SLC17A1

solute carrier family 17 member 1, the group of Solute carrier family 17

Basic information

Region (hg38): 6:25782914-25832052

Previous symbols: [ "NPT1" ]

Links

ENSG00000124568 ∙ NCBI:6568 ∙ OMIM:182308 ∙ HGNC:10929 ∙ Uniprot:Q14916 ∙ 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 SLC17A1 gene.

• Inborn genetic diseases (17 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC17A1 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			14	3		17
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	3	1

Variants in SLC17A1

This is a list of pathogenic ClinVar variants found in the SLC17A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-25798815-C-T			Benign (Apr 02, 2018)
6-25798907-C-T		not specified	Uncertain significance (May 18, 2023)
6-25798909-G-C		not specified	Uncertain significance (May 03, 2023)
6-25800915-G-A		not specified	Uncertain significance (Nov 29, 2023)
6-25811461-G-A		not specified	Likely benign (Feb 27, 2023)
6-25811499-A-T		not specified	Uncertain significance (Dec 20, 2021)
6-25811641-C-T		not specified	Uncertain significance (Jan 26, 2023)
6-25811698-A-T		not specified	Uncertain significance (Jan 09, 2024)
6-25811704-A-G		not specified	Uncertain significance (Nov 19, 2022)
6-25812910-G-A		not specified	Uncertain significance (Aug 22, 2023)
6-25819083-C-T		not specified	Uncertain significance (Apr 04, 2023)
6-25819540-C-T		not specified	Uncertain significance (Dec 20, 2021)
6-25819543-T-A		not specified	Uncertain significance (Dec 28, 2023)
6-25819597-C-G		not specified	Uncertain significance (Jan 16, 2024)
6-25819807-A-G		not specified	Uncertain significance (May 03, 2023)
6-25819867-A-G		not specified	Uncertain significance (Nov 07, 2023)
6-25819902-T-A		not specified	Uncertain significance (Jun 29, 2023)
6-25819909-T-C		not specified	Likely benign (Jan 18, 2023)
6-25819911-G-C		not specified	Uncertain significance (Jun 21, 2022)
6-25826464-T-C		not specified	Uncertain significance (Jul 05, 2023)
6-25826471-T-C		not specified	Uncertain significance (Dec 13, 2023)
6-25826526-C-T		not specified	Uncertain significance (Feb 28, 2024)
6-25826555-G-A		not specified	Likely benign (Apr 25, 2022)
6-25826558-C-T		not specified	Uncertain significance (Jul 30, 2023)
6-25826603-A-C		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC17A1	protein_coding	protein_coding	ENST00000244527	11	49163

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.12e-16	0.0115	125418	1	328	125747	0.00131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.418	235	254	0.926	0.0000126	3030
Missense in Polyphen		70	80.698	0.86743		1038
Synonymous	0.719	83	91.8	0.904	0.00000470	947
Loss of Function	0.110	24	24.6	0.976	0.00000129	273

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0129	0.0129
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000548	0.000545
Middle Eastern	0.000327	0.000326
South Asian	0.000863	0.000850
Other	0.00185	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Important for the resorption of phosphate by the kidney. May be involved in actively transporting phosphate into cells via Na(+) cotransport in the renal brush border membrane. Plays a role in urate transport in the kidney (PubMed:27906618). {ECO:0000269|PubMed:27906618}.
• Pathway: Uricosurics Pathway, Pharmacodynamics;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 (Consensus)

Recessive Scores

• pRec: 0.137

Intolerance Scores

• loftool: 0.928
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.37

Haploinsufficiency Scores

• pHI: 0.0538
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.104

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc17a1

Gene ontology

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