SLC26A7

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

Basic information

Region (hg38): 8:91209494-91398155

Links

ENSG00000147606 ∙ NCBI:115111 ∙ OMIM:608479 ∙ HGNC:14467 ∙ Uniprot:Q8TE54 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital hypothyroidism (Strong), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC26A7 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC26A7 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			32	2	1	35
nonsense		1	1			2
start loss						0
frameshift	1					1
inframe indel				1		1
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding						0
Total	1	2	33	3	1

Highest pathogenic variant AF is 0.00000659

Variants in SLC26A7

This is a list of pathogenic ClinVar variants found in the SLC26A7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-91218920-G-A		not specified	Uncertain significance (Feb 22, 2023)
8-91218965-C-T		not specified	Uncertain significance (Apr 09, 2024)
8-91218993-A-C		not specified	Uncertain significance (Jun 06, 2023)
8-91218993-A-G		not specified	Uncertain significance (Jul 05, 2022)
8-91249683-T-C		Inborn genetic diseases	Uncertain significance (Feb 14, 2023)
8-91249722-T-C		Inborn genetic diseases	Uncertain significance (Dec 01, 2022)
8-91249743-G-A		Inborn genetic diseases	Uncertain significance (May 24, 2024)
8-91249823-G-A		Inborn genetic diseases	Uncertain significance (Dec 20, 2021)
8-91289142-C-T		Inborn genetic diseases	Uncertain significance (Nov 21, 2023)
8-91289199-C-T		Inborn genetic diseases	Uncertain significance (Mar 01, 2024)
8-91289231-C-T		Inborn genetic diseases	Uncertain significance (Jan 20, 2023)
8-91289241-C-T			Uncertain significance (Sep 03, 2021)
8-91295613-G-T		Inborn genetic diseases	Uncertain significance (Nov 21, 2023)
8-91295625-C-A		Inborn genetic diseases	Uncertain significance (Nov 10, 2022)
8-91295639-C-T		Inborn genetic diseases	Uncertain significance (Dec 22, 2023)
8-91318250-C-T		SLC26A7-related disorder	Likely benign (Feb 18, 2022)
8-91318300-A-G		Inborn genetic diseases	Uncertain significance (Nov 12, 2021)
8-91318363-C-T		Inborn genetic diseases	Uncertain significance (Jan 09, 2024)
8-91334332-G-A		Inborn genetic diseases	Likely benign (Apr 17, 2024)
8-91334352-T-A		Inborn genetic diseases	Uncertain significance (Feb 16, 2023)
8-91334356-T-C		Inborn genetic diseases	Uncertain significance (Feb 10, 2022)
8-91334365-T-C		Inborn genetic diseases	Uncertain significance (Oct 27, 2023)
8-91334418-A-G		Inborn genetic diseases	Uncertain significance (Feb 11, 2022)
8-91338163-C-A		Hyperoxaluria	Uncertain significance (May 15, 2023)
8-91338178-G-T		Inborn genetic diseases	Uncertain significance (Oct 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC26A7	protein_coding	protein_coding	ENST00000309536	18	188657

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.91e-9	0.992	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0117	351	352	0.998	0.0000171	4322
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000987	0.000971
Ashkenazi Jewish	0.000108	0.0000992
East Asian	0.000441	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000214	0.000211
Middle Eastern	0.000441	0.000435
South Asian	0.000169	0.000163
Other	0.000848	0.000815

dbNSFP

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}.
• Pathway: 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;Multifunctional anion exchangers (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.101
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62.1

Haploinsufficiency Scores

• pHI: 0.502
• hipred: N
• hipred_score: 0.234
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0745

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc26a7
• Phenotype: digestive/alimentary phenotype; renal/urinary system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: gastric acid secretion;ion transport;anion transport;chloride transport;sulfate transport;bicarbonate transport;oxalate transport;sulfate transmembrane transport;chloride transmembrane transport
• Cellular component: cytoplasm;endosome;plasma membrane;integral component of plasma membrane;basolateral plasma membrane;recycling endosome membrane
• Molecular function: chloride channel activity;secondary active sulfate transmembrane transporter activity;bicarbonate transmembrane transporter activity;chloride transmembrane transporter activity;sulfate transmembrane transporter activity;anion:anion antiporter activity;oxalate transmembrane transporter activity