KCTD1
Basic information
Region (hg38): 18:26454910-26657401
Previous symbols: [ "C18orf5" ]
Links
Phenotypes
GenCC
Source:
- 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
- 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 15 | 17 | ||||
missense | 10 | 131 | 153 | |||
nonsense | 2 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 10 | 3 | 135 | 23 | 2 |
GnomAD
Source:
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:
- 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
- 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