KCTD11

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

Basic information

Region (hg38): 17:7351889-7354944

Previous symbols: [ "C17orf36" ]

Links

ENSG00000213859 ∙ NCBI:147040 ∙ OMIM:609848 ∙ HGNC:21302 ∙ Uniprot:Q693B1 ∙ 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 KCTD11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCTD11 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			11		1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	1

Variants in KCTD11

This is a list of pathogenic ClinVar variants found in the KCTD11 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7352979-C-G		not specified	Uncertain significance (May 15, 2024)
17-7353006-G-A			Benign (Dec 31, 2019)
17-7353075-C-G		not specified	Uncertain significance (Dec 31, 2023)
17-7353132-T-C		not specified	Uncertain significance (Jul 25, 2023)
17-7353162-C-T		not specified	Uncertain significance (Dec 08, 2023)
17-7353243-G-T		not specified	Uncertain significance (Oct 25, 2022)
17-7353317-C-A		not specified	Uncertain significance (Mar 27, 2023)
17-7353348-G-T		not specified	Uncertain significance (Mar 25, 2022)
17-7353349-C-T		not specified	Uncertain significance (Sep 25, 2023)
17-7353355-G-A		not specified	Uncertain significance (Oct 25, 2024)
17-7353367-G-C		not specified	Uncertain significance (Dec 03, 2024)
17-7353388-C-A		not specified	Uncertain significance (Mar 07, 2024)
17-7353486-G-T		not specified	Uncertain significance (Jun 30, 2023)
17-7353501-C-T		not specified	Uncertain significance (Dec 02, 2024)
17-7353504-C-T		not specified	Uncertain significance (Oct 11, 2024)
17-7353513-G-C		not specified	Uncertain significance (Jul 30, 2024)
17-7353535-A-T		not specified	Uncertain significance (Nov 21, 2024)
17-7353587-C-G		not specified	Uncertain significance (Jun 10, 2024)
17-7353589-C-T		not specified	Uncertain significance (May 23, 2023)
17-7353633-C-T		not specified	Uncertain significance (Oct 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCTD11	protein_coding	protein_coding	ENST00000333751	1	3051

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00550	0.732	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	115	159	0.725	0.0000109	1464
Missense in 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

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	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.146
• hipred: Y
• hipred_score: 0.645
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.707

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kctd11

Gene ontology

• Biological process: cell cycle;negative regulation of neuroblast proliferation;protein ubiquitination;regulation of growth;positive regulation of neuron differentiation;negative regulation of smoothened signaling pathway;protein homooligomerization
• Cellular component: cytoplasm
• Molecular function: transferase activity;identical protein binding