KCTD5

potassium channel tetramerization domain containing 5, the group of KCTD family

Basic information

Region (hg38): 16:2682522-2709030

Links

ENSG00000167977 ∙ NCBI:54442 ∙ OMIM:611285 ∙ HGNC:21423 ∙ Uniprot:Q9NXV2 ∙ 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 KCTD5 gene.

• Inborn genetic diseases (9 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCTD5 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in KCTD5

This is a list of pathogenic ClinVar variants found in the KCTD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-2682561-C-T		not specified	Uncertain significance (Apr 07, 2022)
16-2682586-G-T		not specified	Uncertain significance (Apr 10, 2023)
16-2682589-G-T		not specified	Uncertain significance (Dec 19, 2023)
16-2682646-G-C		not specified	Uncertain significance (Oct 26, 2021)
16-2682648-G-C		not specified	Uncertain significance (Jan 23, 2024)
16-2682658-A-G		not specified	Uncertain significance (Oct 26, 2021)
16-2682675-T-C		not specified	Uncertain significance (Nov 22, 2021)
16-2682785-C-A		not specified	Uncertain significance (Jul 09, 2021)
16-2697978-G-A		not specified	Uncertain significance (Jan 09, 2024)
16-2702364-C-T			Likely benign (Jan 01, 2023)
16-2702381-A-G		not specified	Uncertain significance (Mar 22, 2023)
16-2702407-C-T		not specified	Uncertain significance (Jan 18, 2023)
16-2707314-G-A		not specified	Uncertain significance (Jan 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCTD5	protein_coding	protein_coding	ENST00000301738	6	26556

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0543	0.928	125643	0	6	125649	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	83	120	0.694	0.00000659	1495
Missense in Polyphen		11	28.547	0.38533		430
Synonymous	-2.69	80	54.7	1.46	0.00000351	460
Loss of Function	2.07	4	11.6	0.345	5.97e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000105	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000701	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000186	0.0000176
Middle Eastern	0.0000701	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Its interaction with CUL3 suggests that it may act as a substrate adapter in some E3 ligase complex. Does not affect the function of Kv channel Kv2.1/KCNB1, Kv1.2/KCNA2, Kv4.2/KCND2 and Kv3.4/KCNC4.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.434
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.255
• hipred: Y
• hipred_score: 0.673
• ghis: 0.715

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.926

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kctd5

Gene ontology

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