KCTD11

protein-coding

potassium channel tetramerization domain containing 11, the group of KCTD family

Gene summary

Enables identical protein binding activity. Predicted to be involved in positive regulation of neuron differentiation. Predicted to act upstream of or within several processes, including negative regulation of neuroblast proliferation; negative regulation of smoothened signaling pathway; and nervous system development. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C17orf36

MANE transcript

NM_001363642.1

Inheritance

—

ClinVar variants

U:34B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr17:7,351,889-7,354,944

External References & Databases

Ensembl (ENSG00000213859)

Transcript & Mutation Effects

hg38 • Region Span ~3.1 kb

Loading mutation effect viewer...

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 KCTD11 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 34

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001363642.1. 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			34 clinvar		1 clinvar	35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	0	1	35

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001363642.1	RefSeq	NP_001350571.1	1	MANE Select
ENST00000333751.8	Ensembl	ENSP00000328352.5	1	MANE Select
NM_001002914.3	RefSeq	NP_001002914.1	1	Standard
ENST00000576980.2	Ensembl	ENSP00000495203.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell cycle
negative regulation of neuroblast proliferation
protein ubiquitination
regulation of growth
positive regulation of neuron differentiation

Molecular Function

transferase activity
identical protein binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000333751
Coding exons: 1
Length: 3051
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.23	115	159	0.725	0.0000109	1464
Missense (PolyPhen)		39	65.698	0.59363		678
Synonymous	1.38	55	69.6	0.790	0.00000442	540
Loss of Function	0.791	4	6.11	0.655	5.31e-7	46

Population LoF Frequency

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

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role as a marker and a regulator of neuronal differentiation; Up-regulated by a variety of neurogenic signals, such as retinoic acid, epidermal growth factor/EGF and NGFB/nerve growth factor. Induces apoptosis, growth arrest and the expression of cyclin-dependent kinase inhibitor CDKN1B. Plays a role as a tumor repressor and inhibits cell growth and tumorigenicity of medulloblastoma (MDB). Acts as probable substrate-specific adapter for a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex towards HDAC1. Functions as antagonist of the Hedgehog pathway on cell proliferation and differentiation by affecting the nuclear transfer of transcription factor GLI1, thus maintaining cerebellar granule cells in undifferentiated state, this effect probably occurs via HDAC1 down-regulation, keeping GLI1 acetylated and inactive. When knock-down, Hedgehog antagonism is impaired and proliferation of granule cells is sustained. Activates the caspase cascade. {ECO:0000269|PubMed:15249678, ECO:0000269|PubMed:20081843, ECO:0000269|PubMed:21237243}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.276
RVIS EVS: 0.28
RVIS percentile EVS: 71.08

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.707

Gene Damage Prediction

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