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SCAPER S-phase cyclin A associated protein in the ER [ Homo sapiens (human) ]

Gene ID: 49855, updated on 3-Apr-2024

Summary

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Official Symbol
SCAPERprovided by HGNC
Official Full Name
S-phase cyclin A associated protein in the ERprovided by HGNC
Primary source
HGNC:HGNC:13081
See related
Ensembl:ENSG00000140386 MIM:611611; AllianceGenome:HGNC:13081
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
IDDRP; ZNF291; Zfp291; MSTP063
Summary
Predicted to enable nucleic acid binding activity and zinc ion binding activity. Located in cytosol and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 4.5), brain (RPKM 3.0) and 25 other tissues See more
Orthologs
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Genomic context

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See SCAPER in Genome Data Viewer
Location:
15q24.3
Exon count:
46
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (76347904..76905340, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (74219067..74764374, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (76640245..77197681, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene electron transfer flavoprotein subunit alpha Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:76603062-76603562 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:76603563-76604063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9878 Neighboring gene CRISPRi-validated cis-regulatory element chr15.2471 Neighboring gene TYRO3P protein tyrosine kinase pseudogene Neighboring gene Sharpr-MPRA regulatory region 228 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:76629623-76630434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9881 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:76632479-76633234 Neighboring gene uncharacterized LOC124903532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76638487-76638988 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6688 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:76663676-76663893 Neighboring gene tRNA-Lys (anticodon CTT) 16-1 Neighboring gene ISL LIM homeobox 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:76726060-76727259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9883 Neighboring gene microRNA 3713 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6689 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76991672-76992172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76992173-76992673 Neighboring gene RN7SK pseudogene 217 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6690 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6691 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:77197527-77198027 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:77208364-77208864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:77208865-77209365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6693 Neighboring gene uncharacterized LOC105370904 Neighboring gene RNA, 7SL, cytoplasmic 278, pseudogene Neighboring gene reticulocalbin 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Delineating the expanding phenotype associated with SCAPER gene mutation. Fasham J, et al. Am J Med Genet A, 2019 Aug. PMID 31192531, Free PMC Article
  2. Homozygous variants in the gene SCAPER cause syndromic intellectual disability. Kahrizi K, et al. Am J Med Genet A, 2019 Jul. PMID 31069901
  3. SCAPER localizes to primary cilia and its mutation affects cilia length, causing Bardet-Biedl syndrome. Wormser O, et al. Eur J Hum Genet, 2019 Jun. PMID 30723319, Free PMC Article
  4. SCAPER-associated nonsyndromic autosomal recessive retinitis pigmentosa. Jauregui R, et al. Am J Med Genet A, 2019 Feb. PMID 30561111, Free PMC Article
  5. Double identity of SCAPER: a substrate and regulator of cyclin A/Cdk2. Tsang WY, et al. Cell Cycle, 2008 Mar 15. PMID 18245951

See all (38) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Absence of SCAPER causes male infertility in humans and Drosophila by modulating microtubule dynamics during meiosis.
    Title: Absence of SCAPER causes male infertility in humans and Drosophila by modulating microtubule dynamics during meiosis.
  2. Male sterility and reduced female fertility in SCAPER-deficient mice.
    Title: Male sterility and reduced female fertility in SCAPER-deficient mice.
  3. Delineating the expanding phenotype associated with SCAPER gene mutation.
    Title: Delineating the expanding phenotype associated with SCAPER gene mutation.
  4. As SCAPER expression is known to peak at late G1 and S phase, overlapping the timing of ciliary resorption, our data suggest a possible role of SCAPER in ciliary dynamics and disassembly, also affecting microtubule-related mitotic progression.
    Title: SCAPER localizes to primary cilia and its mutation affects cilia length, causing Bardet-Biedl syndrome.
  5. Homozygous variants in the gene SCAPER cause syndromic intellectual disability.
    Title: Homozygous variants in the gene SCAPER cause syndromic intellectual disability.
  6. Unique to our patient's presentation is the absence of intellectual disability and attention-deficit/hyperactivity disorder, suggesting that SCAPER-associated retinitis pigmentosa can also present without systemic manifestations.
    Title: SCAPER-associated nonsyndromic autosomal recessive retinitis pigmentosa.
  7. By sequestering cyclin A/Cdk2, SCAPER is capable of directing the activity of this kinase complex away from the nucleus and regulating cyclin A/Cdk2 equilibrium in distinct subcellular compartments.
    Title: Double identity of SCAPER: a substrate and regulator of cyclin A/Cdk2.
  8. An unstable [CCTG](n) repeat in the second intron of the ZNF291 gene, on chromosome 15q21-24, was identified.
    Title: Detection of an unstable non-coding tandem repeat in the ZNF291 gene.
  9. Study describes the biochemically purification and identification of SCAPER, a novel protein that specifically interacts with cyclin A/Cdk2 in vivo.
    Title: SCAPER, a novel cyclin A-interacting protein that regulates cell cycle progression.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Intellectual developmental disorder and retinitis pigmentosa; IDDRP
MedGen: C4748658 OMIM: 618195 GeneReviews: Not available
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EBI GWAS Catalog

Description
An atlas of genetic influences on human blood metabolites.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ31533, FLJ31953, FLJ46212, KIAA1454

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in antral ovarian follicle growth IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within retina development in camera-type eye IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in seminiferous tubule development IEA
Inferred from Electronic Annotation
more info
  
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear speck IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in ooplasm IEA
Inferred from Electronic Annotation
more info
  
located_in sperm head IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
S phase cyclin A-associated protein in the endoplasmic reticulum
Names
zinc finger protein 291

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001145923.2 → NP_001139395.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AC016343, AC027243, AF119814, BX647285
    Consensus CDS
    CCDS53961.1
    UniProtKB/Swiss-Prot
    Q9BY12
    Related
    ENSP00000442190.2, ENST00000538941.6
    Conserved Domains (2) summary
    PTZ00121
    Location:146 → 524
    PTZ00121; MAEBL; Provisional
    smart00451
    Location:544 → 576
    ZnF_U1; U1-like zinc finger

  2. NM_001353009.2 → NP_001339938.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform c

    Status: VALIDATED

    Source sequence(s)
    AC015798, AC016343, AC027243, AC051643, AC090179, AC090751
    Conserved Domains (3) summary
    smart00451
    Location:796 → 828
    ZnF_U1; U1-like zinc finger
    pfam16501
    Location:89 → 183
    SCAPER_N; S phase cyclin A-associated protein in the endoplasmic reticulum
    cl26511
    Location:395 → 776
    Neuromodulin_N; Gap junction protein N-terminal region

  3. NM_001353010.2 → NP_001339939.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform d

    Status: VALIDATED

    Source sequence(s)
    AC015798, AC016343, AC027243, AC051643, AC090179, AC090751
    Conserved Domains (3) summary
    smart00451
    Location:656 → 688
    ZnF_U1; U1-like zinc finger
    pfam16501
    Location:1 → 49
    SCAPER_N; S phase cyclin A-associated protein in the endoplasmic reticulum
    cl26511
    Location:258 → 636
    Neuromodulin_N; Gap junction protein N-terminal region

  4. NM_001353011.2 → NP_001339940.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform e

    Status: VALIDATED

    Source sequence(s)
    AC015798, AC016343, AC027243, AC051643, AC090179, AC090751
    Conserved Domains (3) summary
    smart00451
    Location:662 → 694
    ZnF_U1; U1-like zinc finger
    pfam16501
    Location:1 → 49
    SCAPER_N; S phase cyclin A-associated protein in the endoplasmic reticulum
    cl26511
    Location:261 → 642
    Neuromodulin_N; Gap junction protein N-terminal region

  5. NM_001353012.2 → NP_001339941.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform d

    Status: VALIDATED

    Source sequence(s)
    AC015798, AC016343, AC027243, AC051643, AC090179, AC090751
    Conserved Domains (3) summary
    smart00451
    Location:656 → 688
    ZnF_U1; U1-like zinc finger
    pfam16501
    Location:1 → 49
    SCAPER_N; S phase cyclin A-associated protein in the endoplasmic reticulum
    cl26511
    Location:258 → 636
    Neuromodulin_N; Gap junction protein N-terminal region

  6. NM_020843.4 → NP_065894.2  S phase cyclin A-associated protein in the endoplasmic reticulum isoform a

    See identical proteins and their annotated locations for NP_065894.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform a.
    Source sequence(s)
    AC015798, AC016343, AC027243, AC051643, AC090179, AC090751
    Consensus CDS
    CCDS53962.1
    UniProtKB/Swiss-Prot
    F5H7X8, H3BNR7, Q3B7X7, Q96BS9, Q9BY12, Q9H3D8, Q9NT03, Q9P274
    Related
    ENSP00000454973.1, ENST00000563290.6
    Conserved Domains (5) summary
    smart00451
    Location:790 → 822
    ZnF_U1; U1-like zinc finger
    pfam00836
    Location:529 → 626
    Stathmin; Stathmin family
    pfam16501
    Location:89 → 183
    SCAPER_N; S phase cyclin A-associated protein in the endoplasmic reticulum
    cd16269
    Location:760 → 770
    GBP_C; coiled coil [structural motif]
    cl20817
    Location:670 → 774
    GBP_C; Guanylate-binding protein, C-terminal domain

RNA

  1. NR_148227.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC015798, AC016343, AC027243, AC051643, AC090179, AC090751

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    76347904..76905340 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017022273.2 → XP_016877762.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X9

    Conserved Domains (3) summary
    smart00451
    Location:656 → 688
    ZnF_U1; U1-like zinc finger
    pfam16501
    Location:1 → 49
    SCAPER_N; S phase cyclin A-associated protein in the endoplasmic reticulum
    cl26511
    Location:258 → 636
    Neuromodulin_N; Gap junction protein N-terminal region

  2. XM_011521653.4 → XP_011519955.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X8

    See identical proteins and their annotated locations for XP_011519955.1

    Conserved Domains (3) summary
    smart00451
    Location:662 → 694
    ZnF_U1; U1-like zinc finger
    pfam16501
    Location:1 → 49
    SCAPER_N; S phase cyclin A-associated protein in the endoplasmic reticulum
    cl26511
    Location:261 → 642
    Neuromodulin_N; Gap junction protein N-terminal region

  3. XM_047432625.1 → XP_047288581.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X6

  4. XM_047432621.1 → XP_047288577.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X2

  5. XM_047432624.1 → XP_047288580.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X5

  6. XM_047432620.1 → XP_047288576.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X1

  7. XM_047432623.1 → XP_047288579.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X4

  8. XM_047432622.1 → XP_047288578.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X3

  9. XM_047432626.1 → XP_047288582.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X7

  10. XM_047432627.1 → XP_047288583.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X10

  11. XM_011521656.4 → XP_011519958.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X20

    Conserved Domains (5) summary
    smart00451
    Location:176 → 208
    ZnF_U1; U1-like zinc finger
    pfam11600
    Location:28 → 182
    CAF-1_p150; Chromatin assembly factor 1 complex p150 subunit, N-terminal
    cd16269
    Location:146 → 156
    GBP_C; coiled coil [structural motif]
    cl00220
    Location:543 → 584
    cysteine_hydrolases; Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It ...
    cl20817
    Location:56 → 160
    GBP_C; Guanylate-binding protein, C-terminal domain

  12. XM_047432633.1 → XP_047288589.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X22

  13. XM_047432629.1 → XP_047288585.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X15

  14. XM_047432628.1 → XP_047288584.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X14

  15. XM_024449942.2 → XP_024305710.2  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X13

  16. XM_024449941.2 → XP_024305709.2  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X12

  17. XM_024449940.2 → XP_024305708.2  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X11

  18. XM_047432630.1 → XP_047288586.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X16

  19. XM_047432632.1 → XP_047288588.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X21

  20. XM_047432631.1 → XP_047288587.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X18

  21. XM_024449944.2 → XP_024305712.2  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X17

  22. XM_017022283.2 → XP_016877772.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X19

    UniProtKB/TrEMBL
    H3BS25
    Related
    ENSP00000456508.1, ENST00000564590.5

  23. XM_047432634.1 → XP_047288590.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X23

RNA

  1. XR_007064448.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    74219067..74764374 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054378112.1 → XP_054234087.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X9

  2. XM_054378111.1 → XP_054234086.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X8

  3. XM_054378109.1 → XP_054234084.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X6

  4. XM_054378105.1 → XP_054234080.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X2

  5. XM_054378108.1 → XP_054234083.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X5

  6. XM_054378104.1 → XP_054234079.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X1

  7. XM_054378107.1 → XP_054234082.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X4

  8. XM_054378106.1 → XP_054234081.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X3

  9. XM_054378110.1 → XP_054234085.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X7

  10. XM_054378113.1 → XP_054234088.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X10

  11. XM_054378123.1 → XP_054234098.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X20

  12. XM_054378125.1 → XP_054234100.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X22

  13. XM_054378118.1 → XP_054234093.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X15

  14. XM_054378116.1 → XP_054234091.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X13

  15. XM_054378115.1 → XP_054234090.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X12

  16. XM_054378117.1 → XP_054234092.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X14

  17. XM_054378114.1 → XP_054234089.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X11

  18. XM_054378119.1 → XP_054234094.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X16

  19. XM_054378124.1 → XP_054234099.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X21

  20. XM_054378121.1 → XP_054234096.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X18

  21. XM_054378120.1 → XP_054234095.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X17

  22. XM_054378122.1 → XP_054234097.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X19

  23. XM_054378126.1 → XP_054234101.1  S phase cyclin A-associated protein in the endoplasmic reticulum isoform X23

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BY12.2 GenPept UniProtKB/Swiss-Prot:Q9BY12

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