SLC6A12

solute carrier family 6 member 12, the group of Solute carrier family 6

Basic information

Region (hg38): 12:190076-214570

Links

ENSG00000111181 ∙ NCBI:6539 ∙ OMIM:603080 ∙ HGNC:11045 ∙ Uniprot:P48065 ∙ 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 SLC6A12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC6A12 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					3	3
missense			25	4		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	25	4	4

Variants in SLC6A12

This is a list of pathogenic ClinVar variants found in the SLC6A12 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-191075-T-G		not specified	Uncertain significance (Oct 12, 2021)
12-191091-C-T		not specified	Uncertain significance (Jul 13, 2021)
12-191096-A-G		not specified	Uncertain significance (Jan 07, 2022)
12-191132-C-T		not specified	Likely benign (Oct 17, 2023)
12-191160-G-A		not specified	Uncertain significance (Mar 29, 2022)
12-191211-G-A		not specified	Uncertain significance (Apr 18, 2024)
12-192519-C-T		not specified	Likely benign (Jul 05, 2023)
12-192583-C-T			Benign (Apr 04, 2018)
12-192597-C-T		not specified	Likely benign (Jul 20, 2021)
12-192633-A-C		not specified	Uncertain significance (Apr 26, 2024)
12-193293-G-T		not specified	Uncertain significance (Apr 19, 2023)
12-193326-C-G			Likely benign (Jan 01, 2023)
12-193333-G-A		not specified	Uncertain significance (May 08, 2023)
12-195274-G-C		not specified	Uncertain significance (Jun 04, 2024)
12-196115-G-C			Benign (Mar 29, 2018)
12-196162-C-G		not specified	Uncertain significance (Feb 21, 2024)
12-196189-G-A		not specified	Uncertain significance (Apr 25, 2023)
12-196203-C-T		not specified	Uncertain significance (Mar 24, 2023)
12-196240-C-T		not specified	Uncertain significance (Feb 17, 2023)
12-196245-C-T		not specified	Uncertain significance (Mar 15, 2024)
12-196772-G-C		not specified	Uncertain significance (Jun 23, 2023)
12-196856-G-A		not specified	Uncertain significance (Dec 16, 2022)
12-196862-C-T		not specified	Uncertain significance (Oct 12, 2021)
12-196879-G-A		not specified	Uncertain significance (Feb 28, 2024)
12-197458-C-T		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC6A12	protein_coding	protein_coding	ENST00000428720	14	24494

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.28e-8	0.987	125702	0	46	125748	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	260	343	0.759	0.0000193	3986
Missense in Polyphen		127	173.64	0.73138		1975
Synonymous	0.427	138	145	0.955	0.00000862	1213
Loss of Function	2.34	18	32.4	0.556	0.00000148	363

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000532	0.000532
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000188	0.000185
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.000336	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transports betaine and GABA. May have a role in regulation of GABAergic transmission in the brain through the reuptake of GABA into presynaptic terminals, as well as in osmotic regulation.
• Pathway: Benzodiazepine Pathway, Pharmacodynamics;Amine compound SLC transporters;Metabolism of polyamines;Metabolism of amino acids and derivatives;Metabolism;Amino acid transport across the plasma membrane;Amino acid and oligopeptide SLC transporters;Transport of inorganic cations/anions and amino acids/oligopeptides;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;Glycine, serine, alanine and threonine metabolism;Creatine metabolism (Consensus)

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.776
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.98

Haploinsufficiency Scores

• pHI: 0.0917
• hipred: N
• hipred_score: 0.290
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.248

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc6a12

Gene ontology

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