CEP104

centrosomal protein 104, the group of Cilia and flagella associated|TOG domain containing

Basic information

Region (hg38): 1:3812086-3857396

Previous symbols: [ "KIAA0562" ]

Links

ENSG00000116198 ∙ NCBI:9731 ∙ OMIM:616690 ∙ HGNC:24866 ∙ Uniprot:O60308 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Joubert syndrome 25 (Moderate), mode of inheritance: AR
• Joubert syndrome 25 (Strong), mode of inheritance: AR
• Joubert syndrome (Supportive), mode of inheritance: AR
• Joubert syndrome 25 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal recessive 77	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	34196201; 35359234

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEP104 gene.

• Joubert_syndrome_25 (236 variants)
• not_provided (145 variants)
• Inborn_genetic_diseases (127 variants)
• CEP104-related_disorder (34 variants)
• Intellectual_developmental_disorder,_autosomal_recessive_77 (25 variants)
• not_specified (17 variants)
• Joubert_syndrome_and_related_disorders (13 variants)
• Autism_spectrum_disorder (2 variants)
• Dystonic_disorder (1 variants)
• Joubert_syndrome (1 variants)
• Global_developmental_delay (1 variants)
• See_cases (1 variants)
• Cerebellar_ataxia (1 variants)
• Ciliopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP104 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014704.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	68	3	72
missense			184	31	2	217
nonsense	3	12	1			16
start loss						0
frameshift	10	11				21
splice donor/acceptor (+/-2bp)	3	8	1	1		13
Total	16	31	187	100	5

Highest pathogenic variant AF is 0.00040422552

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP104	protein_coding	protein_coding	ENST00000378230	21	45134

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.23e-12	0.999	125617	0	131	125748	0.000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.444	503	532	0.946	0.0000312	6046
Missense in Polyphen		144	176.07	0.81784		2011
Synonymous	1.65	171	201	0.852	0.0000126	1737
Loss of Function	3.05	28	51.7	0.542	0.00000291	604

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000765	0.000764
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000163	0.000163
Finnish	0.000508	0.000508
European (Non-Finnish)	0.000785	0.000783
Middle Eastern	0.000163	0.000163
South Asian	0.000229	0.000229
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for ciliogenesis and for structural integrity at the ciliary tip. {ECO:0000269|PubMed:23970417}.
• Disease: DISEASE: Joubert syndrome 25 (JBTS25) [MIM:616781]: 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. JBTS25 clinical manifestations appear to be confined to the neurologic system. JBTS25 inheritance is autosomal recessive. {ECO:0000269|PubMed:26477546}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• rvis_EVS: -0.15
• rvis_percentile_EVS: 42.34

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.443
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cep104

Gene ontology

• Cellular component: spindle pole;centriole;cilium
• Molecular function: protein binding;glycine binding;glutamate binding;thienylcyclohexylpiperidine binding