SLC4A9

protein-coding

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

Gene summary

The protein encoded by this gene is a membrane protein involved in anion exchange. Expression of this gene is mostly limited to the kidney. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]

MANE transcript

NM_031467.3

Inheritance

—

ClinVar variants

U:123B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.85

Max pathogenic AF

—

Genomic locus

chr5:140,360,194-140,375,141

External References & Databases

Ensembl (ENSG00000113073)

Transcript & Mutation Effects

hg38 • Region Span ~14.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC4A9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 122

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031467.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			121 clinvar	4 clinvar		125
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	123	4	1	128

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 61 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031467.3	RefSeq	NP_113655.2	21	MANE Select
ENST00000506757.7	Ensembl	ENSP00000424424.1	21	MANE Select
NM_001258426.2	RefSeq	NP_001245355.1	21	Standard
NM_001258427.2	RefSeq	NP_001245356.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Transport of inorganic cations/anions and amino acids/oligopeptides
SLC-mediated transmembrane transport
Transport of small molecules
Bicarbonate transporters

Biological Process

inorganic anion transport
bicarbonate transport
regulation of intracellular pH
anion transmembrane transport

Molecular Function

inorganic anion exchanger activity
sodium:bicarbonate symporter activity
anion:anion antiporter activity

Cellular Component

plasma membrane
integral component of plasma membrane
apical part of cell

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000230993
Coding exons: 21
Length: 14942
Individuals with no LoFs: 124476
Homozygous LoFs: 2
Heterozygous LoFs: 258
Defined: 124736
p: 0.00104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.06	468	537	0.871	0.0000288	6221
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00072	0.00071	rare
Latino/Admixed American	0.00042	0.00041	rare
Ashkenazi Jewish	0.0019	0.0017	notable
East Asian	0.00079	0.00078	rare
Finnish	0.00037	0.00037	rare
European (Non-Finnish)	0.0013	0.0013	notable
South Asian	0.0015	0.0014	notable
Other	0.0017	0.0016	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable apical anion exchanger of the kidney cortex. {ECO:0000250}.;

Recessive Scores

pRec: 0.166

Intolerance Scores

LoFtool: 0.681
RVIS EVS: -0.44
RVIS percentile EVS: 24.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.200

Gene Damage Prediction

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