SLC38A3

solute carrier family 38 member 3, the group of Solute carrier family 38

Basic information

Region (hg38): 3:50205246-50221486

Links

ENSG00000188338

∙ NCBI:10991 ∙ OMIM:604437 ∙ HGNC:18044 ∙ Uniprot:Q99624 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

developmental and epileptic encephalopathy 102 (Moderate), mode of inheritance: AR
developmental and epileptic encephalopathy 102 (Strong), mode of inheritance: AR
developmental and epileptic encephalopathy 102 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 102	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic; Ophthalmologic	34605855

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC38A3 gene.

Inborn_genetic_diseases (47 variants)
Developmental_and_epileptic_encephalopathy_102 (7 variants)
Short_stature (3 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC38A3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006841.6. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense	1 clinvar		49 clinvar	2 clinvar		52
nonsense	2 clinvar		1 clinvar			3
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)	1 clinvar					1
Total	5	0	50	2	0

Highest pathogenic variant AF is 0.000001373234

Loading clinvar variants...

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Function: FUNCTION: Sodium-dependent amino acid/proton antiporter. Mediates electrogenic cotransport of glutamine and sodium ions in exchange for protons. Also recognizes histidine, asparagine and alanine. May mediate amino acid transport in either direction under physiological conditions. May play a role in nitrogen metabolism and synaptic transmission. {ECO:0000250|UniProtKB:Q9JHZ9, ECO:0000269|PubMed:10823827}.;
Pathway: GABAergic synapse - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);Proximal tubule bicarbonate reclamation - Homo sapiens (human);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;Histidine metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Aminosugars metabolism;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

pRec: 0.182

Haploinsufficiency Scores

pHI: 0.693
hipred
hipred_score
ghis

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
gene_indispensability_pred: E
gene_indispensability_score: 0.731

Mouse Genome Informatics

Gene name: Slc38a3
Phenotype: homeostasis/metabolism phenotype; growth/size/body region 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process: amino acid transmembrane transport;sodium ion transport;amino acid transport;asparagine transport;glutamine transport;brain development;female pregnancy;L-alanine transport;histidine transport;cellular response to potassium ion starvation;positive regulation of transcription from RNA polymerase II promoter in response to acidic pH;L-histidine transmembrane transport;positive regulation of glutamine transport
Cellular component: plasma membrane;integral component of plasma membrane;basolateral plasma membrane
Molecular function: L-histidine transmembrane transporter activity;amino acid transmembrane transporter activity;L-alanine transmembrane transporter activity;L-asparagine transmembrane transporter activity;L-glutamine transmembrane transporter activity;symporter activity;antiporter activity