KCTD19

protein-coding

potassium channel tetramerization domain containing 19, the group of KCTD family

Gene summary

Predicted to enable identical protein binding activity. Predicted to be involved in male meiotic nuclear division. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001100915.3

Inheritance

—

ClinVar variants

P:1U:119B:11

Top phenotype

Cerebral visual impairment and intellectual disability

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr16:67,289,428-67,326,760

External References & Databases

Ensembl (ENSG00000168676)

Transcript & Mutation Effects

hg38 • Region Span ~37.3 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 KCTD19 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 116

not providedTotal: 8

Cerebral visual impairment and intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001100915.3. 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	4 clinvar	2 clinvar	7
missense		1 clinvar	116 clinvar	3 clinvar	1 clinvar	121
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)				1 clinvar		1
Total	0	1	119	8	3	131

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001100915.3	RefSeq	NP_001094385.1	16	MANE Select
ENST00000304372.6	Ensembl	ENSP00000305702.5	16	MANE Select
ENST00000562721.1	Ensembl	ENSP00000462122.1	2	Standard
ENST00000562841.1	Ensembl	ENSP00000463249.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein homooligomerization

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000304372
Coding exons: 16
Length: 37336
Individuals with no LoFs: 124516
Homozygous LoFs: 1
Heterozygous LoFs: 294
Defined: 124811
p: 0.00118

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.29	432	514	0.840	0.0000280	6023
Missense (PolyPhen)		114	148.06	0.76995		1902
Synonymous	-0.0634	216	215	1.01	0.0000125	1852
Loss of Function	2.19	30	46.0	0.652	0.00000231	528

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00058	0.00058	rare
Latino/Admixed American	0.00081	0.00081	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.0022	0.0021	notable
Finnish	0.0038	0.0037	notable
European (Non-Finnish)	0.0010	0.0010	notable
South Asian	0.00036	0.00036	rare
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.862
RVIS EVS: -0.42
RVIS percentile EVS: 25.83

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.567

Gene Damage Prediction

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