SLC13A2

protein-coding

solute carrier family 13 member 2, the group of Solute carrier family 13

Gene summary

The protein encoded by this gene is a sodium-coupled citrate transporter that is regulated by the chaperone activity of cyclophilin b. The encoded protein may play a role in the formation of kidney stones. [provided by RefSeq, Oct 2016]

MANE transcript

NM_003984.4

Inheritance

—

ClinVar variants

U:83B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr17:28,473,293-28,497,781

External References & Databases

Ensembl (ENSG00000007216)

Transcript & Mutation Effects

hg38 • Region Span ~24.5 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 SLC13A2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 87

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003984.4. 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			1 clinvar			1
missense			81 clinvar	6 clinvar		87
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	83	6	0	89

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003984.4	RefSeq	NP_003975.1	12	MANE Select
ENST00000314669.10	Ensembl	ENSP00000316202.6	12	MANE Select
NM_001145975.2	RefSeq	NP_001139447.1	12	Standard
NM_001346683.2	RefSeq	NP_001333612.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Bile salt and organic anion SLC transporters
Sodium-coupled sulphate, di- and tri-carboxylate transporters
Transport of bile salts and organic acids, metal ions and amine compounds
SLC-mediated transmembrane transport
Transport of small molecules

Biological Process

sodium ion transport
dicarboxylic acid transport
transmembrane transport

Molecular Function

low-affinity sodium:dicarboxylate symporter activity

Cellular Component

plasma membrane
integral component of plasma membrane
membrane
integral component of membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000444914
Coding exons: 12
Length: 24489
Individuals with no LoFs: 125620
Homozygous LoFs: 0
Heterozygous LoFs: 128
Defined: 125748
p: 0.000509

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.963	343	397	0.864	0.0000235	4166
Missense (PolyPhen)		131	165	0.79392		1773
Synonymous	-0.253	186	182	1.02	0.0000125	1362
Loss of Function	0.944	23	28.4	0.809	0.00000148	276

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00050	0.00049	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.00060	0.00060	rare
East Asian	0.00071	0.00071	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00055	0.00055	rare
South Asian	0.0010	0.00091	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Cotransport of sodium ions and dicarboxylates such as succinate and citrate.;

Intolerance Scores

LoFtool: 0.874
RVIS EVS: -0.37
RVIS percentile EVS: 28.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.162

Gene Damage Prediction

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