CCP110

centriolar coiled-coil protein 110

Basic information

Region (hg38): 16:19523811-19553408

Links

ENSG00000103540 ∙ NCBI:9738 ∙ OMIM:609544 ∙ HGNC:24342 ∙ Uniprot:O43303 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ciliopathy (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCP110 gene.

• not_specified (112 variants)
• not_provided (4 variants)
• See_cases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCP110 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001323572.2. 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			2	2	2	6
missense			99	5	1	105
nonsense		1	1			2
start loss						0
frameshift		1				1
splice donor/acceptor (+/-2bp)						0
Total	0	2	102	7	3

Highest pathogenic variant AF is 0.00000371769

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCP110	protein_coding	protein_coding	ENST00000381396	14	29598

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00668	0.993	125698	0	46	125744	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	437	519	0.842	0.0000254	6677
Missense in Polyphen		171	216.07	0.7914		2852
Synonymous	1.91	145	177	0.818	0.00000904	1862
Loss of Function	4.46	13	45.5	0.286	0.00000226	609

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000431	0.000427
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000385	0.000381
Finnish	0.0000979	0.0000924
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000385	0.000381
South Asian	0.000165	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Necessary for centrosome duplication at different stages of procentriole formation. Acts as a key negative regulator of ciliogenesis in collaboration with CEP97 by capping the mother centriole thereby preventing cilia formation (PubMed:17719545 PubMed:17681131, PubMed:23486064). Also involved in promoting ciliogenesis. May play a role in the assembly of the mother centriole subdistal appendages (SDA) thereby effecting the fusion of recycling endosomes to basal bodies during cilia formation (By similarity). Required for correct spindle formation and has a role in regulating cytokinesis and genome stability via cooperation with CALM1 and CETN2 (PubMed:16760425). {ECO:0000250|UniProtKB:Q7TSH4, ECO:0000269|PubMed:12361598, ECO:0000269|PubMed:16760425, ECO:0000269|PubMed:17681131, ECO:0000269|PubMed:17719545, ECO:0000269|PubMed:23486064}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Regulation of PLK1 Activity at G2/M Transition;Recruitment of mitotic centrosome proteins and complexes;Loss of Nlp from mitotic centrosomes;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;Ub-specific processing proteases;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;Deubiquitination;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Intolerance Scores

• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.54

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.270
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccp110
• Phenotype: craniofacial phenotype; cellular phenotype; growth/size/body region phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; digestive/alimentary phenotype; vision/eye phenotype; skeleton phenotype; renal/urinary system phenotype; embryo 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;centriole replication;regulation of G2/M transition of mitotic cell cycle;protein deubiquitination;ciliary basal body organization;regulation of cytokinesis;positive regulation of cilium assembly;centrosome duplication;ciliary basal body-plasma membrane docking;negative regulation of cilium assembly
• Cellular component: centrosome;centriole;cytosol;cilium;protein-containing complex
• Molecular function: protein binding