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    SH2D4A SH2 domain containing 4A [ Homo sapiens (human) ]

    Gene ID: 63898, updated on 7-Apr-2024

    Summary

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    Official Symbol
    SH2D4Aprovided by HGNC
    Official Full Name
    SH2 domain containing 4Aprovided by HGNC
    Primary source
    HGNC:HGNC:26102
    See related
    Ensembl:ENSG00000104611 MIM:614968; AllianceGenome:HGNC:26102
    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
    SH2A; PPP1R38
    Summary
    Enables phosphatase binding activity. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in ovary (RPKM 11.6), stomach (RPKM 9.2) and 22 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SH2D4A in Genome Data Viewer
    Location:
    8p21.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (19313693..19396218)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (19578579..19661102)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (19171204..19253729)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379300 Neighboring gene uncharacterized LOC105379306 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:19230007-19230168 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27055 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:19263473-19263973 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:19262972-19263472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27057 Neighboring gene chondroitin sulfate N-acetylgalactosaminyltransferase 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:19394183-19395382 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:19435762-19436961 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:19497293-19497837 Neighboring gene uncharacterized LOC124901900 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:19522068-19523267 Neighboring gene uncharacterized LOC124901899 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:19536806-19537406

    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. SH2D4A downregulation due to loss of chromosome 8p is associated with poor prognosis and low T cell infiltration in colorectal cancer. Matsumoto T, et al. Br J Cancer, 2022 Apr. PMID 34893760, Free PMC Article
    2. SH2D4A is frequently downregulated in hepatocellular carcinoma and cirrhotic nodules. Quagliata L, et al. Eur J Cancer, 2014 Mar. PMID 24315626
    3. [A novel member of SH(2) signaling protein family: cloning and characterization of SH(2)A gene]. Dai S, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2002 Dec. PMID 12476414
    4. Chromosome 8p tumor suppressor genes SH2D4A and SORBS3 cooperate to inhibit interleukin-6 signaling in hepatocellular carcinoma. Ploeger C, et al. Hepatology, 2016 Sep. PMID 27311882, Free PMC Article
    5. Genome-wide association study of urinary albumin excretion rate in patients with type 1 diabetes. Sandholm N, et al. Diabetologia, 2014 Jun. PMID 24595857

    See all (51) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SH2D4A inhibits esophageal squamous cell carcinoma progression through FAK/PI3K/AKT signaling pathway.
      Title: SH2D4A inhibits esophageal squamous cell carcinoma progression through FAK/PI3K/AKT signaling pathway.
    2. SH2D4A downregulation due to loss of chromosome 8p is associated with poor prognosis and low T cell infiltration in colorectal cancer.
      Title: SH2D4A downregulation due to loss of chromosome 8p is associated with poor prognosis and low T cell infiltration in colorectal cancer.
    3. The chromosome 8p tumor suppressor genes SORBS3 and SH2D4A are physically and functionally linked and provide a molecular mechanism of inhibiting STAT3-mediated IL-6 signaling in hepatocellular carcinoma cells.
      Title: Chromosome 8p tumor suppressor genes SH2D4A and SORBS3 cooperate to inhibit interleukin-6 signaling in hepatocellular carcinoma.
    4. New evidence for SH2D4A involvement in hepatocellular carcinoma pathogenesis demonstrating for the first time its deregulation in cirrhotic nodules.
      Title: SH2D4A is frequently downregulated in hepatocellular carcinoma and cirrhotic nodules.
    5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    6. SH2D4A inhibited cell proliferation by suppression of the ERalpha/PLC-gamma/PKC signaling pathway.
      Title: SH2D4A regulates cell proliferation via the ERalpha/PLC-gamma/PKC pathway.
    7. SH2D4A is dispensable for TCR signal transduction in T cells
      Title: Genetic analysis of SH2D4A, a novel adapter protein related to T cell-specific adapter and adapter protein in lymphocytes of unknown function, reveals a redundant function in T cells.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association study of primary dentition pit-and-fissure and smooth surface caries.
    EBI GWAS Catalog
    Genome-wide association study of urinary albumin excretion rate in patients with type 1 diabetes.
    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

    • FLJ20967

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatase binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    SH2 domain-containing protein 4A
    Names
    protein SH(2)A
    protein phosphatase 1 regulatory subunit 38

    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_001174159.2 → NP_001167630.1  SH2 domain-containing protein 4A isoform a

      See identical proteins and their annotated locations for NP_001167630.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AK024799, BC082982, CA418381
      Consensus CDS
      CCDS6009.1
      UniProtKB/Swiss-Prot
      B4DDR1, Q5XKC1, Q6NXE9, Q86YM2, Q96C88, Q9H788, Q9H7F7
      Related
      ENSP00000428684.1, ENST00000519207.5
      Conserved Domains (1) summary
      cd10350
      Location:339 → 442
      SH2_SH2D4A; Src homology 2 domain found in the SH2 domain containing protein 4A (SH2D4A)

    2. NM_001174160.2 → NP_001167631.1  SH2 domain-containing protein 4A isoform b

      See identical proteins and their annotated locations for NP_001167631.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) has a shorter and distinct N-terminus compared to isoform a.
      Source sequence(s)
      AK024799, AK293301, CA418381, DA952240
      Consensus CDS
      CCDS55206.1
      UniProtKB/Swiss-Prot
      Q9H788
      Related
      ENSP00000429482.1, ENST00000518040.5
      Conserved Domains (1) summary
      cd10350
      Location:294 → 397
      SH2_SH2D4A; Src homology 2 domain found in the SH2 domain containing protein 4A (SH2D4A)

    3. NM_001363110.2 → NP_001350039.1  SH2 domain-containing protein 4A isoform c

      Status: VALIDATED

      Source sequence(s)
      AK024799, BC082982, CA418381, DA952240, DB183296
      Conserved Domains (2) summary
      cd10350
      Location:312 → 415
      SH2_SH2D4A; Src homology 2 domain found in the SH2 domain containing protein 4A (SH2D4A)
      cl26511
      Location:99 → 251
      Neuromodulin_N; Gap junction protein N-terminal region

    4. NM_001363111.2 → NP_001350040.1  SH2 domain-containing protein 4A isoform c

      Status: VALIDATED

      Source sequence(s)
      AK024799, BC082982, CA418381, DB183296
      Conserved Domains (2) summary
      cd10350
      Location:312 → 415
      SH2_SH2D4A; Src homology 2 domain found in the SH2 domain containing protein 4A (SH2D4A)
      cl26511
      Location:99 → 251
      Neuromodulin_N; Gap junction protein N-terminal region

    5. NM_022071.4 → NP_071354.2  SH2 domain-containing protein 4A isoform a

      See identical proteins and their annotated locations for NP_071354.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AK024799, BC082982, CA418381, DA952240
      Consensus CDS
      CCDS6009.1
      UniProtKB/Swiss-Prot
      B4DDR1, Q5XKC1, Q6NXE9, Q86YM2, Q96C88, Q9H788, Q9H7F7
      Related
      ENSP00000265807.3, ENST00000265807.8
      Conserved Domains (1) summary
      cd10350
      Location:339 → 442
      SH2_SH2D4A; Src homology 2 domain found in the SH2 domain containing protein 4A (SH2D4A)

    RNA

    1. NR_156444.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC068880, CA418381, DA952240

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      19313693..19396218
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422080.1 → XP_047278036.1  SH2 domain-containing protein 4A isoform X2

    2. XM_047422079.1 → XP_047278035.1  SH2 domain-containing protein 4A isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      19578579..19661102
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054360966.1 → XP_054216941.1  SH2 domain-containing protein 4A isoform X2

    2. XM_054360965.1 → XP_054216940.1  SH2 domain-containing protein 4A isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H788.1 GenPept UniProtKB/Swiss-Prot:Q9H788

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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