SLC9C2

protein-coding

solute carrier family 9 member C2 (putative), the group of Solute carrier family 9

Gene summary

Predicted to enable potassium:proton antiporter activity and sodium:proton antiporter activity. Predicted to be involved in potassium ion transmembrane transport; regulation of intracellular pH; and sodium ion import across plasma membrane. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

SLC9A11

MANE transcript

NM_178527.4

Inheritance

—

ClinVar variants

U:104B:16

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr1:173,500,460-173,603,072

External References & Databases

Ensembl (ENSG00000162753)

Transcript & Mutation Effects

hg38 • Region Span ~102.6 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 SLC9C2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 111

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178527.4. 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						0
missense			100 clinvar	15 clinvar	1 clinvar	116
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	104	15	1	120

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178527.4	RefSeq	NP_848622.2	27	MANE Select
ENST00000367714.4	Ensembl	ENSP00000356687.3	27	MANE Select
ENST00001143010.1	Ensembl	ENSP00000809289.1	27	Standard
XM_011509426.3	RefSeq	XP_011507728.1	27	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Stimuli-sensing channels
Ion channel transport
Transport of small molecules

Biological Process

regulation of intracellular pH
potassium ion transmembrane transport
sodium ion import across plasma membrane
proton transmembrane transport

Molecular Function

sodium:proton antiporter activity
potassium:proton antiporter activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367714
Coding exons: 27
Length: 102631
Individuals with no LoFs: 125697
Homozygous LoFs: 0
Heterozygous LoFs: 41
Defined: 125738
p: 0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.01	429	564	0.761	0.0000272	7421
Missense (PolyPhen)		120	165.81	0.72373		2400
Synonymous	1.69	153	182	0.841	0.00000903	2002
Loss of Function	4.87	18	58.1	0.310	0.00000264	822

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0.00043	0.00040	rare
East Asian	0.00017	0.00016	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00016	0.00015	rare
South Asian	0.00021	0.00020	rare
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in pH regulation. {ECO:0000250}.;

Recessive Scores

pRec: 0.0599

Intolerance Scores

RVIS EVS: 0.38
RVIS percentile EVS: 75.63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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