SLC6A13

solute carrier family 6 member 13, the group of Solute carrier family 6

Basic information

Region (hg38): 12:220620-262873

Links

ENSG00000010379 ∙ NCBI:6540 ∙ OMIM:615097 ∙ HGNC:11046 ∙ Uniprot:Q9NSD5 ∙ 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 SLC6A13 gene.

• Inborn genetic diseases (26 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC6A13 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	4	5
missense			27	1	1	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	27	2	5

Variants in SLC6A13

This is a list of pathogenic ClinVar variants found in the SLC6A13 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-221013-G-T		not specified	Uncertain significance (Aug 14, 2023)
12-221028-G-A		not specified	Uncertain significance (Feb 07, 2023)
12-221064-G-A		not specified	Uncertain significance (Sep 07, 2022)
12-221369-G-A			Benign (Mar 29, 2018)
12-221391-C-A		not specified	Uncertain significance (May 05, 2023)
12-221447-G-C		not specified	Uncertain significance (Jan 03, 2022)
12-221482-G-A		not specified	Uncertain significance (Feb 15, 2023)
12-222566-T-G		not specified	Uncertain significance (Nov 18, 2022)
12-222623-C-T			Uncertain significance (Mar 05, 2018)
12-223137-A-G		not specified	Uncertain significance (Aug 02, 2022)
12-223159-C-T		not specified	Uncertain significance (Jul 10, 2023)
12-223160-G-T		not specified	Uncertain significance (Nov 14, 2023)
12-223172-G-A			Benign (Jun 14, 2018)
12-223231-C-T		not specified	Uncertain significance (Jan 16, 2024)
12-224018-G-T		not specified	Uncertain significance (May 03, 2023)
12-224035-A-G		not specified	Uncertain significance (Mar 01, 2024)
12-224059-C-T			Benign (Aug 09, 2018)
12-224079-G-A			Benign (Mar 29, 2018)
12-224082-A-G			Benign (Aug 09, 2018)
12-224123-A-G		not specified	Uncertain significance (Oct 07, 2022)
12-224417-A-G		not specified	Uncertain significance (May 31, 2023)
12-224425-G-A			Likely benign (Nov 01, 2022)
12-224432-A-C		not specified	Uncertain significance (May 17, 2023)
12-224484-G-A		not specified	Uncertain significance (May 01, 2022)
12-226412-G-C			Benign (Jul 06, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC6A13	protein_coding	protein_coding	ENST00000343164	14	42251

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.22e-11	0.755	125659	1	88	125748	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0232	342	343	0.996	0.0000192	3889
Missense in Polyphen		144	155.75	0.92458		1790
Synonymous	-0.961	161	146	1.10	0.00000902	1200
Loss of Function	1.65	22	32.1	0.685	0.00000144	358

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000297	0.000297
Ashkenazi Jewish	0.000398	0.000397
East Asian	0.000383	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000304	0.000299
Middle Eastern	0.000383	0.000381
South Asian	0.00118	0.00114
Other	0.000186	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium-dependent GABA and taurine transporter. In presynaptic terminals, regulates GABA signaling termination through GABA uptake. May also be involved in beta-alanine transport. {ECO:0000269|PubMed:17502375, ECO:0000269|PubMed:22932902}.
• Pathway: Benzodiazepine Pathway, Pharmacodynamics;GABAergic synapse - Homo sapiens (human);Nuclear Receptors Meta-Pathway;NRF2 pathway;Amine compound SLC transporters;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Neuronal System;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Na+/Cl- dependent neurotransmitter transporters;Reuptake of GABA;GABA synthesis, release, reuptake and degradation;Neurotransmitter release cycle;Transmission across Chemical Synapses (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.724
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.89

Haploinsufficiency Scores

• pHI: 0.0845
• hipred: Y
• hipred_score: 0.528
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.173

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc6a13
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: gamma-aminobutyric acid transport;transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;neuron projection;extracellular exosome
• Molecular function: gamma-aminobutyric acid:sodium symporter activity;neurotransmitter binding