CEP78 (centrosomal protein 78)

Gene

• Entrez ID: 84131
• Gene name: Centrosomal protein 78
• Gene symbol: CEP78
• Synonyms (NCBI Gene): C9orf81, CRDHL, IP63
• Chromosome: 9
• Chromosome location: 9q21.2
• Summary: This gene encodes a centrosomal protein that is both required for the regulation of centrosome-related events during the cell cycle, and required for ciliogenesis. The encoded protein has an N-terminal leucine-rich repeat (LRR) domain with six consecutive

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs745750156	G>A	Pathogenic	Intron variant
rs1014151821	A>G	Likely-pathogenic	Intron variant, splice acceptor variant
rs1057517691	G>T	Pathogenic	Splice donor variant
rs1057517692	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs1057517693	G>A	Pathogenic	Intron variant
rs1057517694	G>A	Pathogenic	Splice acceptor variant
rs1057517695	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs1057518753	A>G	Pathogenic	Splice acceptor variant
rs1273366435	AGAG>-	Likely-pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT026788	hsa-miR-192-5p	Microarray	19074876
MIRT042634	hsa-miR-423-3p	CLASH	23622248
MIRT643674	hsa-miR-3938	HITS-CLIP	23824327
MIRT643673	hsa-miR-3124-3p	HITS-CLIP	23824327
MIRT643672	hsa-miR-3180-5p	HITS-CLIP	23824327
MIRT515083	hsa-miR-4438	PAR-CLIP	23446348
MIRT515082	hsa-miR-6504-3p	PAR-CLIP	23446348
MIRT515081	hsa-miR-4537	PAR-CLIP	23446348
MIRT515080	hsa-miR-5095	PAR-CLIP	23446348
MIRT515079	hsa-miR-7151-3p	PAR-CLIP	23446348
MIRT515078	hsa-miR-619-5p	PAR-CLIP	23446348
MIRT515077	hsa-miR-1228-3p	PAR-CLIP	23446348
MIRT515075	hsa-miR-6765-3p	PAR-CLIP	23446348
MIRT515076	hsa-miR-874-5p	PAR-CLIP	23446348
MIRT515073	hsa-miR-6807-5p	PAR-CLIP	23446348
MIRT515074	hsa-miR-4701-5p	PAR-CLIP	23446348
MIRT643674	hsa-miR-3938	HITS-CLIP	23824327
MIRT643673	hsa-miR-3124-3p	HITS-CLIP	23824327
MIRT643672	hsa-miR-3180-5p	HITS-CLIP	23824327
MIRT515083	hsa-miR-4438	PAR-CLIP	23446348
MIRT515082	hsa-miR-6504-3p	PAR-CLIP	23446348
MIRT515081	hsa-miR-4537	PAR-CLIP	23446348
MIRT515080	hsa-miR-5095	PAR-CLIP	23446348
MIRT515079	hsa-miR-7151-3p	PAR-CLIP	23446348
MIRT515078	hsa-miR-619-5p	PAR-CLIP	23446348
MIRT515077	hsa-miR-1228-3p	PAR-CLIP	23446348
MIRT515075	hsa-miR-6765-3p	PAR-CLIP	23446348
MIRT515076	hsa-miR-874-5p	PAR-CLIP	23446348
MIRT515073	hsa-miR-6807-5p	PAR-CLIP	23446348
MIRT515074	hsa-miR-4701-5p	PAR-CLIP	23446348
MIRT886471	hsa-miR-1243	CLIP-seq
MIRT886472	hsa-miR-1269	CLIP-seq
MIRT886473	hsa-miR-1269b	CLIP-seq
MIRT886474	hsa-miR-1288	CLIP-seq
MIRT886475	hsa-miR-1290	CLIP-seq
MIRT886476	hsa-miR-3167	CLIP-seq
MIRT886477	hsa-miR-34c-3p	CLIP-seq
MIRT886478	hsa-miR-3681	CLIP-seq
MIRT886479	hsa-miR-3942-3p	CLIP-seq
MIRT886480	hsa-miR-4515	CLIP-seq
MIRT886481	hsa-miR-4699-3p	CLIP-seq
MIRT886482	hsa-miR-4740-5p	CLIP-seq
MIRT886483	hsa-miR-876-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IBA
GO:0005813	Component	Centrosome	IDA	28242748, 34259627
GO:0005813	Component	Centrosome	IDA	21399614, 27246242
GO:0005813	Component	Centrosome	IEA
GO:0005814	Component	Centriole	IDA	34259627
GO:0005814	Component	Centriole	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005929	Component	Cilium	IEA
GO:0030030	Process	Cell projection organization	IEA
GO:0030317	Process	Flagellated sperm motility	IEA
GO:0030317	Process	Flagellated sperm motility	IMP	36206347, 36756949
GO:0031397	Process	Negative regulation of protein ubiquitination	IDA	28242748, 34259627
GO:0036064	Component	Ciliary basal body	IBA
GO:0036064	Component	Ciliary basal body	IDA	27588451
GO:0042995	Component	Cell projection	IEA
GO:0044782	Process	Cilium organization	IBA
GO:0044782	Process	Cilium organization	IEA
GO:0044782	Process	Cilium organization	IMP	27588451, 34259627
GO:0044782	Process	Cilium organization	ISS
GO:0061512	Process	Protein localization to cilium	IEA
GO:0061512	Process	Protein localization to cilium	ISS
GO:0071539	Process	Protein localization to centrosome	IDA	28242748

Other IDs

• MIM: 617110
• HGNC: 25740
• e!Ensembl: ENSG00000148019

Protein

• UniProt ID: Q5JTW2
• Protein name: Centrosomal protein of 78 kDa (Cep78)
• Protein function: Centriole wall protein that localizes to mature centrioles and regulates centriole and cilia biogenesis (PubMed:27246242, PubMed:27588451, PubMed:28242748, PubMed:34259627). Involved in centrosome duplication: required for efficient PLK4 centros
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13516	LRR_6	146 → 169	Leucine Rich repeat	Repeat
  PF13516	LRR_6	254 → 277	Leucine Rich repeat	Repeat

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed (PubMed:27588451, PubMed:27588452). Expressed in different retinal cell types with higher expression in cone compared to rod cells (at protein level) (PubMed:27588452). {ECO:0000269|PubMed:27588451, ECO:0000269|PubMed:
• Sequence:

  MIDSVKLRRDSAADFFSHYEYLCALQNSVPLPAVRACLREGVLDFNADRLRGVDWAPLLS
  TLKINKDLPLVSIKSFFQPWLGDTGSDMNKFCRSRVPAIRYKDVTFQLCKALKGCLSISS
  VLKNLELNGLILRERDLTILAKGLNKSASLVHLSLANCPIGDGGLEIICQGIKSSITLKT
  VNFTGCNLTWQGADHMAKILKYQTMRRHEETWAESLRYRRPDLDCMAGLRRITLNCNTLI
  GDLGACAFADSLSEDLWLRALDLQQCGLTNEGAKALLEALETNTTLVVLDIRKNPLIDHS
  MMKAVIKKVLQNGRSAKSEYQWITSPSVKEPSKTAKQKRRTIILGSGHKGKATIRIGLAT
  KKPVSSGRKHSLGKEYYAPAPLPPGVSGFLPWRTAERAKRHRGFPLIKTRDICNQLQQPG
  FPVTVTVESPSSSEVEEVDDSSESVHEVPEKTSIEQEALQEKLEECLKQLKEERVIRLKV
  DKRVSELEHENAQLRNINFSLSEALHAQSLTNMILDDEGVLGSIENSFQKFHAFLDLLKD
  AGLGQLATMAGIDQSDFQLLGHPQMTSTVSNPPKEEKKALEDEKPEPKQNALGQMQNIQF
  QKITGDARIPLPLDSFPVPVSTPEGLGTSSNNLGVPATEQRQESFEGFIARMCSPSPDAT
  SGTGSQRKEEELSRNSRSSSEKKTKTESH

• Sequence length: 689

Pathways

Reactome:

Regulation of PLK1 Activity at G2/M Transition
Loss of Nlp from mitotic centrosomes
Recruitment of mitotic centrosome proteins and complexes
Loss of proteins required for interphase microtubule organization from the centrosome
Recruitment of NuMA to mitotic centrosomes
Anchoring of the basal body to the plasma membrane
AURKA Activation by TPX2

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Cone-rod dystrophy	Pathogenic; Likely pathogenic	rs1057517694, rs1057517695, rs1827340429, rs1196886096	RCV001002940 RCV001002939 RCV001199658 RCV001199659	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cone-rod dystrophy and hearing loss	Likely pathogenic; Pathogenic	rs1210581905	RCV003225969	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cone-rod dystrophy and hearing loss 1	Likely pathogenic; Pathogenic	rs1210581905, rs2118460550, rs761661253, rs769767723, rs760484787, rs1306330581, rs2489451154, rs996333495, rs1057517691, rs1057517692, rs1057517693, rs1057517694, rs1057517695, rs745750156, rs1057518753, rs1196886096, rs759754640, rs778035330	RCV001376465 RCV001523889 RCV001523890 RCV004017881 RCV005860282 RCV005356276 RCV005059115 RCV003222499 RCV000412585 RCV000412668 RCV000412541 RCV000412597 RCV000412648 RCV000412542 RCV000412602 RCV001376466 RCV005001997 RCV001542676	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Familial pancreatic carcinoma	Pathogenic	rs745750156	RCV005900651	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Pathogenic; Likely pathogenic	rs2118460550, rs761661253, rs996333495, rs1057517692, rs1826338661, rs776271026, rs1363491382, rs1042726781, rs1363359148, rs1826145876, rs1826148463	RCV004815547 RCV004815548 RCV004818299 RCV004816635 RCV001075680 RCV001075678 RCV001075728 RCV001073975 RCV001073858 RCV001073973 RCV004813870	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Sensorineural hearing loss disorder	Pathogenic	rs1057517694, rs1057517695	RCV001002940 RCV001002939	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANDROGENETIC ALOPECIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CEP78-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONE-ROD DYSTROPHIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign; Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Moyamoya angiopathy	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Optic atrophy	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
RETINITIS PIGMENTOSA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SENSORINEURAL HEARING LOSS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME TYPE 3	—	GWAS catalog, Orphanet GWAS catalog, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
USHER SYNDROME, TYPE III	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Age related macular degeneration	Age-related macular degeneration	HPO_DG			★☆☆☆☆ Found in Text Mining only
Anxiety	Anxiety Disorder	HPO_DG			★☆☆☆☆ Found in Text Mining only
Astigmatism	Astigmatism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Squamous cell carcinoma	Pubtator	33119552	Stimulate	★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathy	Pubtator	27627988	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	27357513		★☆☆☆☆ Found in Text Mining only
Cone-Rod Dystrophies	Cone-rod dystrophy	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONE-ROD DYSTROPHY AND HEARING LOSS	Cone-Rod Dystrophy And Hearing Loss	BEFREE	27588451		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
CONE-ROD DYSTROPHY AND HEARING LOSS	Cone-Rod Dystrophy And Hearing Loss	CLINGEN_DG	27588451, 27588452, 27627988, 28005958		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
CONE-ROD DYSTROPHY AND HEARING LOSS	Cone-Rod Dystrophy And Hearing Loss	GENOMICS_ENGLAND_DG	27627988		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
CONE-ROD DYSTROPHY AND HEARING LOSS	Cone-Rod Dystrophy And Hearing Loss	CTD_human_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
CONE-ROD DYSTROPHY AND HEARING LOSS	Cone-Rod Dystrophy And Hearing Loss	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Depressive disorder	Mental Depression	HPO_DG			★☆☆☆☆ Found in Text Mining only
Differentiated Thyroid Gland Carcinoma	Thyroid Carcinoma	BEFREE	30884127		★☆☆☆☆ Found in Text Mining only
Hallucinations	Hallucinations	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	31999394, 34021019, 34259627	Associate	★☆☆☆☆ Found in Text Mining only
Hearing Loss Sensorineural	Hearing loss	Pubtator	27588452, 34223797	Associate	★☆☆☆☆ Found in Text Mining only
Hemianopsia	Hemianopsia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Infertility	Infertility	Pubtator	31999394	Associate	★☆☆☆☆ Found in Text Mining only
Infertility Male	Male infertility	Pubtator	31999394	Associate	★☆☆☆☆ Found in Text Mining only
Lymphatic Metastasis	Lymphatic Metastasis	BEFREE	27357513		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	27357513		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	27357513		★☆☆☆☆ Found in Text Mining only
Nyctalopia	Nyctalopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal detachment	Pubtator	34021019	Associate	★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	27588451		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	33119552	Associate	★☆☆☆☆ Found in Text Mining only
Usher Syndrome	Usher Syndrome	BEFREE	27588451, 27588452		★☆☆☆☆ Found in Text Mining only
Usher syndrome type 3	Usher Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Usher Syndrome, Type III	Usher Syndrome	ORPHANET_DG	27627988		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Usher Syndromes	Usher syndrome	Pubtator	27588452, 27627988, 31999394	Associate	★☆☆☆☆ Found in Text Mining only