SLC38A2

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

Basic information

Region (hg38): 12:46358188-46372773

Links

ENSG00000134294 ∙ NCBI:54407 ∙ OMIM:605180 ∙ HGNC:13448 ∙ Uniprot:Q96QD8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	1	2
missense			25	2		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: gnomAD

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: 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

	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