, 2023) | ||
| 12-46239793-T-G | not specified | Uncertain significance (Nov 28, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC38A1 | protein_coding | protein_coding | ENST00000398637 | 15 | 86955 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.931 | 0.0693 | 124754 | 0 | 6 | 124760 | 0.0000240 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.15 | 168 | 267 | 0.630 | 0.0000139 | 3188 |
| Missense in Polyphen | 42 | 102.48 | 0.40983 | 1285 | ||
| Synonymous | 0.365 | 96 | 101 | 0.954 | 0.00000584 | 921 |
| Loss of Function | 4.01 | 4 | 26.1 | 0.153 | 0.00000128 | 338 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000652 | 0.0000646 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000446 | 0.0000442 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Functions as a sodium-dependent amino acid transporter. Mediates the saturable, pH-sensitive and electrogenic cotransport of glutamine and sodium ions with a stoichiometry of 1:1. May also transport small zwitterionic and aliphatic amino acids with a lower affinity. May supply glutamatergic and GABAergic neurons with glutamine which is required for the synthesis of the neurotransmitters glutamate and GABA. {ECO:0000269|PubMed:10891391}.;
- Pathway
- GABAergic synapse - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);Astrocytic Glutamate-Glutamine Uptake And Metabolism;miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Synaptic Vesicle Pathway;Biopterin metabolism;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;Transport of small molecules;Neuronal System;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Valine, leucine and isoleucine degradation;Aminosugars metabolism;Bile acid biosynthesis;Glycerophospholipid metabolism;Neurotransmitter uptake and metabolism In glial cells;Transmission across Chemical Synapses;Glycine, serine, alanine and threonine metabolism
(Consensus)
Recessive Scores
- pRec
- 0.148
Intolerance Scores
- loftool
- 0.175
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 27.88
Haploinsufficiency Scores
- pHI
- 0.569
- hipred
- Y
- hipred_score
- 0.768
- ghis
- 0.607
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.523
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc38a1
- Phenotype
Gene ontology
- Biological process
- neurotransmitter uptake;amino acid transmembrane transport;sodium ion transport;amino acid transport;neutral amino acid transport;L-alpha-amino acid transmembrane transport
- Cellular component
- plasma membrane;integral component of plasma membrane;integral component of membrane;extracellular exosome
- Molecular function
- amino acid:sodium symporter activity;protein binding;amino acid transmembrane transporter activity;neutral amino acid transmembrane transporter activity;L-amino acid transmembrane transporter activity