KCTD2

potassium channel tetramerization domain containing 2, the group of KCTD family

Basic information

Region (hg38): 17:75032574-75065889

Links

ENSG00000180901 ∙ NCBI:23510 ∙ OMIM:613422 ∙ HGNC:21294 ∙ Uniprot:Q14681 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KCTD2 gene.

• Inborn genetic diseases (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCTD2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	10	0	0

Variants in KCTD2

This is a list of pathogenic ClinVar variants found in the KCTD2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-75039234-G-A		not specified	Uncertain significance (Aug 15, 2023)
17-75040126-T-C		not specified	Uncertain significance (Oct 06, 2022)
17-75040148-C-A		not specified	Uncertain significance (Aug 02, 2021)
17-75042246-T-C		not specified	Uncertain significance (Apr 12, 2022)
17-75042578-T-C		not specified	Uncertain significance (Dec 02, 2022)
17-75042593-T-C		not specified	Uncertain significance (May 03, 2023)
17-75047290-G-C		not specified	Uncertain significance (Jul 08, 2022)
17-75047294-G-A		not specified	Uncertain significance (Dec 01, 2022)
17-75047300-G-T		not specified	Uncertain significance (Dec 22, 2023)
17-75047308-G-A		not specified	Uncertain significance (Feb 07, 2023)
17-75047308-G-T		not specified	Uncertain significance (Aug 22, 2023)
17-75047327-G-A		not specified	Uncertain significance (Oct 02, 2023)
17-75047342-C-T		not specified	Uncertain significance (Nov 03, 2022)
17-75047372-C-T		not specified	Uncertain significance (Jan 02, 2024)
17-75047393-C-T		not specified	Uncertain significance (Jun 09, 2022)
17-75049248-G-T		not specified	Uncertain significance (May 09, 2022)
17-75049269-C-A		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCTD2	protein_coding	protein_coding	ENST00000322444	6	33315

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.201	0.790	125739	0	4	125743	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.72	75	130	0.577	0.00000781	1669
Missense in Polyphen		19	42.693	0.44503		469
Synonymous	0.160	56	57.5	0.973	0.00000397	548
Loss of Function	2.26	3	11.1	0.270	4.70e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000703	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000952	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.285
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.330
• hipred: Y
• hipred_score: 0.662
• ghis: 0.641

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.415

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kctd2

Gene ontology

• Biological process: proteasome-mediated ubiquitin-dependent protein catabolic process;protein homooligomerization
• Cellular component: cytoplasm;Cul3-RING ubiquitin ligase complex
• Molecular function: protein-containing complex binding;cullin family protein binding