KCNK9

Chr 8AD

potassium two pore domain channel subfamily K member 9

Also known as: BIBARS, K2p9.1, KT3.2, TASK-3, TASK3, TASK32

NCBI Gene: 51305 ENSG00000169427 UniProt: Q9NPC2 OMIM: 605874

The protein functions as a pH-dependent potassium channel that regulates neuronal excitability by conducting voltage-dependent outward currents and controlling action potential firing in various brain regions including cerebellum and hippocampus. Mutations cause Birk-Barel syndrome, inherited in an autosomal dominant pattern. The gene is highly constrained against loss-of-function variants and shows imprinted expression in the brain with preferential maternal allele expression.

GeneReviews OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a protein that contains multiple transmembrane regions and two pore-forming P domains and functions as a pH-dependent potassium channel. Amplification and overexpression of this gene have been observed in several types of human carcinomas. This gene is imprinted in the brain, with preferential expression from the maternal allele. A mutation in this gene was associated with Birk-Barel dysmorphism syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2017]

GeneReviews OMIM ResearchGenerating clinical summary…

DNmechanismADLOEUF 0.311 OMIM phenotype

Clinical Summary— KCNK9

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.96). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

8 unique Pathogenic / Likely Pathogenic· 53 VUS of 86 total submissions

Explore recent and relevant literature in Research Assistant →

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GeneReview available — KCNK9

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.31LOEUF

pLI 0.955

Z-score 2.89

OE 0.00 (0.00–0.31)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

2.90Z-score

OE missense 0.48 (0.41–0.56)

118 obs / 246.2 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.31)

0≤0.351.4

Missense OE?0.48 (0.41–0.56)

0≤0.61.4

Synonymous OE?1.10

0≤1.21.6

LoF obs/exp: 0 / 9.7Missense obs/exp: 118 / 246.2Syn Z: -0.84

Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗

limitedKCNK9-related Birk-Barel syndromeDNAD

This gene — mechanism propensity

0.6841th %ile

GOF

0.83top 10%

LOF

0.4627th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative, gain-of-function and loss-of-function). The Badonyi & Marsh model scores gain-of-function highest among its predictions, but genomic evidence (constraint, ClinVar variant spectrum, and literature) most strongly supports dominant-negative. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median · 1 literature citation

GOFprediction above median

LOFLOEUF 0.31

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Literature Evidence

DNFurthermore, expression of dominant-negative mutant KCNK9, responsible for the disease, and electrophysiological experiments demonstrated that ion channel function was involved in the migration defect. Calcium imaging revealed that KCNK9 knockdown or expression of dominant-negative mutant KCNK9 incr1

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

References

1.PMID 23236211 ↗

ClinVar Variant Classifications

86 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic2

Likely Pathogenic6

VUS53

Likely Benign12

Benign6

Conflicting2

Pathogenic

Likely Pathogenic

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	2	0	0	2
Likely Pathogenic	0	6	0	0	6
VUS	7	44	2	0	53
Likely Benign	0	2	0	10	12
Benign	0	0	1	5	6
Conflicting	—				2
Total	7	54	3	15	81

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

54 pathogenic / likely-pathogenic (of 59) ClinVar copy-number / structural variants overlap KCNK9 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →