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

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.

• Developmental and epileptic encephalopathy 102 (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.

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						0
missense			29	2		31
nonsense	1		1			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	30	2	0

Variants in SLC38A3

This is a list of pathogenic ClinVar variants found in the SLC38A3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-50214206-G-A		Inborn genetic diseases	Uncertain significance (Jun 10, 2022)
3-50214228-T-C		Inborn genetic diseases	Uncertain significance (Jan 17, 2025)
3-50214261-G-A		Inborn genetic diseases	Uncertain significance (Oct 04, 2024)
3-50214418-C-T		Inborn genetic diseases	Uncertain significance (Oct 02, 2023)
3-50214419-G-A		Inborn genetic diseases	Uncertain significance (Aug 01, 2024)
3-50214656-G-T		Developmental and epileptic encephalopathy 102	Pathogenic (Feb 23, 2023)
3-50214678-T-C		Inborn genetic diseases	Uncertain significance (Mar 04, 2024)
3-50215544-G-A		Inborn genetic diseases	Uncertain significance (Jan 17, 2024)
3-50215574-G-A		Inborn genetic diseases	Uncertain significance (Feb 17, 2024)
3-50215580-T-C		Inborn genetic diseases	Uncertain significance (Oct 17, 2023)
3-50215615-A-G		Inborn genetic diseases	Uncertain significance (May 23, 2024)
3-50215808-G-A		Inborn genetic diseases	Uncertain significance (Jun 01, 2023)
3-50217258-A-G		Inborn genetic diseases	Uncertain significance (Jul 02, 2024)
3-50217312-G-A		Inborn genetic diseases	Uncertain significance (Dec 28, 2024)
3-50217435-G-A		Inborn genetic diseases	Uncertain significance (Feb 13, 2024)
3-50217469-T-C		Short stature	Uncertain significance (Nov 18, 2001)
3-50217697-G-A		Inborn genetic diseases	Uncertain significance (Feb 27, 2023)
3-50217725-A-G		Inborn genetic diseases	Uncertain significance (Dec 12, 2022)
3-50217760-G-C		Inborn genetic diseases	Uncertain significance (Sep 29, 2022)
3-50217787-G-A		Inborn genetic diseases	Uncertain significance (Dec 16, 2022)
3-50217791-C-T		Developmental and epileptic encephalopathy 102	Uncertain significance (Mar 18, 2024)
3-50217827-C-T		Inborn genetic diseases	Uncertain significance (Dec 12, 2022)
3-50217841-G-T		Developmental and epileptic encephalopathy 102	Pathogenic (May 25, 2022)
3-50217962-C-T		Inborn genetic diseases	Uncertain significance (Apr 08, 2022)
3-50218325-A-C		Inborn genetic diseases	Uncertain significance (Nov 29, 2023)

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

Essentials

• 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