SLC17A4

solute carrier family 17 member 4, the group of Solute carrier family 17

Basic information

Region (hg38): 6:25754698-25781199

Links

ENSG00000146039 ∙ NCBI:10050 ∙ OMIM:604216 ∙ HGNC:10932 ∙ Uniprot:Q9Y2C5 ∙ 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 SLC17A4 gene.

• Inborn genetic diseases (24 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC17A4 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						0
missense			21	1	1	23
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	1

Variants in SLC17A4

This is a list of pathogenic ClinVar variants found in the SLC17A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-25761999-G-T		not specified	Conflicting classifications of pathogenicity (Jul 01, 2022)
6-25762001-C-A		not specified	Conflicting classifications of pathogenicity (Jul 01, 2022)
6-25762026-G-A		not specified	Likely benign (Apr 13, 2022)
6-25762027-T-G		not specified	Uncertain significance (Aug 16, 2021)
6-25768985-G-A		not specified	Uncertain significance (Jan 09, 2024)
6-25768996-G-T		not specified	Uncertain significance (Dec 06, 2022)
6-25769076-C-G		not specified	Uncertain significance (Nov 21, 2023)
6-25769173-A-G		not specified	Uncertain significance (Nov 30, 2022)
6-25769174-A-G		not specified	Uncertain significance (Apr 20, 2023)
6-25770251-C-T		not specified	Uncertain significance (Apr 14, 2022)
6-25770286-C-A		not specified	Uncertain significance (May 31, 2023)
6-25770400-G-A		not specified	Uncertain significance (Jan 04, 2024)
6-25770433-C-T		not specified	Uncertain significance (Jul 19, 2023)
6-25770962-G-T		not specified	Uncertain significance (Feb 05, 2024)
6-25770970-C-T		not specified	Uncertain significance (Dec 01, 2022)
6-25770995-A-T		not specified	Uncertain significance (Aug 23, 2021)
6-25773351-T-G		not specified	Uncertain significance (Mar 07, 2024)
6-25773373-G-T		not specified	Uncertain significance (Nov 30, 2022)
6-25773594-T-C		not specified	Uncertain significance (Jul 26, 2022)
6-25773616-C-A		not specified	Uncertain significance (Jul 20, 2022)
6-25773637-C-T		not specified	Uncertain significance (Feb 07, 2023)
6-25773649-C-T		not specified	Uncertain significance (Jun 18, 2021)
6-25773667-T-C		not specified	Uncertain significance (Jul 19, 2023)
6-25776649-G-A		not specified	Uncertain significance (Oct 06, 2022)
6-25776662-C-A		not specified	Uncertain significance (May 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC17A4	protein_coding	protein_coding	ENST00000377905	11	26493

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.57e-9	0.606	123089	30	2619	125738	0.0106

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0881	261	265	0.985	0.0000127	3199
Missense in Polyphen		71	84.033	0.84491		1104
Synonymous	0.127	97	98.6	0.984	0.00000500	1015
Loss of Function	1.27	17	23.6	0.719	0.00000109	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00733	0.00733
Ashkenazi Jewish	0.00576	0.00577
East Asian	0.000326	0.000326
Finnish	0.0246	0.0243
European (Non-Finnish)	0.0151	0.0150
Middle Eastern	0.000326	0.000326
South Asian	0.00333	0.00330
Other	0.0106	0.0106

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a membrane potential-dependent organic anion transporter, the transport requires a low concentration of chloride ions. May be involved in urate extrusion from the intestinal duct. May recognize hydrophilic anionic drugs such as aspirin, salicylate, and ibuprofen as substrates. Able to actively transport inorganic phosphate into cells via Na(+) cotransport (in vitro). {ECO:0000269|PubMed:22460716}.

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.908
• rvis_EVS: 0.0000761
• rvis_percentile_EVS: 53.98

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.304
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.308

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc17a4

Gene ontology

• Biological process: phosphate-containing compound metabolic process;sodium ion transport;sialic acid transport;sodium ion transmembrane transport
• Cellular component: lysosome;integral component of plasma membrane;membrane;integral component of membrane;apical plasma membrane
• Molecular function: sodium:phosphate symporter activity;sialic acid transmembrane transporter activity