SLC12A9

protein-coding

solute carrier family 12 member 9, the group of Solute carrier family 12

Gene summary

Predicted to enable potassium:chloride symporter activity. Predicted to be involved in several processes, including cell volume homeostasis; chloride ion homeostasis; and potassium ion homeostasis. Located in extracellular exosome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_020246.4

Inheritance

ClinVar variants

U:148B:7

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr7:100,826,820-100,867,010

External References & Databases

Ensembl (ENSG00000146828)

Transcript & Mutation Effects

hg38 • Region Span ~40.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0100038

Submitter: Ambry Genetics

complex neurodevelopmental disorderMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0100038

Submitter: G2P

neurodevelopmental disorderSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC12A9 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 139

not providedTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020246.4. 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				1 clinvar	1 clinvar	2
missense			138 clinvar	5 clinvar		143
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	148	6	1	155

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 108 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020246.4	RefSeq	NP_064631.2	13	MANE Select
ENST00000354161.8	Ensembl	ENSP00000275730.4	13	MANE Select
NM_001267812.2	RefSeq	NP_001254741.1	13	Standard
NM_001267814.2	RefSeq	NP_001254743.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell volume homeostasis
chloride ion homeostasis
potassium ion homeostasis
chloride transmembrane transport
potassium ion import across plasma membrane

Molecular Function

cation:chloride symporter activity
potassium:chloride symporter activity

Cellular Component

plasma membrane
integral component of membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000354161
Coding exons: 13
Length: 40190
Individuals with no LoFs: 125596
Homozygous LoFs: 0
Heterozygous LoFs: 152
Defined: 125748
p: 0.000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.44	413	578	0.714	0.0000376	5709
Missense (PolyPhen)		117	198.19	0.59034		2016
Synonymous	-0.346	279	272	1.03	0.0000178	2194
Loss of Function	0.852	26	31.1	0.835	0.00000159	330

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00025	rare
Latino/Admixed American	0.00041	0.00040	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.0034	0.0018	notable
European (Non-Finnish)	0.00073	0.00069	rare
South Asian	0.00036	0.00036	rare
Other	0.00082	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be an inhibitor of SLC12A1. Seems to correspond to a subunit of a multimeric transport system and thus, additional subunits may be required for its function. {ECO:0000269|PubMed:10871601}.;

Recessive Scores

pRec: 0.158

Intolerance Scores

RVIS EVS: -1.17
RVIS percentile EVS: 6.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.772

Gene Damage Prediction

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