SLC17A2

solute carrier family 17 member 2, the group of Solute carrier family 17

Basic information

Region (hg38): 6:25912754-25930691

Links

ENSG00000112337 ∙ NCBI:10246 ∙ OMIM:611049 ∙ HGNC:10930 ∙ Uniprot:O00624 ∙ 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 SLC17A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC17A2 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						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	3	0

Variants in SLC17A2

This is a list of pathogenic ClinVar variants found in the SLC17A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-25913374-C-T		not specified	Likely benign (Aug 08, 2023)
6-25913393-C-T		not specified	Uncertain significance (Apr 25, 2022)
6-25914598-A-G		not specified	Likely benign (Jun 24, 2022)
6-25916722-G-A		not specified	Uncertain significance (Dec 28, 2023)
6-25916755-C-A		not specified	Uncertain significance (Feb 05, 2024)
6-25916773-C-G		not specified	Uncertain significance (May 31, 2022)
6-25916807-C-G		not specified	Uncertain significance (Jul 15, 2021)
6-25916997-T-C		not specified	Uncertain significance (Jul 15, 2021)
6-25917006-C-T		not specified	Uncertain significance (Aug 08, 2022)
6-25921016-A-C		not specified	Uncertain significance (Oct 27, 2022)
6-25921087-C-A		not specified	Uncertain significance (Aug 08, 2022)
6-25921201-C-T		not specified	Uncertain significance (Sep 22, 2023)
6-25921290-C-G		not specified	Uncertain significance (Mar 22, 2023)
6-25921326-A-T		not specified	Uncertain significance (Jun 19, 2024)
6-25921357-T-C		not specified	Likely benign (Feb 21, 2024)
6-25921364-A-T		not specified	Uncertain significance (Dec 15, 2023)
6-25923719-T-C		not specified	Uncertain significance (Nov 21, 2022)
6-25923871-G-C		not specified	Uncertain significance (Apr 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC17A2	protein_coding	protein_coding	ENST00000360488	10	17965

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000142	0.959	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	174	237	0.733	0.0000118	2806
Missense in Polyphen		51	82.585	0.61754		949
Synonymous	-0.696	98	89.6	1.09	0.00000471	902
Loss of Function	1.93	13	23.0	0.566	0.00000126	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000242	0.000242
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000132
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in actively transporting phosphate into cells via Na(+) cotransport. {ECO:0000250}.
• Pathway: Osteoblast Signaling (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.563
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.27

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.310
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.732

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc17a2

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
• Molecular function: sodium:phosphate symporter activity;sialic acid transmembrane transporter activity