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

ENSG00000134504NCBI:284252OMIM:613420HGNC:18249Uniprot:Q719H9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
15
clinvar
1
clinvar
17
missense
10
clinvar
3
clinvar
131
clinvar
8
clinvar
1
clinvar
153
nonsense
2
clinvar
2
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
Total 10 3 135 23 2
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
KCTD1protein_codingprotein_codingENST00000408011 4202492
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8550.144125730021257320.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.82951600.5940.000009881671
Missense in Polyphen1545.4130.3303560
Synonymous1.195466.30.8150.00000459513
Loss of Function2.75110.70.09335.17e-7131

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002950.0000295
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Kctd1
Phenotype

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