SLC26A9

solute carrier family 26 member 9, the group of Solute carrier family 26

Basic information

Region (hg38): 1:205913047-205943460

Links

ENSG00000174502 ∙ NCBI:115019 ∙ OMIM:608481 ∙ HGNC:14469 ∙ Uniprot:Q7LBE3 ∙ 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 SLC26A9 gene.

• Inborn genetic diseases (42 variants)
• not specified (5 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC26A9 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				1	2	3
missense			40	2	3	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	40	3	6

Variants in SLC26A9

This is a list of pathogenic ClinVar variants found in the SLC26A9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-205914934-T-C		not specified	Benign (Mar 29, 2016)
1-205914975-C-T		not specified	Uncertain significance (Dec 09, 2023)
1-205915079-G-A		not specified	Uncertain significance (Feb 28, 2024)
1-205915098-C-T		not specified	Likely benign (Apr 13, 2023)
1-205915112-C-T		not specified	Uncertain significance (Jan 04, 2022)
1-205915125-G-A		not specified	Uncertain significance (Aug 16, 2022)
1-205915146-T-C		not specified	Benign (Mar 29, 2016)
1-205915163-C-T		not specified	Uncertain significance (Aug 21, 2023)
1-205915181-T-C		not specified	Uncertain significance (Mar 14, 2023)
1-205917290-A-G		not specified	Uncertain significance (Jul 31, 2023)
1-205917306-G-A		not specified	Uncertain significance (Mar 22, 2023)
1-205917325-G-A			Likely benign (Aug 29, 2018)
1-205917326-T-C		not specified	Uncertain significance (Jul 26, 2022)
1-205918853-T-C		not specified	Benign (Mar 29, 2016)
1-205918859-G-T		not specified	Uncertain significance (Feb 28, 2024)
1-205918920-C-T		not specified	Uncertain significance (Mar 17, 2023)
1-205918943-T-C		not specified	Uncertain significance (Aug 08, 2023)
1-205920182-T-C		not specified	Uncertain significance (Feb 10, 2022)
1-205920201-C-T		not specified	Benign (Mar 29, 2016)
1-205920226-C-G		not specified	Uncertain significance (Dec 17, 2023)
1-205921551-T-C		not specified	Benign (Mar 29, 2016)
1-205921587-C-T		not specified	Uncertain significance (Feb 28, 2023)
1-205921658-T-C		not specified	Uncertain significance (Nov 09, 2022)
1-205921694-C-T		not specified	Uncertain significance (Jan 06, 2023)
1-205921736-G-A		not specified	Uncertain significance (Sep 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC26A9	protein_coding	protein_coding	ENST00000367134	21	30413

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0127	0.987	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.397	499	525	0.951	0.0000300	5780
Missense in Polyphen		138	182.95	0.75431		2038
Synonymous	-0.559	236	225	1.05	0.0000152	1769
Loss of Function	4.10	11	38.4	0.286	0.00000170	454

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000272	0.000272
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.000163	0.000163
South Asian	0.0000655	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DIDS- and thiosulfate- sensitive anion exchanger mediating chloride, sulfate and oxalate transport. Mediates chloride/bicarbonate exchange or chloride-independent bicarbonate extrusion thus assuring bicarbonate secretion. Inhibited by ammonium and thiosulfate. {ECO:0000269|PubMed:11834742, ECO:0000269|PubMed:15800055}.
• Pathway: Mineral absorption - 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: 0.117

Intolerance Scores

• loftool: 0.0289
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.35

Haploinsufficiency Scores

• pHI: 0.179
• hipred: Y
• hipred_score: 0.600
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.404

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc26a9
• Phenotype: digestive/alimentary phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: ion transport;anion transport;chloride transport;positive regulation of gene expression;bicarbonate transport;oxalate transport;sulfate transmembrane transport;chloride transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;cell surface;apical plasma membrane;extracellular exosome
• 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;ATPase binding