KCTD15

potassium channel tetramerization domain containing 15, the group of KCTD family

Basic information

Region (hg38): 19:33795933-33815763

Links

ENSG00000153885 ∙ NCBI:79047 ∙ OMIM:615240 ∙ HGNC:23297 ∙ Uniprot:Q96SI1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• frontonasal dysplasia (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KCTD15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCTD15 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in KCTD15

This is a list of pathogenic ClinVar variants found in the KCTD15 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-33800459-C-G		not specified	Uncertain significance (Oct 29, 2024)
19-33800482-G-A		not specified	Uncertain significance (Jan 08, 2025)
19-33800498-C-T		not specified	Uncertain significance (May 13, 2022)
19-33801201-G-A		not specified	Uncertain significance (Apr 25, 2022)
19-33801250-G-C		not specified	Uncertain significance (Aug 26, 2024)
19-33806951-C-T		not specified	Uncertain significance (Feb 04, 2025)
19-33806957-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-33806976-C-T		not specified	Uncertain significance (Feb 21, 2025)
19-33811255-T-A		not specified	Uncertain significance (Jul 05, 2024)
19-33811255-T-G		not specified	Uncertain significance (Sep 22, 2022)
19-33811293-C-T		not specified	Uncertain significance (Jun 09, 2022)
19-33811313-C-A		not specified	Uncertain significance (Jun 02, 2024)
19-33811337-C-T		not specified	Uncertain significance (Oct 25, 2022)
19-33811343-C-T		not specified	Uncertain significance (Dec 03, 2024)
19-33811380-C-T		not specified	Uncertain significance (Sep 11, 2024)
19-33811387-C-G		not specified	Uncertain significance (Aug 02, 2021)
19-33811435-G-T		not specified	Uncertain significance (Nov 25, 2024)
19-33811508-A-G		not specified	Uncertain significance (Jun 29, 2023)
19-33811512-G-A		not specified	Uncertain significance (Oct 23, 2024)
19-33811539-T-C		not specified	Uncertain significance (Sep 12, 2023)
19-33812799-C-T		not specified	Uncertain significance (Jan 07, 2025)
19-33812823-G-T		not specified	Uncertain significance (Jan 18, 2023)
19-33812844-G-A		not specified	Uncertain significance (May 25, 2022)
19-33812892-C-T		not specified	Uncertain significance (Nov 20, 2024)
19-33812896-G-A		not specified	Uncertain significance (Aug 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCTD15	protein_coding	protein_coding	ENST00000430256	5	19831

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0355	0.932	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	155	202	0.768	0.0000153	1813
Missense in Polyphen		48	81.673	0.58771		761
Synonymous	0.905	79	89.9	0.879	0.00000714	600
Loss of Function	1.85	4	10.5	0.383	4.45e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000159	0.000159
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000471	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: During embryonic development, interferes with neural crest formation (By similarity). Inhibits AP2 transcriptional activity by interaction with its activation domain. {ECO:0000250, ECO:0000269|PubMed:23382213}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Negative regulation of activity of TFAP2 (AP-2) family transcription factors;Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.362
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.170
• hipred: N
• hipred_score: 0.490
• ghis: 0.638

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.736

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kctd15
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: multicellular organism development;protein homooligomerization
• Molecular function: protein binding;identical protein binding