SLC6A11

solute carrier family 6 member 11, the group of Solute carrier family 6

Basic information

Region (hg38): 3:10816200-10940714

Links

ENSG00000132164 ∙ NCBI:6538 ∙ OMIM:607952 ∙ HGNC:11044 ∙ Uniprot:P48066 ∙ 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 SLC6A11 gene.

• Inborn genetic diseases (22 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC6A11 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					2	2
missense			21	1	2	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	4

Variants in SLC6A11

This is a list of pathogenic ClinVar variants found in the SLC6A11 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-10816336-C-T		not specified	Likely benign (Apr 07, 2023)
3-10816353-A-G		not specified	Uncertain significance (Apr 07, 2023)
3-10816359-G-A		not specified	Uncertain significance (Apr 07, 2023)
3-10816375-G-T		not specified	Uncertain significance (Aug 06, 2021)
3-10816395-G-A		not specified	Uncertain significance (Dec 20, 2021)
3-10816399-A-G		not specified	Uncertain significance (Dec 01, 2022)
3-10816443-G-A		not specified	Uncertain significance (Mar 03, 2023)
3-10819522-T-G		not specified	Uncertain significance (Mar 16, 2022)
3-10819744-C-T		not specified	Uncertain significance (Jan 22, 2024)
3-10819813-G-C		not specified	Uncertain significance (Mar 13, 2023)
3-10844219-G-A		not specified	Uncertain significance (May 06, 2022)
3-10874970-G-A		not specified	Uncertain significance (May 17, 2023)
3-10874970-G-T		not specified	Uncertain significance (May 27, 2022)
3-10874978-G-A			Benign (May 21, 2018)
3-10875021-G-A			Benign (Oct 24, 2018)
3-10875066-C-T		not specified	Uncertain significance (Sep 20, 2023)
3-10912109-C-T		not specified	Uncertain significance (Dec 16, 2023)
3-10912185-C-T			Benign (Feb 01, 2024)
3-10918336-A-G		not specified	Uncertain significance (Dec 14, 2021)
3-10918360-G-A		not specified	Uncertain significance (Jun 12, 2023)
3-10918372-G-A		not specified	Uncertain significance (Oct 06, 2022)
3-10918417-G-A		not specified	Uncertain significance (Oct 03, 2023)
3-10926023-T-G		not specified	Uncertain significance (Jun 28, 2023)
3-10926042-A-G		not specified	Uncertain significance (Jul 13, 2021)
3-10929275-G-A		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC6A11	protein_coding	protein_coding	ENST00000254488	14	124535

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000483	1.00	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.56	227	365	0.623	0.0000203	4126
Missense in Polyphen		79	177.14	0.44598		1963
Synonymous	-0.542	159	151	1.06	0.00000927	1228
Loss of Function	3.15	13	32.3	0.402	0.00000148	374

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000458	0.000456
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000372	0.000370
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Terminates the action of GABA by its high affinity sodium-dependent reuptake into presynaptic terminals.
• Pathway: Benzodiazepine Pathway, Pharmacodynamics;GABAergic synapse - Homo sapiens (human);Nuclear Receptors Meta-Pathway;NRF2 pathway;GABA receptor Signaling;Amine compound SLC transporters;Metabolism of polyamines;Metabolism of amino acids and derivatives;Metabolism;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;Creatine metabolism (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.367
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.53

Haploinsufficiency Scores

• pHI: 0.208
• hipred: Y
• hipred_score: 0.639
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.150

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc6a11
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

• Biological process: brain development;gamma-aminobutyric acid transport;response to drug;transmembrane transport
• Cellular component: cytoplasm;plasma membrane;integral component of membrane;neuron projection;GABA-ergic synapse;integral component of postsynaptic membrane;integral component of presynaptic membrane
• Molecular function: gamma-aminobutyric acid:sodium symporter activity;neurotransmitter binding