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 (Strong), 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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Multinucleated neurons, anhydramnios, renal dysplasia, cerebellar hypoplasia and hydranencephaly (MARCH)	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic; Renal	28264986; 28295209

ClinVar

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

• not provided (5 variants)
• Multinucleated neurons-anhydramnios-renal dysplasia-cerebellar hypoplasia-hydranencephaly syndrome (4 variants)
• Inborn genetic diseases (2 variants)
• CEP55-related disorder (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.

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				7	3	10
missense			35	5	10	50
nonsense	4	4				8
start loss						0
frameshift	2					2
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region	1		1	1		3
non coding					3	3
Total	7	4	35	12	16

Highest pathogenic variant AF is 0.000171

Variants in CEP55

This is a list of pathogenic ClinVar variants found in the CEP55 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-93500056-C-T		Inborn genetic diseases	Uncertain significance (Feb 10, 2023)
10-93500068-C-G		Inborn genetic diseases	Uncertain significance (Feb 07, 2023)
10-93500073-G-T		Multinucleated neurons-anhydramnios-renal dysplasia-cerebellar hypoplasia-hydranencephaly syndrome	Uncertain significance (Jul 19, 2023)
10-93500106-A-G		Inborn genetic diseases	Uncertain significance (Feb 10, 2022)
10-93500121-G-A		Multinucleated neurons-anhydramnios-renal dysplasia-cerebellar hypoplasia-hydranencephaly syndrome	Uncertain significance (Jul 30, 2018)
10-93500145-G-A		Inborn genetic diseases	Uncertain significance (Nov 07, 2023)
10-93500222-C-G		CEP55-related disorder	Benign (Jan 29, 2024)
10-93500226-C-T			Benign (Jan 18, 2024)
10-93500232-G-A		Inborn genetic diseases	Likely benign (Aug 15, 2023)
10-93503119-C-T		Multinucleated neurons-anhydramnios-renal dysplasia-cerebellar hypoplasia-hydranencephaly syndrome	Pathogenic/Likely pathogenic (Apr 23, 2020)
10-93503133-T-A			Benign (Jan 24, 2024)
10-93503166-G-A		CEP55-related disorder	Likely benign (Jun 21, 2019)
10-93503171-A-G			Uncertain significance (Nov 27, 2023)
10-93503185-C-T		Multinucleated neurons-anhydramnios-renal dysplasia-cerebellar hypoplasia-hydranencephaly syndrome • CEP55-related disorder • Inborn genetic diseases	Pathogenic (Sep 01, 2023)
10-93503213-A-G		Inborn genetic diseases	Uncertain significance (Jan 29, 2024)
10-93503223-C-T			Benign (Dec 31, 2019)
10-93503223-CA-TG			Likely benign (Nov 15, 2022)
10-93503224-A-G			Benign (Jan 29, 2024)
10-93503224-A-A			Benign (Oct 11, 2023)
10-93503236-C-T			Pathogenic (Jan 01, 2024)
10-93503252-C-T		Inborn genetic diseases	Uncertain significance (Jul 13, 2021)
10-93503307-C-T			Likely benign (Feb 23, 2023)
10-93503308-G-A		Inborn genetic diseases • Multinucleated neurons-anhydramnios-renal dysplasia-cerebellar hypoplasia-hydranencephaly syndrome	Uncertain significance (Oct 12, 2022)
10-93503308-G-T			Uncertain significance (Jul 17, 2021)
10-93503332-G-A		Inborn genetic diseases	Likely benign (Jun 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP55	protein_coding	protein_coding	ENST00000371485	8	32461

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.96e-12	0.378	125625	0	123	125748	0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.497	211	232	0.908	0.0000117	3022
Missense in Polyphen		37	45.157	0.81937		603
Synonymous	0.677	82	90.2	0.909	0.00000479	841
Loss of Function	1.22	22	29.1	0.756	0.00000173	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000843	0.000843
Ashkenazi Jewish	0.00	0.00
East Asian	0.000436	0.000435
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000564	0.000563
Middle Eastern	0.000436	0.000435
South Asian	0.000493	0.000490
Other	0.000657	0.000652

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

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

Mouse Genome Informatics

• Gene name: Cep55

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