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    DENND2D DENN domain containing 2D [ Homo sapiens (human) ]

    Gene ID: 79961, updated on 10-Dec-2024

    Summary

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    Official Symbol
    DENND2Dprovided by HGNC
    Official Full Name
    DENN domain containing 2Dprovided by HGNC
    Primary source
    HGNC:HGNC:26192
    See related
    Ensembl:ENSG00000162777 MIM:615111; AllianceGenome:HGNC:26192
    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
    Summary
    Enables guanyl-nucleotide exchange factor activity. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in lymph node (RPKM 32.5), appendix (RPKM 17.0) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DENND2D in Genome Data Viewer
    Location:
    1p13.3-p13.2
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (111185969..111204578, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (111200774..111219466, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (111728591..111747200, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 54 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:111644109-111645308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1480 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1481 Neighboring gene DNA damage regulated autophagy modulator 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1180 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1482 Neighboring gene choline/ethanolamine phosphotransferase 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:111729927-111731126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1484 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1483 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1182 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:111756584-111757783 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1487 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1488 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1489 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1491 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:111777146-111778345 Neighboring gene chitinase 3 like 2 Neighboring gene chitinase, acidic pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Suppression of non-small cell lung cancer proliferation and tumorigenicity by DENND2D. Ling B, et al. Lung Cancer, 2013 Feb. PMID 23182661
    2. Downregulation of DENND2D by promoter hypermethylation is associated with early recurrence of hepatocellular carcinoma. Kanda M, et al. Int J Oncol, 2014 Jan. PMID 24189587
    3. Reduced expression of DENND2D through promoter hypermethylation is an adverse prognostic factor in squamous cell carcinoma of the esophagus. Hibino S, et al. Oncol Rep, 2014 Feb. PMID 24317529
    4. Prognostic impact of expression and methylation status of DENN/MADD domain-containing protein 2D in gastric cancer. Kanda M, et al. Gastric Cancer, 2015 Apr. PMID 24695972
    5. Exosomal microRNA miR-1246 induces cell motility and invasion through the regulation of DENND2D in oral squamous cell carcinoma. Sakha S, et al. Sci Rep, 2016 Dec 8. PMID 27929118, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. resulted in increased cell motility and invasive ability. Moreover, miR-1246 increased cell motility by directly targeting DENN/MADD Domain Containing 2D (DENND2D)
      Title: Exosomal microRNA miR-1246 induces cell motility and invasion through the regulation of DENND2D in oral squamous cell carcinoma.
    2. Higher frequency of promoter hypermethylation of DENND2D is associated with gastric cancer.
      Title: Prognostic impact of expression and methylation status of DENN/MADD domain-containing protein 2D in gastric cancer.
    3. DENND2D is a candidate tumor suppressor gene that was inactivated by promoter hypermethylation in patients with esophageal squamous cell carcinoma and may serve as a novel biomarker of esophageal squamous cell carcinoma.
      Title: Reduced expression of DENND2D through promoter hypermethylation is an adverse prognostic factor in squamous cell carcinoma of the esophagus.
    4. DENND2D is a candidate tumor suppressor gene that is inactivated by promoter hypermethylation in patients with Hepatocellular carcinoma and may serve as a novel biomarker of early recurrence of Hepatocellular carcinoma .
      Title: Downregulation of DENND2D by promoter hypermethylation is associated with early recurrence of hepatocellular carcinoma.
    5. Our data show that DENND2D might function as a tumor suppressor-like gene, preventing survival and expansion of cells with genetic damage through apoptosis mechanism. Absence of DENND2D might play a permissive role, as an early event, in tumorigenesis.
      Title: Suppression of non-small cell lung cancer proliferation and tumorigenicity by DENND2D.
    6. Mutations in DENND2D in melanoma by inhibition of nonsense-mediated mRNA decay.
      Title: Identification of ARHGEF17, DENND2D, FGFR3, and RB1 mutations in melanoma by inhibition of nonsense-mediated mRNA decay.
    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 identifies loci influencing concentrations of liver enzymes in plasma.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ22457, FLJ32619

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity 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 cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    DENN domain-containing protein 2D
    Names
    DENN/MADD domain containing 2D
    RP5-1180E21.2

    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_001271833.2 → NP_001258762.1  DENN domain-containing protein 2D isoform b

      See identical proteins and their annotated locations for NP_001258762.1

      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) is shorter and has a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AK026110, AL355816, BP270686
      Consensus CDS
      CCDS60219.1
      UniProtKB/TrEMBL
      B4DWL2
      Related
      ENSP00000358767.5, ENST00000369752.5
      Conserved Domains (3) summary
      smart00801
      Location:369 → 434
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:47 → 139
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      pfam02141
      Location:146 → 330
      DENN; DENN (AEX-3) domain

    2. NM_024901.5 → NP_079177.2  DENN domain-containing protein 2D isoform a

      See identical proteins and their annotated locations for NP_079177.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AL355816, BC004557
      Consensus CDS
      CCDS831.1
      UniProtKB/Swiss-Prot
      Q5T5V6, Q9BSU0, Q9H6A0
      UniProtKB/TrEMBL
      B4DWL2
      Related
      ENSP00000350266.4, ENST00000357640.9
      Conserved Domains (3) summary
      smart00801
      Location:372 → 437
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:50 → 142
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      pfam02141
      Location:149 → 333
      DENN; DENN (AEX-3) 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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      111185969..111204578 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017002388.2 → XP_016857877.1  DENN domain-containing protein 2D isoform X6

      Conserved Domains (2) summary
      smart00801
      Location:192 → 257
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      pfam02141
      Location:4 → 153
      DENN; DENN (AEX-3) domain

    2. XM_017002386.2 → XP_016857875.1  DENN domain-containing protein 2D isoform X6

      Conserved Domains (2) summary
      smart00801
      Location:192 → 257
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      pfam02141
      Location:4 → 153
      DENN; DENN (AEX-3) domain

    3. XM_011542190.3 → XP_011540492.1  DENN domain-containing protein 2D isoform X2

      See identical proteins and their annotated locations for XP_011540492.1

      UniProtKB/TrEMBL
      B4DWL2
      Conserved Domains (3) summary
      smart00801
      Location:360 → 425
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:38 → 130
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      pfam02141
      Location:137 → 321
      DENN; DENN (AEX-3) domain

    4. XM_006710921.3 → XP_006710984.2  DENN domain-containing protein 2D isoform X1

      Conserved Domains (3) summary
      smart00801
      Location:386 → 451
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00800
      Location:64 → 156
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      pfam02141
      Location:163 → 347
      DENN; DENN (AEX-3) domain

    5. XM_017002387.2 → XP_016857876.1  DENN domain-containing protein 2D isoform X6

      Conserved Domains (2) summary
      smart00801
      Location:192 → 257
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      pfam02141
      Location:4 → 153
      DENN; DENN (AEX-3) domain

    6. XM_024449898.2 → XP_024305666.1  DENN domain-containing protein 2D isoform X6

      Conserved Domains (2) summary
      smart00801
      Location:192 → 257
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      pfam02141
      Location:4 → 153
      DENN; DENN (AEX-3) domain

    7. XM_011542189.2 → XP_011540491.1  DENN domain-containing protein 2D isoform X3

      See identical proteins and their annotated locations for XP_011540491.1

      Conserved Domains (2) summary
      smart00801
      Location:316 → 381
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      pfam02141
      Location:93 → 277
      DENN; DENN (AEX-3) domain

    8. XM_047430867.1 → XP_047286823.1  DENN domain-containing protein 2D isoform X4

    9. XM_047430868.1 → XP_047286824.1  DENN domain-containing protein 2D isoform X5

    RNA

    1. XR_946765.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      111200774..111219466 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338841.1 → XP_054194816.1  DENN domain-containing protein 2D isoform X6

    2. XM_054338843.1 → XP_054194818.1  DENN domain-containing protein 2D isoform X6

    3. XM_054338840.1 → XP_054194815.1  DENN domain-containing protein 2D isoform X2

      UniProtKB/TrEMBL
      B4DWL2

    4. XM_054338836.1 → XP_054194811.1  DENN domain-containing protein 2D isoform X1

    5. XM_054338842.1 → XP_054194817.1  DENN domain-containing protein 2D isoform X6

    6. XM_054338844.1 → XP_054194819.1  DENN domain-containing protein 2D isoform X6

    7. XM_054338837.1 → XP_054194812.1  DENN domain-containing protein 2D isoform X3

    8. XM_054338838.1 → XP_054194813.1  DENN domain-containing protein 2D isoform X4

    9. XM_054338839.1 → XP_054194814.1  DENN domain-containing protein 2D isoform X5

    10. XM_054338845.1 → XP_054194820.1  DENN domain-containing protein 2D isoform X7

      UniProtKB/TrEMBL
      Q8TCN6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H6A0.2 GenPept UniProtKB/Swiss-Prot:Q9H6A0

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