KCTD20

protein-coding

potassium channel tetramerization domain containing 20, the group of KCTD family

Gene summary

Predicted to enable identical protein binding activity. Predicted to be involved in positive regulation of phosphorylation. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C6orf69

MANE transcript

NM_173562.5

Inheritance

—

ClinVar variants

U:48

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.44

Max pathogenic AF

—

Genomic locus

chr6:36,442,767-36,491,143

External References & Databases

Ensembl (ENSG00000112078)

Transcript & Mutation Effects

hg38 • Region Span ~48.4 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 KCTD20 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 45

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173562.5. 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			46 clinvar			46
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	48	0	0	48

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 83 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173562.5	RefSeq	NP_775833.2	7	MANE Select
ENST00000373731.7	Ensembl	ENSP00000362836.2	7	MANE Select
NM_001286579.2	RefSeq	NP_001273508.1	4	Standard
NM_001286580.2	RefSeq	NP_001273509.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of phosphorylation

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373731
Coding exons: 7
Length: 48377
Individuals with no LoFs: 125683
Homozygous LoFs: 0
Heterozygous LoFs: 64
Defined: 125747
p: 0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.19	189	241	0.784	0.0000132	2791
Missense (PolyPhen)		58	90.221	0.64286		1043
Synonymous	0.0262	84	84.3	0.996	0.00000442	786
Loss of Function	2.22	8	18.2	0.439	0.00000102	219

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00055	0.00054	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.00023	0.00023	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Promotes the phosphorylation of AKT family members. {ECO:0000250|UniProtKB:Q8CDD8}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.516
RVIS EVS: -0.05
RVIS percentile EVS: 50.22

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.894

Gene Damage Prediction

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