SLC13A4

protein-coding

solute carrier family 13 member 4, the group of Solute carrier family 13

Gene summary

Enables sodium:sulfate symporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001318192.2

Inheritance

—

ClinVar variants

U:64B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr7:135,681,231-135,729,258

External References & Databases

Ensembl (ENSG00000164707)

Transcript & Mutation Effects

hg38 • Region Span ~48.0 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 SLC13A4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 66

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001318192.2. 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						0
missense			63 clinvar	3 clinvar		66
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	64	3	0	67

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001318192.2	RefSeq	NP_001305121.1	16	MANE Select
ENST00000682651.1	Ensembl	ENSP00000508027.1	16	MANE Select
NM_012450.4	RefSeq	NP_036582.2	16	Standard
ENST00000354042.8	Ensembl	ENSP00000297282.5	16	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
sulfate transport
citrate transport
succinate transmembrane transport
sulfate transmembrane transport

Molecular Function

citrate transmembrane transporter activity
succinate transmembrane transporter activity
sodium:sulfate symporter activity
sodium:dicarboxylate symporter activity

Cellular Component

plasma membrane
integral component of plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000354042
Coding exons: 16
Length: 48022
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 18
Defined: 125747
p: 0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.01	256	364	0.703	0.0000204	4089
Missense (PolyPhen)		110	169.67	0.6483		1904
Synonymous	-0.0397	161	160	1.00	0.0000105	1283
Loss of Function	4.26	6	32.0	0.188	0.00000154	352

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.000067	0.000065	rare
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Sodium/sulfate cotransporter that mediates sulfate reabsorption in the high endothelial venules (HEV). {ECO:0000269|PubMed:10535998, ECO:0000269|PubMed:15607730}.;

Recessive Scores

pRec: 0.161

Intolerance Scores

LoFtool: 0.379
RVIS EVS: -0.58
RVIS percentile EVS: 18.72

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.129

Gene Damage Prediction

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