SCAPER (S-phase cyclin A associated protein in the ER)

Gene

• Entrez ID: 49855
• Gene name: S-phase cyclin A associated protein in the ER
• Gene symbol: SCAPER
• Synonyms (NCBI Gene): IDDRP, MSTP063, ZNF291, Zfp291
• Chromosome: 15
• Chromosome location: 15q24.3

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs777893794	G>A	Likely-pathogenic	Stop gained, genic upstream transcript variant, coding sequence variant, non coding transcript variant
rs978336151	G>A,T	Likely-pathogenic	Non coding transcript variant, synonymous variant, coding sequence variant, stop gained
rs1239725461	G>A	Likely-pathogenic, pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs1303625185	GA>-	Likely-pathogenic	Coding sequence variant, genic downstream transcript variant, frameshift variant, non coding transcript variant
rs1305542291	C>T	Likely-pathogenic, pathogenic	Genic downstream transcript variant, missense variant, coding sequence variant, non coding transcript variant
rs1395475624	CTT>-	Likely-pathogenic, pathogenic	Non coding transcript variant, coding sequence variant, genic upstream transcript variant, inframe deletion
rs1462082548	T>-,TT	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1484749107	G>A,C	Likely-pathogenic	Stop gained, coding sequence variant, missense variant, non coding transcript variant, 5 prime UTR variant, genic upstream transcript variant
rs1555447569	ATTG>-	Pathogenic	Genic downstream transcript variant, coding sequence variant, non coding transcript variant, frameshift variant
rs1555558169	T>C	Pathogenic	Splice acceptor variant
rs1567499068	G>-	Pathogenic	Non coding transcript variant, coding sequence variant, genic downstream transcript variant, stop gained
rs1596596355	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant, downstream transcript variant, non coding transcript variant
rs1597752941	C>-	Likely-pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant, non coding transcript variant
rs1598279469	G>C	Likely-pathogenic	Intron variant
rs1598598205	C>T	Likely-pathogenic	Splice donor variant, genic upstream transcript variant
rs1598632432	A>-	Likely-pathogenic	Coding sequence variant, frameshift variant, genic upstream transcript variant, non coding transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT439702	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT439702	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT1328386	hsa-miR-3671	CLIP-seq
MIRT1328387	hsa-miR-888	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001541	Process	Ovarian follicle development	IEA
GO:0001547	Process	Antral ovarian follicle growth	IEA
GO:0003676	Function	Nucleic acid binding	IEA
GO:0005515	Function	Protein binding	IPI	17698606, 32814053
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IEA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005829	Component	Cytosol	IDA
GO:0007283	Process	Spermatogenesis	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0016607	Component	Nuclear speck	IDA
GO:0046872	Function	Metal ion binding	IEA
GO:0060041	Process	Retina development in camera-type eye	IMP	28794130
GO:0061827	Component	Sperm head	IEA
GO:0072520	Process	Seminiferous tubule development	IEA
GO:1990917	Component	Ooplasm	IEA

Other IDs

• MIM: 611611
• HGNC: 13081
• e!Ensembl: ENSG00000140386

Protein

• UniProt ID: Q9BY12
• Protein name: S phase cyclin A-associated protein in the endoplasmic reticulum (S phase cyclin A-associated protein in the ER) (Zinc finger protein 291)
• Protein function: CCNA2/CDK2 regulatory protein that transiently maintains CCNA2 in the cytoplasm.
• PDB: 8BPO
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF16501	SCAPER_N	89 → 186	S phase cyclin A-associated protein in the endoplasmic reticulum	Family
  PF12874	zf-met	792 → 816		Domain

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed with high expression in testis. Isoform 1 is detected in various tissues, including retina, fetal and adult brain. Isoform 2 is expressed in the retina at high levels, and in the brain at very low levels (PubMed:287941
• Sequence:

  MMASFQRSNSHDKVRRIVAEEGRTARNLIAWSVPLESKDDDGKPKCQTGGKSKRTIQGTH
  KTTKQSTAVDCKITSSTTGDKHFDKSPTKTRHPRKIDLRARYWAFLFDNLRRAVDEIYVT
  CESDQSVVECKEVLMMLDNYVRDFKALIDWIQLQEKLEKTDAQSRPTSLAWEVKKMSPGR
  HVIPSPSTDRINVTSNARRSLNFGGSTGTVPAPRLAPTGVSWADKVKAHHTGSTASSEIT
  PAQSCPPMTVQKASRKNERKDAEGWETVQRGRPIRSRSTAVMPKVSLATEATRSKDDSDK
  ENVCLLPDESIQKGQFVGDGTSNTIESHPKDSLHSCDHPLAEKTQFTVSTLDDVKNSGSI
  RDNYVRTSEISAVHIDTECVSVMLQAGTPPLQVNEEKFPAEKARIENEMDPSDISNSMAE
  VLAKKEELADRLEKANEEAIASAIAEEEQLTREIEAEENNDINIETDNDSDFSASMGSGS
  VSFCGMSMDWNDVLADYEARESWRQNTSWGDIVEEEPARPPGHGIHMHEKLSSPSRKRTI
  AESKKKHEEKQMKAQQLREKLREEKTLKLQKLLEREKDVRKWKEELLDQRRRMMEEKLLH
  AEFKREVQLQAIVKKAQEEEAKVNEIAFINTLEAQNKRHDVLSKLKEYEQRLNELQEERQ
  RRQEEKQARDEAVQERKRALEAERQARVEELLMKRKEQEARIEQQRQEKEKAREDAARER
  ARDREERLAALTAAQQEAMEELQKKIQLKHDESIRRHMEQIEQRKEKAAELSSGRHANTD
  YAPKLTPYERKKQCSLCNVLISSEVYLFSHVKGRKHQQAVRENTSIQGRELSDEEVEHLS
  LKKYIIDIVVESTAPAEALKDGEERQKNKKKAKKIKARMNFRAKEYESLMETKNSGSDSP
  YKAKLQRLAKDLLKQVQVQDSGSWANNKVSALDRTLGEITRILEKENVADQIAFQAAGGL
  TALEHILQAVVPATNVNTVLRIPPKSLCNAINVYNLTCNNCSENCSDVLFSNKITFLMDL
  LIHQLTVYVPDENNTILGRNTNKQVFEGLTTGLLKVSAVVLGCLIANRPDGNCQPATPKI
  PTQEMKNKPSQGDPFNNRVQDLISYVVNMGLIDKLCACFLSVQGPVDENPKMAIFLQHAA
  GLLHAMCTLCFAVTGRSYSIFDNNRQDPTGLTAALQATDLAGVLHMLYCVLFHGTILDPS
  TASPKENYTQNTIQVAIQSLRFFNSFAALHLPAFQSIVGAEGLSLAFRHMASSLLGHCSQ
  VSCESLLHEVIVCVGYFTVNHPDNQVIVQSGRHPTVLQKLCQLPFQYFSDPRLIKVLFPS
  LIAACYNNHQNKIILEQEMSCVLLATFIQDLAQTPGQAENQPYQPKGKCLGSQDYLELAN
  RFPQQAWEEARQFFLKKEKK

• Sequence length: 1400

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Attention deficit hyperactivity disorder	Pathogenic	rs1555447569	RCV000515799
Intellectual developmental disorder and retinitis pigmentosa; IDDRP	Likely pathogenic; Pathogenic	rs761149240, rs2050148457, rs757834403, rs2151864247, rs1192028272, rs1555447569, rs1555558169, rs1305542291, rs1395475624, rs1239725461, rs1303625185, rs1596596355, rs1462082548, rs978336151, rs1598632432, rs1484749107, rs1598279469, rs1598598205, rs1597752941, rs777893794	RCV001783712 RCV001783713 RCV001813898 RCV002221861 RCV003989435 RCV000722054 RCV000722053 RCV000722056 RCV000722055 RCV000984530 RCV000984529 RCV000984527 RCV000984523 RCV000984524 RCV000984525 RCV000984528 RCV000984531 RCV000984526 RCV001029901 RCV001029902
Moderate intellectual disability	Pathogenic; Likely pathogenic	rs1555447569, rs1305542291, rs1395475624	RCV000515799 RCV000523592 RCV000520792
Retinitis pigmentosa	Pathogenic	rs1555558169	RCV000578475
Rod-cone dystrophy	Pathogenic; Likely pathogenic	rs1555447569, rs1305542291, rs1395475624	RCV000515799 RCV000523592 RCV000520792
SCAPER-related disorder	Likely pathogenic	rs2050148457, rs2548144366, rs1239045609	RCV004731179 RCV003400295 RCV003397443
Syndromic retinitis pigmentosa	Pathogenic	rs1555558169	RCV001003221

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Acute myeloid leukemia	Conflicting classifications of pathogenicity	rs139187840	RCV005938664
Bardet-Biedl syndrome 1	Uncertain significance	rs771454836	RCV003229559
Cervical cancer	Conflicting classifications of pathogenicity	rs139187840	RCV005938665
Familial cancer of breast	Conflicting classifications of pathogenicity	rs139187840	RCV005938663
Gastric cancer	Conflicting classifications of pathogenicity	rs139187840	RCV005938666
Lung cancer	Conflicting classifications of pathogenicity	rs139187840	RCV005938668
Optic atrophy	Conflicting classifications of pathogenicity	rs200793584	RCV004818440
Ovarian serous cystadenocarcinoma	Conflicting classifications of pathogenicity	rs139187840	RCV005938667
Retinal dystrophy	Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	rs199859385, rs137972092, rs771454836, rs139187840, rs35382573	RCV004818280 RCV004818281 RCV004818306 RCV004818439 RCV004818441
Schizophrenia	Uncertain significance	rs2548136015	RCV002463554

Associations from Text Mining
Disease Name	Relationship Type	References
Attention Deficit Disorder with Hyperactivity	Associate	30561111
Intellectual Disability	Associate	30561111, 37295431
Macular Degeneration	Associate	19412524
Pigmentation Disorders	Associate	31437301
Retinitis Pigmentosa	Associate	30561111, 37295431
RHYNS syndrome	Associate	30561111