CEP162

centrosomal protein 162

Basic information

Region (hg38): 6:84124241-84227643

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

Links

ENSG00000135315 ∙ NCBI:22832 ∙ OMIM:610201 ∙ HGNC:21107 ∙ Uniprot:Q5TB80 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	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: gnomAD

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: 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

• 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_gene_trap: N

Mouse Genome Informatics

• Gene name: Cep162

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