SLC4A9

solute carrier family 4 member 9, the group of Solute carrier family 4

Basic information

Region (hg38): 5:140360194-140375141

Links

ENSG00000113073 ∙ NCBI:83697 ∙ OMIM:610207 ∙ HGNC:11035 ∙ Uniprot:Q96Q91 ∙ 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 SLC4A9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC4A9 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	1
missense			66	3		69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	66	3	3

Variants in SLC4A9

This is a list of pathogenic ClinVar variants found in the SLC4A9 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140360282-G-A		not specified	Uncertain significance (Nov 21, 2023)
5-140360285-C-T		not specified	Uncertain significance (May 08, 2023)
5-140360334-C-T		not specified	Uncertain significance (Oct 29, 2021)
5-140360349-A-C		not specified	Uncertain significance (Jun 07, 2023)
5-140360379-T-C		not specified	Uncertain significance (Feb 28, 2025)
5-140360442-C-T		not specified	Uncertain significance (Feb 19, 2025)
5-140360852-C-T		not specified	Uncertain significance (Jun 29, 2022)
5-140360853-G-A		not specified	Uncertain significance (Oct 12, 2021)
5-140360921-G-A		not specified	Likely benign (May 23, 2024)
5-140360969-G-A		not specified	Uncertain significance (Oct 05, 2021)
5-140361362-G-A		not specified	Uncertain significance (May 31, 2023)
5-140361814-C-T		not specified	Uncertain significance (Dec 06, 2022)
5-140361842-G-T		not specified	Uncertain significance (Dec 21, 2022)
5-140362054-C-G		not specified	Uncertain significance (Oct 13, 2023)
5-140362095-G-A		not specified	Uncertain significance (Aug 20, 2024)
5-140362473-A-T		not specified	Uncertain significance (Dec 05, 2024)
5-140362504-G-A		not specified	Uncertain significance (Dec 28, 2023)
5-140362531-C-T		not specified	Uncertain significance (Aug 04, 2021)
5-140362969-G-C		not specified	Uncertain significance (Nov 09, 2021)
5-140362999-C-T		not specified	Uncertain significance (May 02, 2024)
5-140363009-G-A		not specified	Uncertain significance (Feb 23, 2023)
5-140363032-C-A		not specified	Uncertain significance (Jan 10, 2025)
5-140363037-G-A			Benign (May 14, 2018)
5-140363038-C-T		not specified	Uncertain significance (Oct 06, 2021)
5-140363045-G-A		not specified	Uncertain significance (May 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC4A9	protein_coding	protein_coding	ENST00000230993	21	14942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.21e-22	0.0146	124476	2	258	124736	0.00104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	468	537	0.871	0.0000288	6221
Missense in Polyphen		186	215.22	0.86422		2735
Synonymous	1.76	185	218	0.849	0.0000113	2100
Loss of Function	0.936	37	43.7	0.847	0.00000194	508

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00114	0.00113
Ashkenazi Jewish	0.00185	0.00169
East Asian	0.000788	0.000779
Finnish	0.000374	0.000371
European (Non-Finnish)	0.00132	0.00127
Middle Eastern	0.000788	0.000779
South Asian	0.00147	0.00137
Other	0.00169	0.00165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable apical anion exchanger of the kidney cortex. {ECO:0000250}.
• Pathway: Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Bicarbonate transporters (Consensus)

Recessive Scores

• pRec: 0.166

Intolerance Scores

• loftool: 0.681
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.68

Haploinsufficiency Scores

• pHI: 0.166
• hipred: N
• hipred_score: 0.146
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.200

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc4a9
• Phenotype: renal/urinary system phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: inorganic anion transport;bicarbonate transport;regulation of intracellular pH;anion transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;apical part of cell
• Molecular function: inorganic anion exchanger activity;sodium:bicarbonate symporter activity;anion:anion antiporter activity