SLC17A3

solute carrier family 17 member 3, the group of Solute carrier family 17

Basic information

Region (hg38): 6:25833066-25882286

Links

ENSG00000124564 ∙ NCBI:10786 ∙ OMIM:611034 ∙ HGNC:10931 ∙ Uniprot:O00476 ∙ 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 SLC17A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC17A3 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			24	2	2	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	4

Variants in SLC17A3

This is a list of pathogenic ClinVar variants found in the SLC17A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-25845389-C-A		not specified	Uncertain significance (Jul 25, 2023)
6-25845389-C-T		not specified	Uncertain significance (Dec 27, 2023)
6-25845390-G-A		not specified	Uncertain significance (Jun 07, 2024)
6-25845396-G-A		not specified	Uncertain significance (Jun 13, 2024)
6-25845410-G-A		not specified	Uncertain significance (May 26, 2022)
6-25845472-G-A		SLC17A3-related disorder	Benign (Mar 18, 2019)
6-25845498-T-A		not specified	Uncertain significance (Dec 22, 2023)
6-25849417-G-C		not specified	Uncertain significance (Dec 20, 2023)
6-25849420-A-G		not specified	Uncertain significance (Dec 19, 2022)
6-25849462-T-C		not specified	Uncertain significance (Jul 14, 2021)
6-25849847-C-T		not specified	Uncertain significance (Dec 19, 2022)
6-25849853-G-A		not specified	Uncertain significance (Jun 11, 2021)
6-25849866-A-T		SLC17A3-related disorder	Benign (Aug 01, 2019)
6-25849936-T-C		SLC17A3-related disorder	Benign (Jul 15, 2020)
6-25850541-A-G		Uric acid concentration, serum, quantitative trait locus 4	association (Nov 05, 2010)
6-25850599-G-T		not specified	Uncertain significance (Sep 29, 2023)
6-25850617-C-T		SLC17A3-related disorder	Benign (Nov 26, 2019)
6-25850620-C-T		not specified	Uncertain significance (Aug 02, 2022)
6-25850827-C-T		not specified	Uncertain significance (Jul 12, 2022)
6-25855230-C-T		not specified	Uncertain significance (Nov 22, 2022)
6-25861672-A-C		not specified	Uncertain significance (Jan 09, 2024)
6-25862321-G-A		not specified	Uncertain significance (Sep 13, 2023)
6-25862323-G-T		not specified	Uncertain significance (Dec 01, 2022)
6-25862334-T-G		Uric acid concentration, serum, quantitative trait locus 4	risk factor (Nov 05, 2010)
6-25862348-A-G		not specified	Uncertain significance (Mar 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC17A3	protein_coding	protein_coding	ENST00000397060	11	49221

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.93e-22	0.000368	125611	0	137	125748	0.000545

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.298	272	259	1.05	0.0000127	3200
Missense in Polyphen		68	63.467	1.0714		835
Synonymous	-0.0527	94	93.4	1.01	0.00000477	1023
Loss of Function	-0.489	31	28.2	1.10	0.00000157	309

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00146	0.00143
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000164	0.000163
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000538	0.000536
Middle Eastern	0.000164	0.000163
South Asian	0.000954	0.000948
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 2: voltage-driven, multispecific, organic anion transporter able to transport para-aminohippurate (PAH), estrone sulfate, estradiol-17-beta-glucuronide, bumetanide, and ochratoxin A. Isoform 2 functions as urate efflux transporter on the apical side of renal proximal tubule and is likely to act as an exit path for organic anionic drugs as well as urate in vivo. May be involved in actively transporting phosphate into cells via Na(+) cotransport.
• Pathway: Uricosurics Pathway, Pharmacodynamics;Stimuli-sensing channels;Ion channel transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.0945

Intolerance Scores

• loftool: 0.983
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62

Haploinsufficiency Scores

• pHI: 0.0884
• hipred: N
• hipred_score: 0.139
• ghis: 0.383

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0557

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc17a3

Gene ontology

• Biological process: sodium ion transport;phosphate ion transport;drug transmembrane transport;organic anion transport;sialic acid transport;urate transport;glucose-6-phosphate transport;drug transport;ion transmembrane transport;sodium ion transmembrane transport;urate metabolic process;toxin transport
• Cellular component: cytoplasm;lysosome;endoplasmic reticulum membrane;plasma membrane;integral component of plasma membrane;integral component of membrane;apical plasma membrane;brush border membrane;perinuclear region of cytoplasm
• Molecular function: sodium:phosphate symporter activity;voltage-gated anion channel activity;organic anion transmembrane transporter activity;sialic acid transmembrane transporter activity;urate transmembrane transporter activity;drug transmembrane transporter activity;efflux transmembrane transporter activity;toxin transmembrane transporter activity