KCTD1

potassium channel tetramerization domain containing 1, the group of MicroRNA protein coding host genes|KCTD family

Basic information

Region (hg38): 18:26454909-26657401

Previous symbols: [ "C18orf5" ]

Links

ENSG00000134504 ∙ NCBI:284252 ∙ OMIM:613420 ∙ HGNC:18249 ∙ Uniprot:Q719H9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• scalp-ear-nipple syndrome (Definitive), mode of inheritance: AD
• scalp-ear-nipple syndrome (Strong), mode of inheritance: AD
• scalp-ear-nipple syndrome (Supportive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KCTD1 gene.

• Inborn genetic diseases (40 variants)
• not provided (36 variants)
• Scalp-ear-nipple syndrome (4 variants)
• KCTD1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCTD1 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				5	3	8
missense	1	1	44	4		50
nonsense						0
start loss						0
frameshift			1			1
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region			1	1		2
non coding				4	11	15
Total	1	1	45	13	15

Variants in KCTD1

This is a list of pathogenic ClinVar variants found in the KCTD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-26455686-TTTTG-T			Benign (May 14, 2021)
18-26455711-T-C			Benign (May 12, 2021)
18-26455775-C-T		not specified	Conflicting classifications of pathogenicity (Jan 05, 2024)
18-26455780-G-A		not specified	Uncertain significance (Jan 10, 2023)
18-26455781-G-A		not specified	Uncertain significance (Feb 17, 2024)
18-26455786-C-T		not specified	Uncertain significance (Jan 17, 2024)
18-26455787-G-A		not specified	Uncertain significance (Feb 06, 2023)
18-26455796-G-A			Likely benign (Oct 03, 2023)
18-26455808-G-A		not specified	Uncertain significance (Dec 08, 2023)
18-26455810-C-T			Uncertain significance (Dec 18, 2023)
18-26455824-G-A		KCTD1-related disorder	Benign (Jan 30, 2024)
18-26455836-C-G			Likely benign (Aug 20, 2023)
18-26455860-G-A			Likely benign (Feb 14, 2023)
18-26455865-C-T			Uncertain significance (Sep 09, 2023)
18-26455866-G-A			Likely benign (Aug 23, 2018)
18-26455896-G-A			Likely benign (Jan 24, 2023)
18-26455912-A-G			Likely benign (Nov 01, 2022)
18-26455913-C-A			Likely benign (Jun 10, 2022)
18-26455916-G-A			Likely benign (Jun 11, 2023)
18-26455918-C-A			Benign (Oct 17, 2022)
18-26455940-GTAAGTCC-G			Benign (May 16, 2021)
18-26455981-A-G			Benign (May 16, 2021)
18-26459525-A-C			Benign (May 12, 2021)
18-26459645-C-G			Uncertain significance (Nov 03, 2023)
18-26459672-G-A		not specified	Uncertain significance (Mar 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KCTD1	protein_coding	protein_coding	ENST00000408011	4	202492

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.855	0.144	125730	0	2	125732	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	95	160	0.594	0.00000988	1671
Missense in Polyphen		15	45.413	0.3303		560
Synonymous	1.19	54	66.3	0.815	0.00000459	513
Loss of Function	2.75	1	10.7	0.0933	5.17e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000295	0.0000295
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	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May repress the transcriptional activity of AP-2 family members, including TFAP2A, TFAP2B and TFAP2C to various extent. {ECO:0000269|PubMed:18358072, ECO:0000269|PubMed:19115315}.
• Disease: DISEASE: Scalp-ear-nipple syndrome (SENS) [MIM:181270]: A disease characterized by aplasia cutis congenita of the scalp, breast anomalies that range from hypothelia or athelia to amastia, and minor anomalies of the external ears. Less frequent clinical characteristics include nail dystrophy, dental anomalies, cutaneous syndactyly of the digits, and renal malformations. Penetrance appears to be high, although there is substantial variable expressivity within families. {ECO:0000269|PubMed:23541344}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• 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: 0.113

Intolerance Scores

• loftool: 0.0836
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.201
• hipred: Y
• hipred_score: 0.728
• ghis: 0.670

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.148

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kctd1

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;negative regulation of transcription, DNA-templated;protein homooligomerization
• Cellular component: nucleus;nucleoplasm
• Molecular function: transcription corepressor activity;protein binding;transcription factor binding;identical protein binding