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

Gene ID: 8631, updated on 3-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (48133442..48445061, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (48996813..49308533, complement)
105.20220307 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. 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
  2. Integration of T cell receptor-dependent signaling pathways by adapter proteins. Clements JL, et al. Annu Rev Immunol, 1999. PMID 10358754
  3. 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
  4. 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
  5. THUMPD3-AS1 facilitates cell growth and aggressiveness by the miR-218-5p/SKAP1 axis in colorectal cancer. Pu Y, et al. Cell Biochem Biophys, 2022 Sep. PMID 35538197

See all (46) 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)

Genotypes

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_2023_10

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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