GeneBe

CEP55

centrosomal protein 55

Basic information

Region (hg38): 10:93496612-93529092

Previous symbols: [ "C10orf3" ]

Links

ENSG00000138180 ∙ NCBI:55165 ∙ OMIM:610000 ∙ HGNC:1161 ∙ Uniprot:Q53EZ4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • multinucleated neurons-anhydramnios-renal dysplasia-cerebellar hypoplasia-hydranencephaly syndrome (Moderate), mode of inheritance: AR
  • multinucleated neurons-anhydramnios-renal dysplasia-cerebellar hypoplasia-hydranencephaly syndrome (Moderate), mode of inheritance: AR
  • complex neurodevelopmental disorder (Moderate), mode of inheritance: AR
  • multinucleated neurons-anhydramnios-renal dysplasia-cerebellar hypoplasia-hydranencephaly syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Multinucleated neurons, anhydramnios, renal dysplasia, cerebellar hypoplasia and hydranencephaly (MARCH)ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingNeurologic; Renal28264986; 28295209

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEP55 gene.

  • Inborn_genetic_diseases (57 variants)
  • not_provided (39 variants)
  • Multinucleated_neurons-anhydramnios-renal_dysplasia-cerebellar_hypoplasia-hydranencephaly_syndrome (12 variants)
  • CEP55-related_disorder (10 variants)
  • not_specified (3 variants)
  • Abnormality_of_prenatal_development_or_birth (1 variants)
  • Encephalopathy,_lethal,_due_to_defective_mitochondrial_peroxisomal_fission_1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP55 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018131.5. 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
11
clinvar
3
clinvar
 14
missense
59
clinvar
10
clinvar
4
clinvar
 73
nonsense
4
clinvar
4
clinvar
 8
start loss
0
frameshift
2
clinvar
 2
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 7 4 59 21 7

Highest pathogenic variant AF is 0.00044866113

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CEP55protein_codingprotein_codingENST00000371485 832461
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.96e-120.37812562501231257480.000489
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4972112320.9080.00001173022
Missense in Polyphen3745.1570.81937603
Synonymous0.6778290.20.9090.00000479841
Loss of Function1.222229.10.7560.00000173334

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008430.000843
Ashkenazi Jewish0.000.00
East Asian0.0004360.000435
Finnish0.0001850.000185
European (Non-Finnish)0.0005640.000563
Middle Eastern0.0004360.000435
South Asian0.0004930.000490
Other0.0006570.000652

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays a role in mitotic exit and cytokinesis (PubMed:16198290, PubMed:17853893). Recruits PDCD6IP and TSG101 to midbody during cytokinesis. Required for successful completion of cytokinesis (PubMed:17853893). Not required for microtubule nucleation (PubMed:16198290). Plays a role in the development of the brain and kidney (PubMed:28264986). {ECO:0000269|PubMed:16198290, ECO:0000269|PubMed:17853893, ECO:0000269|PubMed:28264986}.;
Disease
DISEASE: Multinucleated neurons, anhydramnios, renal dysplasia, cerebellar hypoplasia and hydranencephaly (MARCH) [MIM:236500]: An autosomal recessive, congenital disease characterized by severe hydranencephaly with multinucleated neurons, renal aplasia or dysplasia, and hypoplastic kidneys. Hydranencephaly is an anomaly leading to replacement of the cerebral hemispheres with a fluid- filled cyst. MARCH results in death in utero or in the perinatal period. {ECO:0000269|PubMed:28264986, ECO:0000269|PubMed:28295209}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.0922

Intolerance Scores

loftool
0.872
rvis_EVS
1.62
rvis_percentile_EVS
96

Haploinsufficiency Scores

pHI
0.390
hipred
Y
hipred_score
0.562
ghis
0.471

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.798

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cep55
Phenotype

Zebrafish Information Network

Gene name
cep55l
Affected structure
proximal convoluted tubule
Phenotype tag
abnormal
Phenotype quality
decreased area

Gene ontology

Biological process
mitotic cytokinesis;nucleus organization;mitotic metaphase plate congression;regulation of phosphatidylinositol 3-kinase signaling;establishment of protein localization;midbody abscission;renal system development;cranial skeletal system development
Cellular component
centrosome;centriole;microtubule organizing center;plasma membrane;membrane;midbody;cleavage furrow;intercellular bridge;Flemming body
Molecular function
protein binding