CEP170

centrosomal protein 170

Basic information

Region (hg38): 1:243124427-243255348

Previous symbols: [ "KIAA0470" ]

Links

ENSG00000143702 ∙ NCBI:9859 ∙ OMIM:613023 ∙ HGNC:28920 ∙ Uniprot:Q5SW79 ∙ 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 CEP170 gene.

• Inborn genetic diseases (54 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP170 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			53	1		54
nonsense						0
start loss					1	1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		1	2
Total	0	0	54	3	2

Variants in CEP170

This is a list of pathogenic ClinVar variants found in the CEP170 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-243126601-T-C		not specified	Uncertain significance (Apr 25, 2022)
1-243126617-G-C		not specified	Uncertain significance (Feb 15, 2023)
1-243126622-G-A		not specified	Uncertain significance (Jul 09, 2021)
1-243126634-C-T		not specified	Uncertain significance (Apr 25, 2022)
1-243126654-G-A		not specified	Uncertain significance (Dec 07, 2021)
1-243136134-T-A			Benign (May 30, 2017)
1-243136167-A-G		not specified	Uncertain significance (Jun 03, 2022)
1-243136168-T-C		not specified	Uncertain significance (Feb 05, 2024)
1-243136186-T-C		not specified	Uncertain significance (Apr 13, 2023)
1-243136201-C-T		not specified	Uncertain significance (Dec 28, 2022)
1-243136217-A-T		not specified	Uncertain significance (Oct 06, 2022)
1-243140017-A-G		not specified	Uncertain significance (Oct 13, 2023)
1-243140049-T-C		not specified	Uncertain significance (May 05, 2023)
1-243140065-T-A		not specified	Uncertain significance (Jan 02, 2024)
1-243142447-C-T		not specified	Uncertain significance (Dec 14, 2023)
1-243156259-G-A			Benign/Likely benign (May 01, 2022)
1-243156283-G-C		not specified	Uncertain significance (Jul 11, 2023)
1-243156309-T-C			Benign (Dec 31, 2019)
1-243156323-C-A		not specified	Uncertain significance (Aug 02, 2023)
1-243156333-G-A		not specified	Uncertain significance (Aug 30, 2022)
1-243164385-A-G		not specified	Uncertain significance (Dec 08, 2023)
1-243164389-G-C		not specified	Uncertain significance (May 08, 2023)
1-243164410-T-C		not specified	Uncertain significance (Dec 15, 2023)
1-243164452-T-C		not specified	Uncertain significance (Nov 22, 2023)
1-243164472-G-A		not specified	Uncertain significance (Sep 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP170	protein_coding	protein_coding	ENST00000366542	19	130921

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000321	124625	0	12	124637	0.0000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.20	593	764	0.776	0.0000396	10269
Missense in Polyphen		159	299.6	0.5307		3987
Synonymous	1.92	222	262	0.849	0.0000133	3040
Loss of Function	6.58	6	61.8	0.0970	0.00000357	846

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000156	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000180	0.000167
Finnish	0.0000471	0.0000464
European (Non-Finnish)	0.0000266	0.0000265
Middle Eastern	0.000180	0.000167
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in microtubule organization (PubMed:15616186). Required for centriole subdistal appendage assembly (PubMed:28422092). {ECO:0000269|PubMed:15616186, ECO:0000269|PubMed:28422092}.

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.871
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.82

Haploinsufficiency Scores

• pHI: 0.515
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.929

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cep170

Gene ontology

• Cellular component: centrosome;centriole;spindle;cytosol;microtubule;plasma membrane;centriolar subdistal appendage
• Molecular function: protein binding