CEP162

centrosomal protein 162

Basic information

Region (hg38): 6:84124241-84227643

Previous symbols: [ "C6orf84", "KIAA1009" ]

Links

ENSG00000135315NCBI:22832OMIM:610201HGNC:21107Uniprot:Q5TB80AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEP162 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
2
missense
161
clinvar
16
clinvar
177
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 161 17 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CEP162protein_codingprotein_codingENST00000403245 26103394
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.53e-270.052812543901511255900.000601
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.2446466291.030.00003019279
Missense in Polyphen196192.51.01823035
Synonymous0.03782162170.9970.00001062358
Loss of Function1.705064.80.7720.00000284986

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001400.00140
Ashkenazi Jewish0.000.00
East Asian0.001810.00180
Finnish0.0001400.000139
European (Non-Finnish)0.0005900.000564
Middle Eastern0.001810.00180
South Asian0.0005970.000555
Other0.0005210.000490

dbNSFP

Source: dbNSFP

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