CNTRL

centriolin

Basic information

Region (hg38): 9:121074659-121177729

Previous symbols: [ "CEP1", "CEP110" ]

Links

ENSG00000119397 ∙ NCBI:11064 ∙ OMIM:605496 ∙ HGNC:1858 ∙ Uniprot:Q7Z7A1 ∙ 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 CNTRL gene.

• Inborn genetic diseases (78 variants)
• not provided (19 variants)
• C5-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNTRL 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	4	6
missense			71	12	5	88
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1			1
Total	0	0	72	14	9

Variants in CNTRL

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

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

Position	Type	Phenotype	Significance	ClinVar
9-121074757-CA-C			Likely pathogenic (-)
9-121074774-G-T		C5-related disorder	Uncertain significance (Sep 12, 2023)
9-121088358-C-A		not specified	Uncertain significance (Feb 28, 2023)
9-121088364-C-A			Likely benign (Jul 11, 2018)
9-121088405-A-G		not specified	Uncertain significance (Feb 28, 2024)
9-121088508-A-G		not specified	Uncertain significance (Mar 20, 2023)
9-121088538-A-G		not specified	Uncertain significance (Jul 12, 2023)
9-121090350-C-T		not specified	Uncertain significance (Dec 18, 2023)
9-121090387-C-T			Benign (Dec 31, 2019)
9-121090388-G-A		not specified	Uncertain significance (Jul 12, 2023)
9-121094988-G-A		not specified	Uncertain significance (Aug 16, 2021)
9-121096529-G-A		not specified	Uncertain significance (Aug 10, 2021)
9-121096562-C-T		not specified	Uncertain significance (Jan 02, 2024)
9-121098401-A-C		not specified	Uncertain significance (Dec 11, 2023)
9-121098418-A-G			Benign (May 21, 2018)
9-121098471-A-G		not specified	Uncertain significance (Aug 01, 2022)
9-121098483-C-G		not specified	Uncertain significance (Jun 28, 2023)
9-121107843-A-G		not specified	Uncertain significance (Mar 14, 2023)
9-121107873-A-G		not specified	Uncertain significance (Feb 13, 2024)
9-121107948-C-G		not specified	Uncertain significance (Dec 27, 2023)
9-121112538-T-C		not specified	Uncertain significance (Aug 13, 2021)
9-121113503-A-G		not specified	Uncertain significance (May 09, 2023)
9-121113542-T-C		not specified	Uncertain significance (Jul 07, 2022)
9-121113557-A-T		not specified	Uncertain significance (Jan 31, 2024)
9-121113566-A-G		not specified	Uncertain significance (Mar 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNTRL	protein_coding	protein_coding	ENST00000373855	42	102748

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.89e-54	0.00483	125344	2	402	125748	0.00161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.218	1113	1.13e+3	0.982	0.0000570	15373
Missense in Polyphen		276	295.3	0.93463		4303
Synonymous	0.845	384	406	0.947	0.0000192	4132
Loss of Function	2.62	102	135	0.757	0.00000738	1660

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00337	0.00335
Ashkenazi Jewish	0.000700	0.000695
East Asian	0.00150	0.00141
Finnish	0.000742	0.000739
European (Non-Finnish)	0.00169	0.00167
Middle Eastern	0.00150	0.00141
South Asian	0.00255	0.00239
Other	0.00218	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in cell cycle progression and cytokinesis. During the late steps of cytokinesis, anchors exocyst and SNARE complexes at the midbody, thereby allowing secretory vesicle- mediated abscission. {ECO:0000269|PubMed:12732615, ECO:0000269|PubMed:16213214}.
• Pathway: Disease;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;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Signaling by FGFR in disease;Cell Cycle;Signaling by cytosolic FGFR1 fusion mutants;FGFR1 mutant receptor activation;Signaling by FGFR1 in disease;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Diseases of signal transduction;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.23

Haploinsufficiency Scores

• pHI: 0.0928
• hipred: N
• hipred_score: 0.336
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Cntrl
• Phenotype: 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); renal/urinary system phenotype; vision/eye phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;regulation of G2/M transition of mitotic cell cycle;peptidyl-tyrosine phosphorylation;cell division;regulation of cytoskeleton organization;ciliary basal body-plasma membrane docking
• Cellular component: centrosome;microtubule organizing center;cytosol;membrane;Flemming body;centriolar subdistal appendage
• Molecular function: protein tyrosine kinase activity;protein binding;cytoskeletal protein binding