SLC38A2
Basic information
Region (hg38): 12:46358188-46372773
Links
Phenotypes
GenCC
Source:
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 SLC38A2 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 | 2 | |||||
missense | 25 | 27 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 25 | 3 | 1 |
Variants in SLC38A2
This is a list of pathogenic ClinVar variants found in the SLC38A2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
12-46361166-C-G | not specified | Uncertain significance (Oct 25, 2024) | ||
12-46362331-T-C | not specified | Uncertain significance (Oct 26, 2022) | ||
12-46362364-T-C | not specified | Uncertain significance (Aug 02, 2021) | ||
12-46362379-C-A | not specified | Uncertain significance (Jul 30, 2024) | ||
12-46363074-G-A | not specified | Uncertain significance (Feb 13, 2025) | ||
12-46363080-T-C | not specified | Uncertain significance (May 30, 2024) | ||
12-46363746-A-G | not specified | Uncertain significance (Apr 25, 2022) | ||
12-46363952-C-T | not specified | Likely benign (Jan 30, 2024) | ||
12-46364412-G-A | not specified | Uncertain significance (Aug 12, 2024) | ||
12-46364427-C-A | not specified | Uncertain significance (Apr 24, 2024) | ||
12-46364429-T-C | not specified | Uncertain significance (Jun 28, 2023) | ||
12-46364445-G-A | not specified | Uncertain significance (Jul 12, 2022) | ||
12-46364468-G-A | not specified | Uncertain significance (Sep 14, 2021) | ||
12-46364478-T-A | not specified | Uncertain significance (Feb 13, 2023) | ||
12-46364522-A-G | not specified | Uncertain significance (Jan 16, 2025) | ||
12-46365162-C-T | Benign (Aug 08, 2018) | |||
12-46366885-G-A | not specified | Likely benign (Feb 12, 2025) | ||
12-46366911-C-G | not specified | Uncertain significance (Feb 26, 2024) | ||
12-46366925-T-C | not specified | Uncertain significance (Apr 12, 2022) | ||
12-46366943-T-A | not specified | Uncertain significance (Jan 07, 2025) | ||
12-46367082-T-C | not specified | Uncertain significance (Jun 07, 2024) | ||
12-46367083-G-A | Benign/Likely benign (Mar 01, 2023) | |||
12-46367275-T-C | not specified | Uncertain significance (Jul 06, 2021) | ||
12-46367276-T-C | not specified | Uncertain significance (Dec 21, 2023) | ||
12-46370519-G-A | not specified | Uncertain significance (Mar 15, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SLC38A2 | protein_coding | protein_coding | ENST00000256689 | 15 | 14679 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.997 | 0.00291 | 125735 | 0 | 13 | 125748 | 0.0000517 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.797 | 227 | 263 | 0.862 | 0.0000127 | 3284 |
Missense in 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 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000107 | 0.000107 |
Ashkenazi Jewish | 0.000107 | 0.0000992 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000926 | 0.0000924 |
European (Non-Finnish) | 0.0000354 | 0.0000352 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000102 | 0.0000980 |
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 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}.;
- Pathway
- 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;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Endochondral Ossification;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;Histidine metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Aminosugars metabolism;Bile acid biosynthesis;Glycerophospholipid metabolism;EGFR1;Glutamate Neurotransmitter Release Cycle;Neurotransmitter release cycle;Transmission across Chemical Synapses;Glycine, serine, alanine and threonine metabolism
(Consensus)
Recessive Scores
- pRec
- 0.121
Intolerance Scores
- loftool
- 0.460
- rvis_EVS
- 0.13
- rvis_percentile_EVS
- 63.36
Haploinsufficiency Scores
- pHI
- 0.523
- hipred
- Y
- hipred_score
- 0.595
- ghis
- 0.461
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.773
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc38a2
- Phenotype
- limbs/digits/tail phenotype; skeleton phenotype; immune system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- amino acid transmembrane transport;sodium ion transport;amino acid transport;glutamine transport;female pregnancy;glutamate secretion;cerebral cortex development;glycine betaine transport;alanine transport;cellular response to amino acid starvation;cellular response to mechanical stimulus
- Cellular component
- plasma membrane;integral component of plasma membrane;brush border;axon;dendrite;sarcolemma;neuronal cell body
- Molecular function
- protein binding;amino acid transmembrane transporter activity;L-glutamine transmembrane transporter activity;symporter activity