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    SKAP1 src kinase associated phosphoprotein 1 [ Homo sapiens (human) ]

    Gene ID: 8631, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SKAP1provided by HGNC
    Official Full Name
    src kinase associated phosphoprotein 1provided by HGNC
    Primary source
    HGNC:HGNC:15605
    See related
    Ensembl:ENSG00000141293 MIM:604969; AllianceGenome:HGNC:15605
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SCAP1; SKAP55; HEL-S-81p
    Summary
    This gene encodes a T cell adaptor protein, a class of intracellular molecules with modular domains capable of recruiting additional proteins but that exhibit no intrinsic enzymatic activity. The encoded protein contains a unique N-terminal region followed by a PH domain and C-terminal SH3 domain. Along with the adhesion and degranulation-promoting adaptor protein, the encoded protein plays a critical role in inside-out signaling by coupling T-cell antigen receptor stimulation to the activation of integrins. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in lymph node (RPKM 9.4), spleen (RPKM 4.5) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SKAP1 in Genome Data Viewer
    Location:
    17q21.32
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (48133442..48445061, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (48996813..49308533, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (46210804..46507576, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46171341-46171930 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46178573-46179172 Neighboring gene RNA, U6 small nuclear 1201, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8650 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:46186828-46187001 Neighboring gene chromobox 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12327 Neighboring gene uncharacterized LOC124904018 Neighboring gene VISTA enhancer hs697 Neighboring gene sorting nexin 11 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:46237721-46238266 Neighboring gene microRNA 1203 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:46269531-46270148 Neighboring gene RNA, U6 small nuclear 1152, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:46296699-46297541 Neighboring gene LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12328 Neighboring gene SKAP1 antisense RNA 2 Neighboring gene Sharpr-MPRA regulatory region 12941 Neighboring gene small nucleolar RNA U3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8651 Neighboring gene uncharacterized LOC101927166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12331 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:46560473-46561672 Neighboring gene uncharacterized LOC124904019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12332 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:46593890-46594400 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:46597283-46597974 Neighboring gene uncharacterized LOC105371808 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:46597975-46598664 Neighboring gene Sharpr-MPRA regulatory region 4378

    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. SKAP1 Is a Novel Biomarker and Therapeutic Target for Gastric Cancer: Evidence from Expression, Functional, and Bioinformatic Analyses. Zhu L, et al. Int J Mol Sci, 2023 Jul 24. PMID 37511629, Free PMC Article
    2. Molecular analysis of the fyn-complex: cloning of SKAP55 and SLAP-130, two novel adaptor proteins which associate with fyn and may participate in the regulation of T cell receptor-mediated signaling. Schraven B, et al. Immunol Lett, 1997 Jun 1. PMID 9232446
    3. The N terminus of SKAP55 enables T cell adhesion to TCR and integrin ligands via distinct mechanisms. Ophir MJ, et al. J Cell Biol, 2013 Dec 23. PMID 24368808, Free PMC Article
    4. Integration of T cell receptor-dependent signaling pathways by adapter proteins. Clements JL, et al. Annu Rev Immunol, 1999. PMID 10358754
    5. Splicing annotation of endometrial cancer GWAS risk loci reveals potentially causal variants and supports a role for NF1 and SKAP1 as susceptibility genes. Canson DM, et al. HGG Adv, 2023 Apr 13. PMID 36908940, Free PMC Article

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SKAP1 Is a Novel Biomarker and Therapeutic Target for Gastric Cancer: Evidence from Expression, Functional, and Bioinformatic Analyses.
      Title: SKAP1 Is a Novel Biomarker and Therapeutic Target for Gastric Cancer: Evidence from Expression, Functional, and Bioinformatic Analyses.
    2. Splicing annotation of endometrial cancer GWAS risk loci reveals potentially causal variants and supports a role for NF1 and SKAP1 as susceptibility genes.
      Title: Splicing annotation of endometrial cancer GWAS risk loci reveals potentially causal variants and supports a role for NF1 and SKAP1 as susceptibility genes.
    3. THUMPD3-AS1 facilitates cell growth and aggressiveness by the miR-218-5p/SKAP1 axis in colorectal cancer.
      Title: THUMPD3-AS1 facilitates cell growth and aggressiveness by the miR-218-5p/SKAP1 axis in colorectal cancer.
    4. The Multiple Roles of the Cytosolic Adapter Proteins ADAP, SKAP1 and SKAP2 for TCR/CD3 -Mediated Signaling Events.
      Title: The Multiple Roles of the Cytosolic Adapter Proteins ADAP, SKAP1 and SKAP2 for TCR/CD3 -Mediated Signaling Events.
    5. K152 and D120 within the PH domain of SKAP55 regulate plasma membrane targeting and T cell receptor-mediated activation of LFA-1.
      Title: D120 and K152 within the PH Domain of T Cell Adapter SKAP55 Regulate Plasma Membrane Targeting of SKAP55 and LFA-1 Affinity Modulation in Human T Lymphocytes.
    6. SKAP55 dimers stabilize SLP-76 microclusters, couple SLP-76 to the force-generating systems responsible for microcluster movement, and enable adhesion via the TCR by mechanisms independent of RIAM, talin, and beta1 integrins.
      Title: The N terminus of SKAP55 enables T cell adhesion to TCR and integrin ligands via distinct mechanisms.
    7. single-nucleotide polymorphisms in ARRDC3, FLT1, and SKAP1 were significant predictors for survival androgen-deprivation therapy in prostate cancer patients.
      Title: Genetic polymorphisms in androgen receptor-binding sites predict survival in prostate cancer patients receiving androgen-deprivation therapy.
    8. N-terminal myr-tagged SKAP1 for membrane binding facilitated constitutive RapL membrane and Rap1 binding and effectively substituted for PI3K and TCR ligation in the activation of LFA-1 in T cells.
      Title: SKAP1 protein PH domain determines RapL membrane localization and Rap1 protein complex formation for T cell receptor (TCR) activation of LFA-1.
    9. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24.
    10. Single nucleotide polymorphism in SKAP1 is associated with ovarian cancer.
      Title: A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    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

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24.
    EBI GWAS Catalog
    Genome-wide association analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32
    EBI GWAS Catalog
    GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer.
    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)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 downregulates the expression of src kinase associated phosphoprotein 1 (SKAP1) in human B cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SH2 domain binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables SH3 domain binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein phosphatase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in T cell receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of adaptive immune response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of cell-cell adhesion mediated by integrin IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in positive regulation of cell-matrix adhesion IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in positive regulation of heterotypic cell-cell adhesion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of integrin activation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of leukocyte cell-cell adhesion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein localization to plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of T cell receptor complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell-cell junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in immunological synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane raft IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    src kinase-associated phosphoprotein 1
    Names
    SKAP-55
    epididymis secretory sperm binding protein Li 81p
    pp55
    src family-associated phosphoprotein 1
    src kinase-associated phosphoprotein of 55 kDa

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001075099.2 → NP_001068567.1  src kinase-associated phosphoprotein 1 isoform 2

      See identical proteins and their annotated locations for NP_001068567.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate, in-frame splice site in the coding region, compared to variant 1. The encoded protein (isoform 2) is shorter but has identical N- and C-termini, compared to isoform 1.
      Source sequence(s)
      BC047870, DR007155
      UniProtKB/TrEMBL
      A8K453, V9HW03
      Conserved Domains (2) summary
      cd12044
      Location:297 → 349
      SH3_SKAP1; Src Homology 3 domain of Src Kinase-Associated Phosphoprotein 1
      cd13380
      Location:108 → 213
      PH_Skap1; Src kinase-associated phosphoprotein 1 Pleckstrin homology (PH) domain

    2. NM_003726.4 → NP_003717.3  src kinase-associated phosphoprotein 1 isoform 1

      See identical proteins and their annotated locations for NP_003717.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      BC047870, DR007155, Y11215
      Consensus CDS
      CCDS32674.1
      UniProtKB/Swiss-Prot
      D3DTV1, O15268, Q86WV1
      UniProtKB/TrEMBL
      A8K453
      Related
      ENSP00000338171.6, ENST00000336915.11
      Conserved Domains (3) summary
      cd12044
      Location:298 → 350
      SH3_SKAP1; Src Homology 3 domain of Src Kinase-Associated Phosphoprotein 1
      cd13380
      Location:108 → 213
      PH_Skap1; Src kinase-associated phosphoprotein 1 Pleckstrin homology (PH) domain
      pfam00169
      Location:108 → 210
      PH; PH domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      48133442..48445061 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005257755.5 → XP_005257812.1  src kinase-associated phosphoprotein 1 isoform X6

      UniProtKB/TrEMBL
      A8K453
      Conserved Domains (3) summary
      cd12044
      Location:280 → 332
      SH3_SKAP1; Src Homology 3 domain of Src Kinase-Associated Phosphoprotein 1
      cd13380
      Location:108 → 213
      PH_Skap1; Src kinase-associated phosphoprotein 1 Pleckstrin homology (PH) domain
      pfam00169
      Location:108 → 210
      PH; PH domain

    2. XM_017025258.2 → XP_016880747.1  src kinase-associated phosphoprotein 1 isoform X10

    3. XM_047436976.1 → XP_047292932.1  src kinase-associated phosphoprotein 1 isoform X5

    4. XM_047436975.1 → XP_047292931.1  src kinase-associated phosphoprotein 1 isoform X4

    5. XM_047436973.1 → XP_047292929.1  src kinase-associated phosphoprotein 1 isoform X2

    6. XM_047436972.1 → XP_047292928.1  src kinase-associated phosphoprotein 1 isoform X1

    7. XM_047436974.1 → XP_047292930.1  src kinase-associated phosphoprotein 1 isoform X3

    8. XM_047436980.1 → XP_047292936.1  src kinase-associated phosphoprotein 1 isoform X11

    9. XM_047436979.1 → XP_047292935.1  src kinase-associated phosphoprotein 1 isoform X9

    10. XM_047436978.1 → XP_047292934.1  src kinase-associated phosphoprotein 1 isoform X8

    11. XM_047436977.1 → XP_047292933.1  src kinase-associated phosphoprotein 1 isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      48996813..49308533 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054317637.1 → XP_054173612.1  src kinase-associated phosphoprotein 1 isoform X6

    2. XM_054317642.1 → XP_054173617.1  src kinase-associated phosphoprotein 1 isoform X10

    3. XM_054317643.1 → XP_054173618.1  src kinase-associated phosphoprotein 1 isoform X11

    4. XM_054317641.1 → XP_054173616.1  src kinase-associated phosphoprotein 1 isoform X9

    5. XM_054317640.1 → XP_054173615.1  src kinase-associated phosphoprotein 1 isoform X8

    6. XM_054317636.1 → XP_054173611.1  src kinase-associated phosphoprotein 1 isoform X5

    7. XM_054317634.1 → XP_054173609.1  src kinase-associated phosphoprotein 1 isoform X3

    8. XM_054317638.1 → XP_054173613.1  src kinase-associated phosphoprotein 1 isoform X12

    9. XM_054317635.1 → XP_054173610.1  src kinase-associated phosphoprotein 1 isoform X4

    10. XM_054317633.1 → XP_054173608.1  src kinase-associated phosphoprotein 1 isoform X2

    11. XM_054317632.1 → XP_054173607.1  src kinase-associated phosphoprotein 1 isoform X1

    12. XM_054317639.1 → XP_054173614.1  src kinase-associated phosphoprotein 1 isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86WV1.3 GenPept UniProtKB/Swiss-Prot:Q86WV1

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