SLC6A12

protein-coding

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

Gene summary

Enables gamma-aminobutyric acid:sodium:chloride symporter activity. Involved in gamma-aminobutyric acid transport and monocarboxylic acid transport. Predicted to be located in basolateral plasma membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001122848.3

Inheritance

—

ClinVar variants

U:66B:17

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr12:190,077-214,570

External References & Databases

Ensembl (ENSG00000111181)

Transcript & Mutation Effects

hg38 • Region Span ~24.5 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC6A12 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 73

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001122848.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					4 clinvar	4
missense			64 clinvar	13 clinvar		77
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	66	13	4	83

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 69 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001122848.3	RefSeq	NP_001116320.1	14	MANE Select
ENST00000684302.1	Ensembl	ENSP00000508194.1	14	MANE Select
NM_001122847.3	RefSeq	NP_001116319.1	14	Standard
NM_001206931.2	RefSeq	NP_001193860.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Benzodiazepine Pathway, Pharmacodynamics
Amine compound SLC transporters
Metabolism of polyamines
Metabolism of amino acids and derivatives
Metabolism

Biological Process

amino acid transmembrane transport
amino acid transport
gamma-aminobutyric acid transport

Molecular Function

gamma-aminobutyric acid:sodium symporter activity
protein binding
amino acid transmembrane transporter activity
neurotransmitter binding

Cellular Component

plasma membrane
integral component of plasma membrane
integral component of membrane
neuron projection

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000428720
Coding exons: 14
Length: 24494
Individuals with no LoFs: 125702
Homozygous LoFs: 0
Heterozygous LoFs: 46
Defined: 125748
p: 0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.59	260	343	0.759	0.0000193	3986
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00035	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00013	0.00013	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.131

Intolerance Scores

LoFtool: 0.776
RVIS EVS: -0.4
RVIS percentile EVS: 26.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Indispensability pred.: N
Indispensability score: 0.248

Gene Damage Prediction

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