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
ciliopathy (Definitive), 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 (365 variants)
Inborn_genetic_diseases (139 variants)
not_provided (131 variants)
CEP120-related_disorder (30 variants)
Joubert_syndrome_31 (17 variants)
not_specified (10 variants)
Chuvash_polycythemia (1 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. These statistics are base on transcript: NM_001375405.1. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				88 clinvar		88
missense	3 clinvar	3 clinvar	223 clinvar	31 clinvar	2 clinvar	262
nonsense	7 clinvar	6 clinvar	1 clinvar			14
start loss			1			1
frameshift	5 clinvar	3 clinvar	1 clinvar			9
splice donor/acceptor (+/-2bp)		11 clinvar				11
Total	15	23	226	119	2

Highest pathogenic variant AF is 0.00002360835

Loading clinvar variants...

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
essential_gene_gene_trap
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