SLC17A2

protein-coding

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

Gene summary

Predicted to enable urate transmembrane transporter activity. Predicted to be involved in phosphate-containing compound metabolic process and sodium ion transport. Predicted to be located in plasma membrane. Predicted to be active in apical plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001286123.3

Inheritance

—

ClinVar variants

U:61B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr6:25,912,754-25,930,691

External References & Databases

Ensembl (ENSG00000112337)

Transcript & Mutation Effects

hg38 • Region Span ~17.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC17A2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 61

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001286123.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	2 clinvar		5
missense			57 clinvar	1 clinvar		58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	61	3	0	64

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 51 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001286123.3	RefSeq	NP_001273052.1	11	MANE Select
ENST00000377850.8	Ensembl	ENSP00000367081.3	11	MANE Select
NM_001286125.2	RefSeq	NP_001273054.1	10	Standard
NM_005835.4	RefSeq	NP_005826.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Osteoblast Signaling

Biological Process

phosphate-containing compound metabolic process
sodium ion transport
sialic acid transport
sodium ion transmembrane transport

Molecular Function

sodium:phosphate symporter activity
sialic acid transmembrane transporter activity

Cellular Component

lysosome
integral component of plasma membrane
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360488
Coding exons: 10
Length: 17965
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125748
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.46	174	237	0.733	0.0000118	2806
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00014	0.00013	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in actively transporting phosphate into cells via Na(+) cotransport. {ECO:0000250}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.563
RVIS EVS: 0.22
RVIS percentile EVS: 68.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.732

Gene Damage Prediction

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