KCTD9

protein-coding

potassium channel tetramerization domain containing 9, the group of KCTD family|BTB domain containing

Gene summary

Enables cullin family protein binding activity and identical protein binding activity. Predicted to be involved in intracellular signal transduction; protein homooligomerization; and protein ubiquitination. Predicted to act upstream of or within several processes, including NK T cell lineage commitment; natural killer cell activation; and response to virus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_017634.4

Inheritance

—

ClinVar variants

U:21

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr8:25,427,847-25,458,476

External References & Databases

Ensembl (ENSG00000104756)

Transcript & Mutation Effects

hg38 • Region Span ~30.6 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 KCTD9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 17

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017634.4. 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
missense			19 clinvar			19
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	0	0	21

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017634.4	RefSeq	NP_060104.2	12	MANE Select
ENST00000221200.9	Ensembl	ENSP00000221200.4	12	MANE Select
ENST00000519665.5	Ensembl	ENSP00000466874.1	2	Standard
ENST00000523140.5	Ensembl	ENSP00000467904.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein ubiquitination
intracellular signal transduction
protein homooligomerization

Molecular Function

protein binding
identical protein binding
protein self-association
cullin family protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000221200
Coding exons: 12
Length: 30627
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125746
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.60	62	208	0.297	0.0000105	2532
Missense (PolyPhen)		15	98.477	0.15232		1278
Synonymous	0.597	66	72.5	0.911	0.00000344	751
Loss of Function	3.35	7	25.1	0.278	0.00000164	278

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00020	0.00018	rare
Latino/Admixed American	0.00016	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex, which mediates the ubiquitination of target proteins, leading to their degradation by the proteasome. {ECO:0000305}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.496
RVIS EVS: -0.12
RVIS percentile EVS: 44.89

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.471

Gene Damage Prediction

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