SLC26A6

solute carrier family 26 member 6, the group of MicroRNA protein coding host genes|Solute carrier family 26

Basic information

Region (hg38): 3:48625722-48635493

Links

ENSG00000225697 ∙ NCBI:65010 ∙ OMIM:610068 ∙ HGNC:14472 ∙ Uniprot:Q9BXS9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC26A6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC26A6 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				2	1	3
missense			42	4	2	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		1	2
non coding					7	7
Total	0	0	42	6	10

Variants in SLC26A6

This is a list of pathogenic ClinVar variants found in the SLC26A6 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-48626219-G-A		not specified	Likely benign (Jun 10, 2022)
3-48626228-C-T		not specified	Uncertain significance (May 23, 2023)
3-48626234-G-T		not specified	Uncertain significance (Apr 25, 2023)
3-48626277-G-A		not specified	Uncertain significance (Mar 25, 2024)
3-48626338-C-A		not specified	Uncertain significance (Feb 07, 2023)
3-48626353-G-T		not specified	Uncertain significance (Jun 26, 2023)
3-48626671-G-C		not specified	Uncertain significance (Jan 04, 2022)
3-48626678-T-A			Uncertain significance (-)
3-48626736-G-C			Benign (May 15, 2021)
3-48626959-G-T		not specified	Uncertain significance (Sep 27, 2022)
3-48626985-C-T		not specified	Uncertain significance (May 09, 2023)
3-48627040-C-T			Benign (May 05, 2021)
3-48627047-G-A			Uncertain significance (-)
3-48627096-G-A			Benign (May 16, 2021)
3-48627947-A-G		not specified	Uncertain significance (Apr 05, 2023)
3-48628021-G-A			Benign (Mar 29, 2018)
3-48628484-C-T		not specified	Uncertain significance (Aug 30, 2022)
3-48628496-G-A		not specified	Uncertain significance (Jul 06, 2021)
3-48628513-G-T		not specified	Uncertain significance (Nov 02, 2023)
3-48628536-ACCACACTG-A		Hyperoxaluria	Uncertain significance (May 15, 2023)
3-48628647-A-G		not specified	Uncertain significance (Jan 17, 2024)
3-48628656-T-C		not specified	Uncertain significance (Jan 09, 2023)
3-48628661-A-T			Uncertain significance (-)
3-48628683-C-T			Uncertain significance (-)
3-48628696-C-G			Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC26A6	protein_coding	protein_coding	ENST00000395550	21	9771

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.90e-13	0.889	124746	0	104	124850	0.000417

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.618	410	447	0.918	0.0000264	4873
Missense in Polyphen		123	145.12	0.84759		1609
Synonymous	-0.464	200	192	1.04	0.0000117	1600
Loss of Function	1.98	25	38.2	0.655	0.00000180	431

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00131	0.00130
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.00151	0.00150
Finnish	0.00	0.00
European (Non-Finnish)	0.000322	0.000318
Middle Eastern	0.00151	0.00150
South Asian	0.000327	0.000327
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Apical membrane anion-exchanger with wide epithelial distribution that plays a role as a component of the pH buffering system for maintaining acid-base homeostasis. Acts as a versatile DIDS-sensitive inorganic and organic anion transporter that mediates the uptake of monovalent anions like chloride, bicarbonate, formate and hydroxyl ion and divalent anions like sulfate and oxalate. Function in multiple exchange modes involving pairs of these anions, which include chloride-bicarbonate, chloride-oxalate, oxalate-formate, oxalate-sulfate and chloride- formate exchange. Apical membrane chloride-bicarbonate exchanger that mediates luminal chloride absorption and bicarbonate secretion by the small intestinal brush border membrane and contributes to intracellular pH regulation in the duodenal upper villous epithelium during proton-coupled peptide absorption, possibly by providing a bicarbonate import pathway. Mediates also intestinal chloride absorption and oxalate secretion, thereby preventing hyperoxaluria and calcium oxalate urolithiasis. Transepithelial oxalate secretion, chloride-formate, chloride- oxalate and chloride-bicarbonate transport activities in the duodenum are inhibited by PKC activation in a calcium-independent manner. The apical membrane chloride-bicarbonate exchanger provides also a major route for fluid and bicarbonate secretion into the proximal tubules of the kidney as well as into the proximal part of the interlobular pancreatic ductal tree, where it mediates electrogenic chloride-bicarbonate exchange with a chloride-bicarbonate stoichiometry of 1:2, and hence will dilute and alkalinize protein-rich acinar secretion. Mediates also the transcellular sulfate absorption and oxalate secretion across the apical membrane in the duodenum and the formate ion efflux at the apical brush border of cells in the proximal tubules of kidney. Plays a role in sperm capacitation by increasing intracellular pH.
• Pathway: Mineral absorption - Homo sapiens (human);Biopterin metabolism;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: 0.245

Intolerance Scores

• loftool: 0.0775
• rvis_EVS: -0.06
• rvis_percentile_EVS: 48.84

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.270
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.140

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc26a6
• Phenotype: digestive/alimentary phenotype; renal/urinary system phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: ion transport;chloride transport;sulfate transport;bicarbonate transport;formate transport;mannitol transport;oxalate transport;transepithelial chloride transport;epithelial fluid transport;oxalic acid secretion;sperm capacitation;intestinal absorption;regulation of intracellular pH;intracellular pH elevation;transepithelial transport;cellular response to cAMP;cellular response to fructose stimulus;cellular response to interferon-gamma;sulfate transmembrane transport;chloride transmembrane transport;positive regulation of dipeptide transmembrane transport
• Cellular component: endoplasmic reticulum;plasma membrane;integral component of plasma membrane;vesicle membrane;membrane;integral component of membrane;basolateral plasma membrane;apical plasma membrane;cytoplasmic vesicle membrane;brush border membrane;vesicle;chloride channel complex;sperm midpiece
• Molecular function: chloride channel activity;inorganic anion exchanger activity;secondary active sulfate transmembrane transporter activity;bicarbonate transmembrane transporter activity;chloride transmembrane transporter activity;sulfate transmembrane transporter activity;anion:anion antiporter activity;formate transmembrane transporter activity;efflux transmembrane transporter activity;formate efflux transmembrane transporter activity;oxalate transmembrane transporter activity;PDZ domain binding