SLC38A2

solute carrier family 38 member 2, the group of Solute carrier family 38

Basic information

Region (hg38): 12:46358188-46372773

Links

ENSG00000134294NCBI:54407OMIM:605180HGNC:13448Uniprot:Q96QD8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC38A2 gene.

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
1
clinvar
1
clinvar
2
missense
25
clinvar
2
clinvar
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)3444319
12-46362331-T-C not specified Uncertain significance (Oct 26, 2022)2320236
12-46362364-T-C not specified Uncertain significance (Aug 02, 2021)2228795
12-46362379-C-A not specified Uncertain significance (Jul 30, 2024)3444320
12-46363074-G-A not specified Uncertain significance (Feb 13, 2025)3797695
12-46363080-T-C not specified Uncertain significance (May 30, 2024)3319703
12-46363746-A-G not specified Uncertain significance (Apr 25, 2022)2285966
12-46363952-C-T not specified Likely benign (Jan 30, 2024)3164567
12-46364412-G-A not specified Uncertain significance (Aug 12, 2024)3444321
12-46364427-C-A not specified Uncertain significance (Apr 24, 2024)3319705
12-46364429-T-C not specified Uncertain significance (Jun 28, 2023)2593130
12-46364445-G-A not specified Uncertain significance (Jul 12, 2022)2382670
12-46364468-G-A not specified Uncertain significance (Sep 14, 2021)2228180
12-46364478-T-A not specified Uncertain significance (Feb 13, 2023)2483053
12-46364522-A-G not specified Uncertain significance (Jan 16, 2025)3797696
12-46365162-C-T Benign (Aug 08, 2018)715519
12-46366885-G-A not specified Likely benign (Feb 12, 2025)3797694
12-46366911-C-G not specified Uncertain significance (Feb 26, 2024)3164565
12-46366925-T-C not specified Uncertain significance (Apr 12, 2022)2283260
12-46366943-T-A not specified Uncertain significance (Jan 07, 2025)3797697
12-46367082-T-C not specified Uncertain significance (Jun 07, 2024)3319706
12-46367083-G-A Benign/Likely benign (Mar 01, 2023)791632
12-46367275-T-C not specified Uncertain significance (Jul 06, 2021)2387195
12-46367276-T-C not specified Uncertain significance (Dec 21, 2023)3164564
12-46370519-G-A not specified Uncertain significance (Mar 15, 2024)3319704

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC38A2protein_codingprotein_codingENST00000256689 1514679
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9970.002911257350131257480.0000517
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7972272630.8620.00001273284
Missense in Polyphen6592.6780.701351147
Synonymous-0.80710695.91.100.00000488971
Loss of Function4.36226.00.07700.00000110364

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001070.000107
Ashkenazi Jewish0.0001070.0000992
East Asian0.000.00
Finnish0.00009260.0000924
European (Non-Finnish)0.00003540.0000352
Middle Eastern0.000.00
South Asian0.0001020.0000980
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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