KCTD1

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

Basic information

Region (hg38): 18:26454910-26657401

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 (Limited), 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.

• not_specified (117 variants)
• not_provided (44 variants)
• Scalp-ear-nipple_syndrome (41 variants)
• KCTD1-related_disorder (7 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. These statistics are base on transcript: NM_001142730.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	15	1	17
missense	10	3	131	8	1	153
nonsense			2			2
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	10	3	135	23	2

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