U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 79961, updated on 3-Apr-2024

Summary

Go to the top of the page Help
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. Predicted to be involved in regulation of catalytic activity. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in lymph node (RPKM 32.5), appendix (RPKM 17.0) and 20 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See DENND2D in Genome Data Viewer
Location:
1p13.3-p13.2
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (111185969..111204578, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (111200774..111219466, complement)
105.20220307 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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. 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
  2. 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
  3. 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
  4. Suppression of non-small cell lung cancer proliferation and tumorigenicity by DENND2D. Ling B, et al. Lung Cancer, 2013 Feb. PMID 23182661
  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

Go to the top of the page Help

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

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help
Preferred Names
DENN domain-containing protein 2D
Names
DENN/MADD domain containing 2D
RP5-1180E21.2

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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_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_2023_10

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

  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

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

Gene LinkOut

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

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous