SLC26A7

protein-coding

solute carrier family 26 member 7, the group of Solute carrier family 26

Gene summary

This gene is one member of a family of sulfate/anion transporter genes. Family members are well conserved in gene structure and protein length yet have markedly different tissue expression patterns. This gene has abundant and specific expression in the kidney. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Aug 2013]

MANE transcript

NM_052832.4

Inheritance

ClinVar variants

P:4U:102B:6

Top phenotype

congenital hypothyroidism

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr8:91,209,494-91,398,155

External References & Databases

Ensembl (ENSG00000147606)

Transcript & Mutation Effects

hg38 • Region Span ~188.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

congenital hypothyroidismSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0018612

Submitter: Ambry Genetics

congenital hypothyroidismSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0018612

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC26A7 variants in ClinVar

5 Conditions Cataloged

Inborn genetic diseasesTotal: 96

not providedTotal: 7

Congenital hypothyroidismTotal: 3

HyperoxaluriaTotal: 1

SLC26A7-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052832.4. 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			2 clinvar			2
missense		1 clinvar	95 clinvar	5 clinvar	1 clinvar	102
nonsense		1 clinvar	1 clinvar			2
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)		1 clinvar	4 clinvar			5
Total	1	3	102	5	1	112

Highest pathogenic variant AF is 0.000015064985

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_052832.4	RefSeq	NP_439897.1	18	MANE Select
ENST00000276609.8	Ensembl	ENSP00000276609.3	18	MANE Select
NM_001282356.2	RefSeq	NP_001269285.1	18	Standard
NM_001282357.2	RefSeq	NP_001269286.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gastric acid secretion - Homo sapiens (human)
Transport of inorganic cations/anions and amino acids/oligopeptides
SLC-mediated transmembrane transport
Transport of small molecules
Methionine and cysteine metabolism

Biological Process

gastric acid secretion
ion transport
anion transport
chloride transport
sulfate transport

Molecular Function

chloride channel activity
secondary active sulfate transmembrane transporter activity
bicarbonate transmembrane transporter activity
chloride transmembrane transporter activity
sulfate transmembrane transporter activity

Cellular Component

cytoplasm
endosome
plasma membrane
integral component of plasma membrane
basolateral plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000309536
Coding exons: 18
Length: 188657
Individuals with no LoFs: 125683
Homozygous LoFs: 0
Heterozygous LoFs: 65
Defined: 125748
p: 0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0117	351	352	0.998	0.0000171	4322
Missense (PolyPhen)		145	142.22	1.0196		1742
Synonymous	-0.150	130	128	1.02	0.00000685	1265
Loss of Function	2.48	20	36.1	0.554	0.00000178	449

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00063	0.00062	rare
Latino/Admixed American	0.00036	0.00035	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00044	0.00044	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00021	0.00021	rare
South Asian	0.00017	0.00016	rare
Other	0.00085	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a sodium-independent DIDS-sensitive anion exchanger mediating bicarbonate, chloride, sulfate and oxalate transport. May play a role in the maintenance of the electrolyte and acid-base homeostasis in the kidney, by acting as a distal excretory segment-specific anion exchanger. Plays a major role in gastric acid secretion. {ECO:0000250|UniProtKB:Q8R2Z3, ECO:0000269|PubMed:11834742, ECO:0000269|PubMed:12736153}.;

Recessive Scores

pRec: 0.127

Intolerance Scores

LoFtool: 0.101
RVIS EVS: 0.11
RVIS percentile EVS: 62.1

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0745

Gene Damage Prediction

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