SLC17A6

solute carrier family 17 member 6, the group of Solute carrier family 17

Basic information

Region (hg38): 11:22338381-22379503

Links

ENSG00000091664 ∙ NCBI:57084 ∙ OMIM:607563 ∙ HGNC:16703 ∙ Uniprot:Q9P2U8 ∙ 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 SLC17A6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC17A6 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			26		1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	3

Variants in SLC17A6

This is a list of pathogenic ClinVar variants found in the SLC17A6 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-22338573-G-A		not specified	Uncertain significance (Feb 23, 2023)
11-22338580-T-G		not specified	Uncertain significance (Nov 10, 2022)
11-22338610-A-G		not specified	Uncertain significance (Apr 18, 2023)
11-22341550-A-G		not specified	Uncertain significance (Jul 26, 2022)
11-22341556-G-A		not specified	Uncertain significance (Jun 11, 2021)
11-22341556-G-C		not specified	Uncertain significance (Oct 08, 2024)
11-22341610-G-T		not specified	Uncertain significance (Apr 07, 2022)
11-22341622-G-T		not specified	Uncertain significance (Oct 27, 2021)
11-22341647-G-T		not specified	Uncertain significance (Nov 13, 2024)
11-22341664-A-G		not specified	Uncertain significance (Sep 13, 2022)
11-22341741-C-G		not specified	Uncertain significance (May 09, 2022)
11-22341751-A-T		not specified	Uncertain significance (Aug 05, 2024)
11-22341764-G-A		not specified	Uncertain significance (Feb 07, 2023)
11-22343254-A-G		not specified	Uncertain significance (Dec 07, 2024)
11-22359432-C-A		not specified	Uncertain significance (Dec 03, 2021)
11-22362817-A-G		not specified	Uncertain significance (Apr 09, 2024)
11-22365560-G-A		not specified	Uncertain significance (Feb 16, 2023)
11-22365570-A-C		not specified	Uncertain significance (Oct 16, 2024)
11-22365603-G-C		not specified	Uncertain significance (Dec 19, 2023)
11-22365633-C-T		not specified	Uncertain significance (Sep 27, 2021)
11-22365634-G-A		not specified	Uncertain significance (Apr 12, 2023)
11-22365672-C-A		not specified	Uncertain significance (Dec 03, 2024)
11-22365678-G-A		not specified	Uncertain significance (Oct 22, 2021)
11-22370097-T-C		not specified	Uncertain significance (Jun 28, 2024)
11-22374759-G-A		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC17A6	protein_coding	protein_coding	ENST00000263160	12	41407

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.162	0.838	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	246	324	0.760	0.0000155	3790
Missense in Polyphen		32	74.079	0.43197		837
Synonymous	-0.127	117	115	1.01	0.00000566	1124
Loss of Function	3.68	7	28.0	0.250	0.00000118	355

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000618	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000892	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the uptake of glutamate into synaptic vesicles at presynaptic nerve terminals of excitatory neural cells. May also mediate the transport of inorganic phosphate. {ECO:0000269|PubMed:10820226, ECO:0000269|PubMed:11698620}.
• Pathway: Synaptic vesicle cycle - Homo sapiens (human);Retrograde endocannabinoid signaling - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);Nicotine addiction - Homo sapiens (human);Synaptic Vesicle Pathway;Organic anion transporters;Amino acid and oligopeptide SLC transporters;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Histidine metabolism (Consensus)

Recessive Scores

• pRec: 0.286

Intolerance Scores

• loftool: 0.590
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.43

Haploinsufficiency Scores

• pHI: 0.235
• hipred: Y
• hipred_score: 0.793
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.650

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc17a6
• Phenotype: homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; normal phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype

Zebrafish Information Network

• Gene name: slc17a6b
• Affected structure: retinal ganglion cell
• Phenotype tag: abnormal
• Phenotype quality: structure

Gene ontology

• Biological process: ion transport;sodium ion transport;L-glutamate transmembrane transport;synaptic transmission, glutamatergic;regulation of synapse structure or activity;neurotransmitter loading into synaptic vesicle
• Cellular component: integral component of membrane;cell junction;integral component of synaptic vesicle membrane;synaptic vesicle membrane;neuron projection;excitatory synapse
• Molecular function: L-glutamate transmembrane transporter activity;neurotransmitter transporter activity;symporter activity