CEP97

centrosomal protein 97

Basic information

Region (hg38): 3:101724534-101770562

Previous symbols: [ "LRRIQ2" ]

Links

ENSG00000182504 ∙ NCBI:79598 ∙ OMIM:615864 ∙ HGNC:26244 ∙ Uniprot:Q8IW35 ∙ 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 CEP97 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP97 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			1	38	7	46
missense		1	123	11	4	139
nonsense			2			2
start loss						0
frameshift			4			4
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			4	6		10
non coding			1	10	2	13
Total	0	1	132	59	13

Variants in CEP97

This is a list of pathogenic ClinVar variants found in the CEP97 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-101724690-G-T			Likely benign (Dec 11, 2023)
3-101724702-C-G		not specified	Uncertain significance (Dec 03, 2024)
3-101724704-T-C			Likely benign (Nov 20, 2022)
3-101724726-C-G			Likely benign (Feb 19, 2022)
3-101724726-C-T			Likely benign (Jan 19, 2023)
3-101724736-C-T			Likely benign (Jul 14, 2022)
3-101726581-G-A			Benign (Jan 08, 2024)
3-101726605-A-C		not specified	Uncertain significance (Feb 28, 2024)
3-101726625-A-G			Likely benign (Feb 03, 2023)
3-101726638-C-A			Uncertain significance (Oct 19, 2023)
3-101726653-GA-G			Uncertain significance (Oct 24, 2023)
3-101726667-C-G		not specified	Uncertain significance (Mar 01, 2023)
3-101726683-A-G		not specified	Uncertain significance (Dec 07, 2024)
3-101726707-A-G		not specified	Uncertain significance (Nov 28, 2024)
3-101726726-G-A			Benign (Jan 26, 2024)
3-101726739-A-T			Uncertain significance (Jan 12, 2022)
3-101727363-AAT-A			Benign (Jan 31, 2024)
3-101727363-A-ATTT			Likely benign (Dec 18, 2023)
3-101727378-T-C			Likely benign (Feb 10, 2023)
3-101727381-A-T			Uncertain significance (Aug 16, 2023)
3-101727383-T-C			Uncertain significance (Jul 23, 2022)
3-101727401-C-T		not specified	Uncertain significance (Sep 25, 2023)
3-101727410-C-T		not specified	Uncertain significance (Aug 02, 2022)
3-101727426-C-T			Uncertain significance (Jan 12, 2023)
3-101727435-C-T			Uncertain significance (Jun 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP97	protein_coding	protein_coding	ENST00000341893	11	46638

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.04e-11	0.991	125684	0	64	125748	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.682	410	451	0.910	0.0000225	5676
Missense in Polyphen		84	101.84	0.82482		1293
Synonymous	0.758	157	170	0.926	0.00000849	1663
Loss of Function	2.53	24	41.6	0.577	0.00000211	492

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000441	0.000440
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000550	0.000544
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000266	0.000264
Middle Eastern	0.000550	0.000544
South Asian	0.000131	0.000131
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a key negative regulator of ciliogenesis in collaboration with CCP110 by capping the mother centriole thereby preventing cilia formation. Required for recruitment of CCP110 to the centrosome. {ECO:0000269|PubMed:17719545}.
• Pathway: Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.0988

Intolerance Scores

• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.21

Haploinsufficiency Scores

• pHI: 0.400
• hipred: N
• hipred_score: 0.414
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.862

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cep97
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: ciliary basal body-plasma membrane docking;regulation of mitotic spindle assembly;negative regulation of cilium assembly
• Cellular component: centrosome;microtubule organizing center;cytosol;protein-containing complex
• Molecular function: protein binding;calmodulin binding