CEP120

centrosomal protein 120

Basic information

Region (hg38): 5:123344890-123423592

Previous symbols: [ "CCDC100" ]

Links

ENSG00000168944 ∙ NCBI:153241 ∙ OMIM:613446 ∙ HGNC:26690 ∙ Uniprot:Q8N960 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Jeune syndrome (Supportive), mode of inheritance: AR
• Joubert syndrome (Supportive), mode of inheritance: AR
• Joubert syndrome with ocular defect (Supportive), mode of inheritance: AR
• Joubert syndrome 31 (Strong), mode of inheritance: AR
• short-rib thoracic dysplasia 13 with or without polydactyly (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Joubert syndrome 31; Short-rib thoracic dysplasia 13 with or without polydactyly	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	Craniofacial; Endocrine; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic	25361962; 27208211

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEP120 gene.

• Short-rib thoracic dysplasia 13 with or without polydactyly (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP120 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				73	2	75
missense		3	160	12	4	179
nonsense	6	2				8
start loss			1			1
frameshift	5	2				7
inframe indel			2			2
splice donor/acceptor (+/-2bp)		8				8
splice region			8	20	3	31
non coding		1	1	92	53	147
Total	11	16	164	177	59

Highest pathogenic variant AF is 0.0000526

Variants in CEP120

This is a list of pathogenic ClinVar variants found in the CEP120 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-123346272-A-T			Likely benign (Oct 05, 2018)
5-123346460-T-G			Benign (Jul 06, 2018)
5-123346519-T-C		Short-rib thoracic dysplasia 13 with or without polydactyly	Likely benign (Jun 23, 2023)
5-123346526-C-T		Inborn genetic diseases	Uncertain significance (Oct 11, 2021)
5-123346549-C-T		Short-rib thoracic dysplasia 13 with or without polydactyly	Likely benign (Sep 20, 2023)
5-123346554-T-C		Short-rib thoracic dysplasia 13 with or without polydactyly	Uncertain significance (Aug 19, 2022)
5-123346555-G-A		Short-rib thoracic dysplasia 13 with or without polydactyly	Likely benign (Nov 16, 2022)
5-123346556-A-C		Short-rib thoracic dysplasia 13 with or without polydactyly	Pathogenic (Nov 06, 2017)
5-123346563-G-A		Short-rib thoracic dysplasia 13 with or without polydactyly	Conflicting classifications of pathogenicity (Sep 10, 2024)
5-123346583-C-T		Inborn genetic diseases	Uncertain significance (Jul 25, 2023)
5-123346591-G-A		Short-rib thoracic dysplasia 13 with or without polydactyly • CEP120-related disorder	Likely benign (Sep 22, 2022)
5-123346605-C-T		Inborn genetic diseases	Uncertain significance (Mar 25, 2024)
5-123346640-C-T		Short-rib thoracic dysplasia 13 with or without polydactyly	Benign (Jan 30, 2024)
5-123346641-G-A		Short-rib thoracic dysplasia 13 with or without polydactyly	Uncertain significance (Sep 21, 2023)
5-123346654-A-G		Short-rib thoracic dysplasia 13 with or without polydactyly • Joubert syndrome 31	Benign (Jan 31, 2024)
5-123346656-C-T		Short-rib thoracic dysplasia 13 with or without polydactyly	Uncertain significance (Apr 16, 2022)
5-123346662-C-T		Inborn genetic diseases	Uncertain significance (May 13, 2024)
5-123346673-A-C		Inborn genetic diseases	Uncertain significance (Jan 11, 2023)
5-123346681-A-G		Short-rib thoracic dysplasia 13 with or without polydactyly	Likely benign (Apr 09, 2021)
5-123346695-T-G		Short-rib thoracic dysplasia 13 with or without polydactyly	Uncertain significance (Aug 16, 2022)
5-123346699-T-A		Short-rib thoracic dysplasia 13 with or without polydactyly	Likely benign (Aug 15, 2022)
5-123346709-A-G		Inborn genetic diseases	Uncertain significance (Apr 23, 2024)
5-123346727-T-A		Short-rib thoracic dysplasia 13 with or without polydactyly	Uncertain significance (May 27, 2022)
5-123346737-G-A		Short-rib thoracic dysplasia 13 with or without polydactyly	Pathogenic (Feb 03, 2023)
5-123346740-C-T		Short-rib thoracic dysplasia 13 with or without polydactyly	Uncertain significance (Jul 30, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP120	protein_coding	protein_coding	ENST00000306467	20	78708

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.09e-15	0.995	125675	0	73	125748	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.233	525	510	1.03	0.0000265	6432
Missense in Polyphen		135	144.54	0.93401		1848
Synonymous	-0.228	180	176	1.02	0.00000887	1836
Loss of Function	2.78	32	54.1	0.592	0.00000270	680

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000668	0.000664
Ashkenazi Jewish	0.00	0.00
East Asian	0.00106	0.000979
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000277	0.000255
Middle Eastern	0.00106	0.000979
South Asian	0.000144	0.000131
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the microtubule-dependent coupling of the nucleus and the centrosome. Involved in the processes that regulate centrosome-mediated interkinetic nuclear migration (INM) of neural progenitors and for proper positioning of neurons during brain development. Also implicated in the migration and selfrenewal of neural progenitors. Required for centriole duplication and maturation during mitosis and subsequent ciliogenesis (By similarity). Required for the recruitment of CEP295 to the proximal end of new-born centrioles at the centriolar microtubule wall during early S phase in a PLK4- dependent manner (PubMed:27185865). {ECO:0000250|UniProtKB:Q7TSG1, ECO:0000269|PubMed:27185865}.
• Disease: DISEASE: Short-rib thoracic dysplasia 13 with or without polydactyly (SRTD13) [MIM:616300]: A form of short-rib thoracic dysplasia, a group of autosomal recessive ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a 'trident' appearance of the acetabular roof. Polydactyly is variably present. Non-skeletal involvement can include cleft lip/palate as well as anomalies of major organs such as the brain, eye, heart, kidneys, liver, pancreas, intestines, and genitalia. Some forms of the disease are lethal in the neonatal period due to respiratory insufficiency secondary to a severely restricted thoracic cage, whereas others are compatible with life. Disease spectrum encompasses Ellis-van Creveld syndrome, asphyxiating thoracic dystrophy (Jeune syndrome), Mainzer-Saldino syndrome, and short rib-polydactyly syndrome. {ECO:0000269|PubMed:25361962}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Joubert syndrome 31 (JBTS31) [MIM:617761]: A form of Joubert syndrome, a disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy, renal disease, liver fibrosis, and polydactyly. JBTS31 inheritance is autosomal recessive. {ECO:0000269|PubMed:27208211}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• loftool: 0.954
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.12

Haploinsufficiency Scores

• pHI: 0.202
• hipred: Y
• hipred_score: 0.544
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.135

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cep120
• 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); embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); 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); cellular phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: cep120
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: centrosome cycle;positive regulation of centrosome duplication;cerebral cortex development;neurogenesis;interkinetic nuclear migration;astral microtubule organization;positive regulation of cilium assembly;positive regulation of centriole elongation;positive regulation of establishment of protein localization
• Cellular component: centrosome;centriole
• Molecular function: protein binding;protein C-terminus binding