KCTD21

potassium channel tetramerization domain containing 21, the group of KCTD family

Basic information

Region (hg38): 11:78171249-78188626

Links

ENSG00000188997 ∙ NCBI:283219 ∙ OMIM:618790 ∙ HGNC:27452 ∙ Uniprot:Q4G0X4 ∙ 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 KCTD21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCTD21 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					1	1
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	1

Variants in KCTD21

This is a list of pathogenic ClinVar variants found in the KCTD21 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-78173834-A-C		not specified	Uncertain significance (Oct 29, 2021)
11-78173834-A-G		not specified	Uncertain significance (Oct 12, 2021)
11-78173855-C-T		not specified	Uncertain significance (Aug 08, 2022)
11-78173864-C-T		not specified	Uncertain significance (Feb 17, 2022)
11-78173865-G-A			Benign (Jun 29, 2018)
11-78173917-G-A		not specified	Uncertain significance (Apr 07, 2023)
11-78173918-C-A		not specified	Uncertain significance (Apr 07, 2023)
11-78173938-T-C		not specified	Uncertain significance (Jan 04, 2024)
11-78174115-T-A		not specified	Uncertain significance (Dec 06, 2022)
11-78174146-A-T		not specified	Uncertain significance (Nov 10, 2022)
11-78174190-G-A		not specified	Uncertain significance (Feb 12, 2024)
11-78174200-G-A		not specified	Uncertain significance (Oct 05, 2021)
11-78174215-T-C		not specified	Uncertain significance (Feb 12, 2024)
11-78174238-G-A		not specified	Uncertain significance (May 13, 2024)
11-78174247-A-C		not specified	Uncertain significance (Aug 04, 2023)
11-78174257-C-G		not specified	Uncertain significance (Oct 27, 2021)
11-78174302-C-A		not specified	Uncertain significance (Jan 08, 2024)
11-78174339-C-G		not specified	Uncertain significance (Jun 16, 2024)
11-78174398-C-T		not specified	Uncertain significance (Oct 27, 2022)
11-78174461-T-C		not specified	Uncertain significance (Sep 19, 2022)
11-78174548-C-T		not specified	Uncertain significance (Jun 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCTD21	protein_coding	protein_coding	ENST00000340067	1	17574

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00306	0.608	125728	0	17	125745	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.505	138	156	0.886	0.00000962	1735
Missense in Polyphen		41	55.144	0.74351		532
Synonymous	-0.277	70	67.1	1.04	0.00000431	517
Loss of Function	0.427	4	5.03	0.794	2.18e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000261	0.000261
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable substrate-specific adapter of a BCR (BTB-CUL3- RBX1) E3 ubiquitin-protein ligase complex mediating the ubiquitination and subsequent proteasomal degradation of target proteins. Promotes the ubiquitination of HDAC1. Can function as antagonist of the Hedgehog pathway by affecting the nuclear transfer of transcription factor GLI1; the function probably occurs via HDAC1 down-regulation, keeping GLI1 acetylated and inactive. Inhibits cell growth and tumorigenicity of medulloblastoma (MDB) (PubMed:21472142). {ECO:0000269|PubMed:21472142}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.308
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

• pHI: 0.243
• hipred: N
• hipred_score: 0.459
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kctd21

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination;regulation of growth;negative regulation of smoothened signaling pathway;protein homooligomerization
• Molecular function: identical protein binding;histone deacetylase binding;cullin family protein binding