SLC6A6

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

Basic information

Region (hg38): 3:14402576-14489349

Links

ENSG00000131389 ∙ NCBI:6533 ∙ OMIM:186854 ∙ HGNC:11052 ∙ Uniprot:P31641 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hypotaurinemic retinal degeneration and cardiomyopathy (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypotaurinemic retinal degeneration and cardiomyopathy	AR	Biochemical; Cardiovascular	Oral taurine supplementation has been described as being beneficial; Individuals have been described with cardiomyopathy, and awareness may allow early diagnosis and management of cardiac sequelae	Biochemical; Cardiovascular; Ophthalmologic	31345061; 31903486

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC6A6 gene.

• Retinal dystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC6A6 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	1	2	39		1	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	2	39	1	1

Variants in SLC6A6

This is a list of pathogenic ClinVar variants found in the SLC6A6 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-14443702-G-C		not specified	Uncertain significance (Jun 01, 2023)
3-14443750-C-T		not specified	Uncertain significance (Feb 15, 2023)
3-14443779-G-A			Uncertain significance (Jan 01, 2019)
3-14445720-C-A		Retinal degeneration • Hypotaurinemic retinal degeneration and cardiomyopathy	Likely pathogenic (Feb 14, 2020)
3-14445827-G-A		not specified	Uncertain significance (Dec 14, 2023)
3-14447599-G-A			Benign (Apr 01, 2024)
3-14447606-T-C		not specified	Uncertain significance (Aug 30, 2021)
3-14447747-G-A		not specified	Uncertain significance (Jun 06, 2023)
3-14447775-C-G		not specified	Uncertain significance (Aug 04, 2021)
3-14447780-C-A		not specified	Uncertain significance (Mar 01, 2024)
3-14457952-G-A		not specified	Uncertain significance (Aug 20, 2024)
3-14458065-G-A		not specified	Uncertain significance (Jan 24, 2024)
3-14458072-C-G		not specified	Uncertain significance (Jan 06, 2023)
3-14466529-C-T		Retinal dystrophy	Pathogenic (May 27, 2024)
3-14466597-G-A		not specified	Uncertain significance (May 04, 2022)
3-14467918-G-A		not specified	Likely benign (Dec 15, 2023)
3-14468146-A-G		not specified	Uncertain significance (Aug 27, 2024)
3-14468191-A-G		not specified	Uncertain significance (Feb 06, 2023)
3-14472217-C-T		not specified	Uncertain significance (Apr 10, 2023)
3-14472304-G-T		Retinal degeneration • Hypotaurinemic retinal degeneration and cardiomyopathy	Likely pathogenic (Feb 14, 2020)
3-14477307-A-C		not specified	Uncertain significance (Oct 26, 2021)
3-14477329-C-T		not specified	Uncertain significance (Nov 09, 2024)
3-14478473-T-G		not specified	Uncertain significance (Aug 10, 2023)
3-14479117-A-G		not specified	Uncertain significance (Aug 22, 2023)
3-14479129-C-T		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC6A6	protein_coding	protein_coding	ENST00000454876	13	86782

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.990	0.0101	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.39	191	376	0.508	0.0000219	4045
Missense in Polyphen		55	181.42	0.30317		2047
Synonymous	0.263	155	159	0.973	0.0000107	1230
Loss of Function	4.53	4	31.4	0.127	0.00000143	352

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium-dependent taurine and beta-alanine transporter. Chloride ions are necessary for optimal uptake. {ECO:0000269|PubMed:8382624}.
• Pathway: Nuclear Receptors Meta-Pathway;NRF2 pathway;Amine compound SLC transporters;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;Bile acid biosynthesis;Na+/Cl- dependent neurotransmitter transporters (Consensus)

Intolerance Scores

• loftool: 0.301
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.328
• hipred: Y
• hipred_score: 0.728
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.266

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc6a6
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye phenotype; muscle 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); growth/size/body region phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: slc6a6b
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: lethal (sensu genetics)

Gene ontology

• Biological process: amino acid transmembrane transport;cellular amino acid metabolic process;neurotransmitter transport;amino acid transport;taurine transport
• Cellular component: plasma membrane;integral component of plasma membrane;integral component of membrane
• Molecular function: neurotransmitter:sodium symporter activity;taurine:sodium symporter activity;amino acid transmembrane transporter activity