GeneBe

CEP250

centrosomal protein 250

Basic information

Region (hg38): 20:35455164-35519280

Previous symbols: [ "CEP2" ]

Links

ENSG00000126001 ∙ NCBI:11190 ∙ OMIM:609689 ∙ HGNC:1859 ∙ Uniprot:Q9BV73 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • cone-rod dystrophy and hearing loss 2 (Strong), mode of inheritance: AR
  • retinitis pigmentosa (Limited), mode of inheritance: AR
  • cone-rod dystrophy and hearing loss 2 (Limited), mode of inheritance: AR
  • male infertility with azoospermia or oligozoospermia due to single gene mutation (Disputed Evidence), mode of inheritance: AR
  • cone-rod dystrophy and hearing loss 2 (Strong), mode of inheritance: AR
  • cone-rod dystrophy and hearing loss 2 (Strong), mode of inheritance: AR
  • cone-rod dystrophy and hearing loss 2 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Cone-rod dystrophy and hearing loss 2ARAudiologic/OtolaryngologicThe condition can involve early-onset hearing impairment, and early recognition and treatment may improve outcomes, including speech and language developmentAudiologic/Otolaryngologic; Ophthalmologic24780881; 28005958; 29718797; 30459346

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEP250 gene.

  • not_provided (1424 variants)
  • not_specified (250 variants)
  • CEP250-related_disorder (43 variants)
  • Cone-rod_dystrophy_and_hearing_loss_2 (34 variants)
  • Retinal_dystrophy (15 variants)
  • Optic_atrophy (4 variants)
  • Usher_syndrome (2 variants)
  • EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
  • Monogenic_hearing_loss (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP250 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007186.6. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
6
clinvar
391
clinvar
17
clinvar
 415
missense
1
clinvar
762
clinvar
33
clinvar
17
clinvar
 813
nonsense
36
clinvar
5
clinvar
1
clinvar
 42
start loss
0
frameshift
37
clinvar
2
clinvar
5
clinvar
 44
splice donor/acceptor (+/-2bp)
2
clinvar
11
clinvar
 13
Total 77 18 774 424 34

Highest pathogenic variant AF is 0.0003270709

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CEP250protein_codingprotein_codingENST00000397527 3256820
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
9.45e-331.0012545002981257480.00119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.3311361.27e+30.8950.000072615721
Missense in Polyphen332394.360.841875341
Synonymous2.444515220.8640.00002664791
Loss of Function5.17771440.5350.000008091476

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002570.00254
Ashkenazi Jewish0.0003020.000298
East Asian0.0008820.000870
Finnish0.003240.00273
European (Non-Finnish)0.001020.00100
Middle Eastern0.0008820.000870
South Asian0.0006650.000621
Other0.001850.00179

dbNSFP

Source: dbNSFP

Function
FUNCTION: Probably plays an important role in centrosome cohesion during interphase.;
Pathway
Mesodermal Commitment Pathway;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;Cell Cycle;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

pRec
0.112

Intolerance Scores

loftool
0.939
rvis_EVS
-0.77
rvis_percentile_EVS
13.17

Haploinsufficiency Scores

pHI
0.144
hipred
N
hipred_score
0.328
ghis
0.580

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.987

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cep250
Phenotype

Gene ontology

Biological process
G2/M transition of mitotic cell cycle;mitotic cell cycle;protein localization;regulation of G2/M transition of mitotic cell cycle;centriole-centriole cohesion;regulation of centriole-centriole cohesion;protein localization to organelle;ciliary basal body-plasma membrane docking;positive regulation of protein localization to centrosome;non-motile cilium assembly
Cellular component
centrosome;centriole;microtubule organizing center;cytosol;cilium;protein-containing complex;perinuclear region of cytoplasm;extracellular exosome
Molecular function
protein binding;protein C-terminus binding;protein kinase binding;protein domain specific binding