CEP89

centrosomal protein 89

Basic information

Region (hg38): 19:32875925-32971991

Previous symbols: [ "CCDC123" ]

Links

ENSG00000121289 ∙ NCBI:84902 ∙ OMIM:615470 ∙ HGNC:25907 ∙ Uniprot:Q96ST8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEP89 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEP89 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			2	36	6	44
missense			117	10	10	137
nonsense			8			8
start loss						0
frameshift			2			2
inframe indel			1			1
splice donor/acceptor (+/-2bp)			4		1	5
splice region			3	9	1	13
non coding			3	23	12	38
Total	0	0	137	69	29

Variants in CEP89

This is a list of pathogenic ClinVar variants found in the CEP89 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-32879163-T-A			Uncertain significance (Mar 23, 2023)
19-32879164-A-G			Benign (Feb 01, 2024)
19-32879169-G-A		not specified	Uncertain significance (Sep 27, 2024)
19-32879175-G-T		not specified	Uncertain significance (Dec 04, 2024)
19-32879178-T-A			Benign (Feb 01, 2024)
19-32879185-T-G		not specified	Uncertain significance (Sep 27, 2021)
19-32879193-T-C			Uncertain significance (Jan 16, 2023)
19-32879196-G-A		not specified	Uncertain significance (Dec 10, 2024)
19-32879204-A-G			Likely benign (Jan 15, 2025)
19-32879206-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-32879212-C-T			Uncertain significance (Jan 02, 2024)
19-32879213-G-A			Likely benign (Feb 25, 2023)
19-32879228-C-G		not specified	Uncertain significance (Nov 06, 2023)
19-32879236-C-T			Uncertain significance (Nov 19, 2022)
19-32879237-G-A			Likely benign (Jan 16, 2024)
19-32879255-A-C			Benign (Feb 01, 2024)
19-32879277-T-A		not specified	Uncertain significance (Feb 06, 2023)
19-32879282-G-A			Likely benign (Oct 05, 2023)
19-32879292-G-A		not specified	Uncertain significance (Jun 06, 2023)
19-32879317-G-A			Uncertain significance (Jan 22, 2024)
19-32879325-C-T			Uncertain significance (Dec 24, 2021)
19-32879344-A-G		not specified	Uncertain significance (Sep 27, 2024)
19-32881830-G-T			Likely benign (Dec 23, 2024)
19-32881832-C-T			Likely benign (May 27, 2022)
19-32881853-T-C		not specified	Uncertain significance (Oct 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEP89	protein_coding	protein_coding	ENST00000305768	19	92996

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.35e-26	0.000808	125314	0	433	125747	0.00172

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.475	395	422	0.935	0.0000231	5105
Missense in Polyphen		71	79.036	0.89832		1046
Synonymous	0.196	161	164	0.981	0.00000942	1434
Loss of Function	0.364	40	42.6	0.940	0.00000213	527

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00295	0.00289
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.00101	0.000979
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00255	0.00251
Middle Eastern	0.00101	0.000979
South Asian	0.00181	0.00177
Other	0.00168	0.00163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for ciliogenesis. Also plays a role in mitochondrial metabolism where it may modulate complex IV activity. {ECO:0000269|PubMed:23348840, ECO:0000269|PubMed:23575228}.
• Disease: DISEASE: Note=Homozygous deletion comprising CEP89 and SLC7A9 genes has been reported in a patient with isolated complex IV deficiency, intellectual disability and multisystemic problems that include cystinuria, cataract, broad based walking pattern and deafness. {ECO:0000269|PubMed:23575228}.
• Pathway: Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.0744

Intolerance Scores

• rvis_EVS: 1.82
• rvis_percentile_EVS: 97.03

Haploinsufficiency Scores

• pHI: 0.0375
• hipred: N
• hipred_score: 0.144
• ghis: 0.427

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	High	Medium	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Cep89

Gene ontology

• Biological process: mitochondrion organization;chemical synaptic transmission;cilium assembly;ciliary basal body-plasma membrane docking;non-motile cilium assembly
• Cellular component: spindle pole;mitochondrial intermembrane space;centrosome;centriole;cytosol;plasma membrane;motile cilium;ciliary transition fiber;non-motile cilium
• Molecular function: protein binding