CEP250 (centrosomal protein 250)

Gene

• Entrez ID: 11190
• Gene name: Centrosomal protein 250
• Gene symbol: CEP250
• Synonyms (NCBI Gene): C-NAP1, CEP2, CNAP1, CRDHL2
• Chromosome: 20
• Chromosome location: 20q11.22
• Summary: This gene encodes a core centrosomal protein required for centriole-centriole cohesion during interphase of the cell cycle. The encoded protein dissociates from the centrosomes when parental centrioles separate at the beginning of mitosis. The protein ass

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs749314857	C>A,T	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained, synonymous variant
rs774702094	C>G,T	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained, missense variant
rs1341298773	C>T	Pathogenic	Genic upstream transcript variant, stop gained, coding sequence variant, non coding transcript variant, upstream transcript variant, 5 prime UTR variant
rs1369076411	C>T	Pathogenic	5 prime UTR variant, coding sequence variant, non coding transcript variant, genic upstream transcript variant, stop gained
rs1568820302	A>T	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT046692	hsa-miR-222-3p	CLASH	23622248
MIRT042169	hsa-miR-484	CLASH	23622248
MIRT040255	hsa-miR-615-3p	CLASH	23622248
MIRT1962756	hsa-miR-1252	CLIP-seq
MIRT1962757	hsa-miR-1253	CLIP-seq
MIRT1962758	hsa-miR-3173-3p	CLIP-seq
MIRT1962759	hsa-miR-3689d	CLIP-seq
MIRT1962760	hsa-miR-425	CLIP-seq
MIRT1962761	hsa-miR-4428	CLIP-seq
MIRT1962762	hsa-miR-4434	CLIP-seq
MIRT1962763	hsa-miR-4516	CLIP-seq
MIRT1962764	hsa-miR-642b	CLIP-seq
MIRT2199083	hsa-miR-105	CLIP-seq
MIRT2199084	hsa-miR-1236	CLIP-seq
MIRT2199085	hsa-miR-124	CLIP-seq
MIRT2199086	hsa-miR-125a-3p	CLIP-seq
MIRT2199087	hsa-miR-1262	CLIP-seq
MIRT2199088	hsa-miR-1292	CLIP-seq
MIRT2199089	hsa-miR-1321	CLIP-seq
MIRT2199090	hsa-miR-1343	CLIP-seq
MIRT2199091	hsa-miR-1915	CLIP-seq
MIRT2199092	hsa-miR-219-1-3p	CLIP-seq
MIRT2199093	hsa-miR-3152-5p	CLIP-seq
MIRT2199094	hsa-miR-3162-5p	CLIP-seq
MIRT2199095	hsa-miR-326	CLIP-seq
MIRT2199096	hsa-miR-330-5p	CLIP-seq
MIRT2199097	hsa-miR-3678-3p	CLIP-seq
MIRT2199098	hsa-miR-3682-5p	CLIP-seq
MIRT2199099	hsa-miR-4259	CLIP-seq
MIRT2199100	hsa-miR-4471	CLIP-seq
MIRT2199101	hsa-miR-4646-5p	CLIP-seq
MIRT2199102	hsa-miR-4699-3p	CLIP-seq
MIRT2199103	hsa-miR-4701-3p	CLIP-seq
MIRT2199104	hsa-miR-4708-3p	CLIP-seq
MIRT2199105	hsa-miR-4726-3p	CLIP-seq
MIRT2199106	hsa-miR-4739	CLIP-seq
MIRT2199107	hsa-miR-4756-5p	CLIP-seq
MIRT2199108	hsa-miR-4774-3p	CLIP-seq
MIRT2199109	hsa-miR-506	CLIP-seq
MIRT2199110	hsa-miR-571	CLIP-seq
MIRT2199111	hsa-miR-587	CLIP-seq
MIRT2199112	hsa-miR-629	CLIP-seq
MIRT2199090	hsa-miR-1343	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000278	Process	Mitotic cell cycle	IDA	12140259
GO:0001750	Component	Photoreceptor outer segment	IEA
GO:0001750	Component	Photoreceptor outer segment	ISS
GO:0001917	Component	Photoreceptor inner segment	IEA
GO:0001917	Component	Photoreceptor inner segment	ISS
GO:0005515	Function	Protein binding	IPI	9647649, 10880350, 18851962, 20300119, 20708153, 30404835, 32814053, 36217029
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IBA
GO:0005813	Component	Centrosome	IDA	9647649, 21399614, 31974111
GO:0005813	Component	Centrosome	IEA
GO:0005814	Component	Centriole	IBA
GO:0005814	Component	Centriole	IDA	11076968
GO:0005814	Component	Centriole	IDA	18851962, 24421332, 26337392, 27623382, 36282799
GO:0005814	Component	Centriole	IEA
GO:0005815	Component	Microtubule organizing center	NAS	9647649
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005929	Component	Cilium	IEA
GO:0008104	Process	Intracellular protein localization	IMP	18851962, 23213374
GO:0010457	Process	Centriole-centriole cohesion	IDA	36282799
GO:0010457	Process	Centriole-centriole cohesion	IMP	11076968, 18851962, 23213374, 24554434
GO:0019904	Function	Protein domain specific binding	IPI	24554434
GO:0030030	Process	Cell projection organization	IEA
GO:0030997	Process	Regulation of centriole-centriole cohesion	IDA	9647649
GO:0031616	Component	Spindle pole centrosome	IEA
GO:0032991	Component	Protein-containing complex	IMP	10880350
GO:0033365	Process	Protein localization to organelle	IMP	24554434
GO:0036064	Component	Ciliary basal body	IDA
GO:0036064	Component	Ciliary basal body	IEA
GO:0036064	Component	Ciliary basal body	ISS
GO:0042995	Component	Cell projection	IEA
GO:0048471	Component	Perinuclear region of cytoplasm	IEA
GO:0050908	Process	Detection of light stimulus involved in visual perception	IEA
GO:0050908	Process	Detection of light stimulus involved in visual perception	ISS
GO:0060271	Process	Cilium assembly	IBA
GO:0060271	Process	Cilium assembly	IMP	28005958
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:0071539	Process	Protein localization to centrosome	IMP	30404835
GO:1904781	Process	Positive regulation of protein localization to centrosome	IMP	27623382
GO:1905515	Process	Non-motile cilium assembly	IMP	23789104

Other IDs

• MIM: 609689
• HGNC: 1859
• e!Ensembl: ENSG00000126001

Protein

• UniProt ID: Q9BV73
• Protein name: Centrosome-associated protein CEP250 (250 kDa centrosomal protein) (Cep250) (Centrosomal Nek2-associated protein 1) (C-Nap1) (Centrosomal protein 2)
• Protein function: Plays an important role in centrosome cohesion during interphase (PubMed:30404835, PubMed:36282799). Recruits CCDC102B to the proximal ends of centrioles (PubMed:30404835). Maintains centrosome cohesion by forming intercentriolar linkages (PubMe
• PDB: 6OQA
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF15035	Rootletin	39 → 215		Family

• Tissue specificity: TISSUE SPECIFICITY: Ubiquitously and weakly expressed.
• Sequence:

  METRSPGLNNMKPQSLQLVLEEQVLALQQQMAENQAASWRKLKNSQEAQQRQATLVRKLQ
  AKVLQYRSWCQELEKRLEATGGPIPQRWENVEEPNLDELLVRLEEEQQRCESLAEVNTQL
  RLHMEKADVVNKALREDVEKLTVDWSRARDELMRKESQWQMEQEFFKGYLKGEHGRLLSL
  WREVVTFRRHFLEMKSATDRDLMELKAEHVRLSGSLLTCCLRLTVGAQSREPNGSGRMDG
  REPAQLLLLLAKTQELEKEAHERSQELIQLKSQGDLEKAELQDRVTELSALLTQSQKQNE
  DYEKMIKALRETVEILETNHTELMEHEASLSRNAQEEKLSLQQVIKDITQVMVEEGDNIA
  QGSGHENSLELDSSIFSQFDYQDADKALTLVRSVLTRRRQAVQDLRQQLAGCQEAVNLLQ
  QQHDQWEEEGKALRQRLQKLTGERDTLAGQTVDLQGEVDSLSKERELLQKAREELRQQLE
  VLEQEAWRLRRVNVELQLQGDSAQGQKEEQQEELHLAVRERERLQEMLMGLEAKQSESLS
  ELITLREALESSHLEGELLRQEQTEVTAALARAEQSIAELSSSENTLKTEVADLRAAAVK
  LSALNEALALDKVGLNQQLLQLEEENQSVCSRMEAAEQARNALQVDLAEAEKRREALWEK
  NTHLEAQLQKAEEAGAELQADLRDIQEEKEEIQKKLSESRHQQEAATTQLEQLHQEAKRQ
  EEVLARAVQEKEALVREKAALEVRLQAVERDRQDLAEQLQGLSSAKELLESSLFEAQQQN
  SVIEVTKGQLEVQIQTVTQAKEVIQGEVRCLKLELDTERSQAEQERDAAARQLAQAEQEG
  KTALEQQKAAHEKEVNQLREKWEKERSWHQQELAKALESLEREKMELEMRLKEQQTEMEA
  IQAQREEERTQAESALCQMQLETEKERVSLLETLLQTQKELADASQQLERLRQDMKVQKL
  KEQETTGILQTQLQEAQRELKEAARQHRDDLAALQEESSSLLQDKMDLQKQVEDLKSQLV
  AQDDSQRLVEQEVQEKLRETQEYNRIQKELEREKASLTLSLMEKEQRLLVLQEADSIRQQ
  ELSALRQDMQEAQGEQKELSAQMELLRQEVKEKEADFLAQEAQLLEELEASHITEQQLRA
  SLWAQEAKAAQLQLRLRSTESQLEALAAEQQPGNQAQAQAQLASLYSALQQALGSVCESR
  PELSGGGDSAPSVWGLEPDQNGARSLFKRGPLLTALSAEAVASALHKLHQDLWKTQQTRD
  VLRDQVQKLEERLTDTEAEKSQVHTELQDLQRQLSQNQEEKSKWEGKQNSLESELMELHE
  TMASLQSRLRRAELQRMEAQGERELLQAAKENLTAQVEHLQAAVVEARAQASAAGILEED
  LRTARSALKLKNEEVESERERAQALQEQGELKVAQGKALQENLALLTQTLAEREEEVETL
  RGQIQELEKQREMQKAALELLSLDLKKRNQEVDLQQEQIQELEKCRSVLEHLPMAVQERE
  QKLTVQREQIRELEKDRETQRNVLEHQLLELEKKDQMIESQRGQVQDLKKQLVTLECLAL
  ELEENHHKMECQQKLIKELEGQRETQRVALTHLTLDLEERSQELQAQSSQIHDLESHSTV
  LARELQERDQEVKSQREQIEELQRQKEHLTQDLERRDQELMLQKERIQVLEDQRTRQTKI
  LEEDLEQIKLSLRERGRELTTQRQLMQERAEEGKGPSKAQRGSLEHMKLILRDKEKEVEC
  QQEHIHELQELKDQLEQQLQGLHRKVGETSLLLSQREQEIVVLQQQLQEAREQGELKEQS
  LQSQLDEAQRALAQRDQELEALQQEQQQAQGQEERVKEKADALQGALEQAHMTLKERHGE
  LQDHKEQARRLEEELAVEGRRVQALEEVLGDLRAESREQEKALLALQQQCAEQAQEHEVE
  TRALQDSWLQAQAVLKERDQELEALRAESQSSRHQEEAARARAEALQEALGKAHAALQGK
  EQHLLEQAELSRSLEASTATLQASLDACQAHSRQLEEALRIQEGEIQDQDLRYQEDVQQL
  QQALAQRDEELRHQQEREQLLEKSLAQRVQENMIQEKQNLGQEREEEEIRGLHQSVRELQ
  LTLAQKEQEILELRETQQRNNLEALPHSHKTSPMEEQSLKLDSLEPRLQRELERLQAALR
  QTEAREIEWREKAQDLALSLAQTKASVSSLQEVAMFLQASVLERDSEQQRLQDELELTRR
  ALEKERLHSPGATSTAELGSRGEQGVQLGEVSGVEAEPSPDGMEKQSWRQRLEHLQQAVA
  RLEIDRSRLQRHNVQLRSTLEQVERERRKLKREAMRAAQAGSLEISKATASSPTQQDGRG
  QKNSDAKCVAELQKEVVLLQAQLTLERKQKQDYITRSAQTSRELAGLHHSLSHSLLAVAQ
  APEATVLEAETRRLDESLTQSLTSPGPVLLHPSPSTTQAASR

• Sequence length: 2442

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
CEP250-related disorder	Likely pathogenic; Pathogenic	rs1243282597, rs2063839688, rs1568806160	RCV003399201 RCV004753586 RCV003966712	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cone-rod dystrophy and hearing loss 2	Pathogenic; Likely pathogenic	rs200263031, rs774612231, rs1051944154, rs757158876, rs749883566, rs1345217165, rs749314857, rs1341298773, rs1369076411, rs1568820302, rs774702094, rs2064077764, rs2064092893, rs2064043746	RCV004774443 RCV004795347 RCV004795348 RCV004774700 RCV005356156 RCV004795349 RCV000761198 RCV000761199 RCV000761200 RCV000761201 RCV000761202 RCV005418968 RCV005418955 RCV004795345	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Gastric cancer	Likely pathogenic; Pathogenic	rs774702094	RCV005897332	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Pathogenic	rs1388902455	RCV004816832	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Thyroid cancer, nonmedullary, 1	Pathogenic	rs774612231	RCV005924302	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Usher syndrome	Likely pathogenic; Pathogenic	rs749314857	RCV001002934	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Monogenic hearing loss	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Optic atrophy	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Ovarian serous cystadenocarcinoma	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA	—	Disgenet, GWAS catalog Disgenet, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Squamous cell lung carcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	33109182	Associate	★☆☆☆☆ Found in Text Mining only
Cone-Rod Dystrophies	Cone-rod dystrophy	BEFREE	29718797, 30459346		★☆☆☆☆ Found in Text Mining only
Cone-Rod Dystrophy 2	Cone-rod dystrophy	BEFREE	29718797, 30459346		★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	30459346	Associate	★☆☆☆☆ Found in Text Mining only
Hearing Loss Sensorineural	Hearing loss	Pubtator	29718797, 34223797	Associate	★☆☆☆☆ Found in Text Mining only
Hypoalphalipoproteinemias	Hypoalphalipoproteinemia	Pubtator	32541515	Associate	★☆☆☆☆ Found in Text Mining only
Lymphoma	Lymphoma	Pubtator	21887344	Associate	★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	21887344		★☆☆☆☆ Found in Text Mining only
Nasopharyngeal Carcinoma	Nasopharyngeal carcinoma	Pubtator	32541515	Associate	★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	38203311	Associate	★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal detachment	Pubtator	34223797	Associate	★☆☆☆☆ Found in Text Mining only
Retinitis Pigmentosa	Retinitis Pigmentosa	BEFREE	29718797, 30998843		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Retinitis Pigmentosa	Retinitis pigmentosa	Pubtator	29718797	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Rod-Cone Dystrophy	Rod-cone dystrophy	BEFREE	29718797, 30459346		★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	BEFREE	24780881, 29718797		★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Usher Syndrome	Usher Syndrome	BEFREE	24780881, 27588452, 29718797, 30459346		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Usher Syndrome	Usher Syndrome	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Usher Syndromes	Usher syndrome	Pubtator	27588452, 29718797, 30459346	Associate	★☆☆☆☆ Found in Text Mining only
Vision Disorders	Visual disorder	Pubtator	30459346	Associate	★☆☆☆☆ Found in Text Mining only