CEP162
Basic information
Region (hg38): 6:84124241-84227643
Previous symbols: [ "C6orf84", "KIAA1009" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (174 variants)
- not_provided (7 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP162 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014895.4. 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 | 2 | |||||
missense | 161 | 16 | 177 | |||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 161 | 17 | 1 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CEP162 | protein_coding | protein_coding | ENST00000403245 | 26 | 103394 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.53e-27 | 0.0528 | 125439 | 0 | 151 | 125590 | 0.000601 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.244 | 646 | 629 | 1.03 | 0.0000301 | 9279 |
Missense in Polyphen | 196 | 192.5 | 1.0182 | 3035 | ||
Synonymous | 0.0378 | 216 | 217 | 0.997 | 0.0000106 | 2358 |
Loss of Function | 1.70 | 50 | 64.8 | 0.772 | 0.00000284 | 986 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00140 | 0.00140 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00181 | 0.00180 |
Finnish | 0.000140 | 0.000139 |
European (Non-Finnish) | 0.000590 | 0.000564 |
Middle Eastern | 0.00181 | 0.00180 |
South Asian | 0.000597 | 0.000555 |
Other | 0.000521 | 0.000490 |
dbNSFP
Source:
- Function
- FUNCTION: Required to promote assembly of the transition zone in primary cilia. Acts by specifically recognizing and binding the axonemal microtubule. Localizes to the distal ends of centrioles before ciliogenesis and directly binds to axonemal microtubule, thereby promoting and restricting transition zone formation specifically at the cilia base. Required to mediate CEP290 association with microtubules. {ECO:0000269|PubMed:23644468}.;
- Pathway
- Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.0891
Intolerance Scores
- loftool
- rvis_EVS
- 1.13
- rvis_percentile_EVS
- 92.13
Haploinsufficiency Scores
- pHI
- 0.386
- hipred
- N
- hipred_score
- 0.123
- ghis
- 0.469
Essentials
- essential_gene_CRISPR
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- gene_indispensability_score
Mouse Genome Informatics
- Gene name
- Cep162
- Phenotype
Zebrafish Information Network
- Gene name
- cep162
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- cilium assembly;ciliary basal body-plasma membrane docking
- Cellular component
- nucleus;centrosome;centriole;spindle;cytosol;axonemal microtubule
- Molecular function
- protein binding