SLC13A1

protein-coding

solute carrier family 13 member 1, the group of Solute carrier family 13

Gene summary

The protein encoded by this gene is an apical membrane Na(+)-sulfate cotransporter involved in sulfate homeostasis in the kidney. Defects in this gene lead to many pathophysiologic problems. [provided by RefSeq, May 2016]

MANE transcript

NM_022444.4

Inheritance

ClinVar variants

P:4U:69B:16

Top phenotype

HYPOSULFATEMIA WITH SKELETAL DYSPLASIA

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr7:123,113,531-123,199,972

External References & Databases

Ensembl (ENSG00000081800)

Transcript & Mutation Effects

hg38 • Region Span ~86.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

sulfation-related bone disorderMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0019688

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC13A1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 79

not providedTotal: 5

HYPOSULFATEMIA WITH SKELETAL DYSPLASIATotal: 5

Abnormality of neuronal migrationTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022444.4. 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				3 clinvar		3
missense	2 clinvar		69 clinvar	9 clinvar	4 clinvar	84
nonsense	2 clinvar					2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	4	0	69	12	4	89

Highest pathogenic variant AF is 0.0024079205

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022444.4	RefSeq	NP_071889.2	15	MANE Select
ENST00000194130.7	Ensembl	ENSP00000194130.2	15	MANE Select
NM_001324400.1	RefSeq	NP_001311329.1	11	Standard
ENST00000427975.5	Ensembl	ENSP00000388403.1	2	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 membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000194130
Coding exons: 15
Length: 86456
Individuals with no LoFs: 125046
Homozygous LoFs: 1
Heterozygous LoFs: 701
Defined: 125748
p: 0.00280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.503	293	318	0.921	0.0000157	3840
Missense (PolyPhen)		132	140.69	0.9382		1762
Synonymous	0.400	111	116	0.953	0.00000638	1196
Loss of Function	0.557	28	31.4	0.893	0.00000156	378

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00080	0.00080	rare
Latino/Admixed American	0.0025	0.0025	notable
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.0044	0.0044	notable
South Asian	0.0025	0.0025	notable
Other	0.0038	0.0038	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Sodium/sulfate cotransporter that mediates sulfate reabsorption in the kidney.;

Recessive Scores

pRec: 0.145

Intolerance Scores

LoFtool: 0.899
RVIS EVS: 0.42
RVIS percentile EVS: 77.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0434

Gene Damage Prediction

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