SLC32A1

solute carrier family 32 member 1, the group of Solute carrier family 32

Basic information

Region (hg38): 20:38724486-38729372

Previous symbols: [ "VIAAT" ]

Links

ENSG00000101438 ∙ NCBI:140679 ∙ OMIM:616440 ∙ HGNC:11018 ∙ Uniprot:Q9H598 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• developmental and epileptic encephalopathy 114 (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Generalized epilepsy with febrile seizures plus, type 12; Developmental and epileptic encephalopathy 114	AD	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	34038384; 36073542

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC32A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC32A1 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
missense		3	43		1	47
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	3	44	1	1

Variants in SLC32A1

This is a list of pathogenic ClinVar variants found in the SLC32A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-38724778-C-G		Inborn genetic diseases	Uncertain significance (Oct 05, 2021)
20-38724788-G-A		Inborn genetic diseases	Uncertain significance (Dec 13, 2021)
20-38724801-G-T		Inborn genetic diseases	Uncertain significance (Oct 20, 2023)
20-38724805-G-A		Inborn genetic diseases	Uncertain significance (Jul 31, 2024)
20-38724840-A-G		Inborn genetic diseases	Uncertain significance (Jul 21, 2021)
20-38724851-G-T		Generalized epilepsy with febrile seizures plus	Uncertain significance (Jan 01, 2020)
20-38724868-C-A			Uncertain significance (Jan 31, 2024)
20-38724902-A-G			Uncertain significance (Sep 06, 2024)
20-38724903-T-G		Early infantile epileptic encephalopathy with suppression bursts	Uncertain significance (Sep 19, 2024)
20-38724933-G-A			Uncertain significance (Jan 26, 2023)
20-38724940-C-G		Inborn genetic diseases	Uncertain significance (Jun 16, 2024)
20-38724947-G-T		Inborn genetic diseases	Uncertain significance (Jul 20, 2022)
20-38724995-G-A		Seizure;Intellectual disability	Uncertain significance (Dec 10, 2021)
20-38724996-C-G			Likely pathogenic (Apr 11, 2024)
20-38725016-T-C			Uncertain significance (Apr 20, 2022)
20-38725020-A-G		Inborn genetic diseases	Uncertain significance (Apr 27, 2022)
20-38725026-A-T		Inborn genetic diseases	Uncertain significance (Jun 29, 2023)
20-38725057-C-G			Uncertain significance (Sep 01, 2024)
20-38725068-A-G		Inborn genetic diseases	Uncertain significance (Dec 25, 2024)
20-38725074-C-A			Uncertain significance (Sep 17, 2024)
20-38727453-G-T		Inborn genetic diseases	Uncertain significance (Oct 05, 2023)
20-38727471-T-C			Uncertain significance (Sep 26, 2024)
20-38727486-T-C			Uncertain significance (Apr 04, 2024)
20-38727563-G-T		Inborn genetic diseases	Uncertain significance (Aug 21, 2024)
20-38727602-C-A		SLC32A1-related epilepsy	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC32A1	protein_coding	protein_coding	ENST00000217420	2	4911

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.967	0.0332	125729	0	3	125732	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.30	188	300	0.626	0.0000141	3404
Missense in Polyphen		25	83.639	0.2989		997
Synonymous	-0.425	144	138	1.05	0.00000689	1111
Loss of Function	3.35	1	15.0	0.0668	6.55e-7	154

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000921	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the uptake of GABA and glycine into the synaptic vesicles. {ECO:0000250|UniProtKB:O35458}.
• Pathway: Benzodiazepine Pathway, Pharmacodynamics;Synaptic vesicle cycle - Homo sapiens (human);Retrograde endocannabinoid signaling - Homo sapiens (human);GABAergic synapse - Homo sapiens (human);Nicotine addiction - Homo sapiens (human);Morphine addiction - Homo sapiens (human);Synaptic Vesicle Pathway;GABA receptor Signaling;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;Pyrimidine metabolism;Histidine metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Bile acid biosynthesis;Porphyrin metabolism;GABA synthesis, release, reuptake and degradation;Neurotransmitter release cycle;Transmission across Chemical Synapses (Consensus)

Recessive Scores

• pRec: 0.169

Intolerance Scores

• loftool: 0.123
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.746
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.386

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Slc32a1
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype; muscle phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; embryo 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); normal phenotype; digestive/alimentary phenotype; 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)

Gene ontology

• Biological process: amino acid transmembrane transport;ion transport;neurotransmitter secretion;aging;gamma-aminobutyric acid transport;glycine transport;hippocampus development;neurotransmitter loading into synaptic vesicle
• Cellular component: plasma membrane;integral component of synaptic vesicle membrane;dendrite;synaptic vesicle membrane;neuron projection;dendrite terminus;neuron projection terminus;cone cell pedicle;presynaptic active zone;cell tip;inhibitory synapse;clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane;GABA-ergic synapse
• Molecular function: amino acid transmembrane transporter activity;glycine transmembrane transporter activity;gamma-aminobutyric acid:proton symporter activity