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.

• not_specified (108 variants)
• not_provided (3 variants)

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. These statistics are base on transcript: NM_000031467.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			104	4		108
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	104	4	1

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