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DENND2C DENN domain containing 2C [ Homo sapiens (human) ]

Gene ID: 163259, updated on 5-Mar-2024

Summary

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Official Symbol
DENND2Cprovided by HGNC
Official Full Name
DENN domain containing 2Cprovided by HGNC
Primary source
HGNC:HGNC:24748
See related
Ensembl:ENSG00000175984 AllianceGenome:HGNC:24748
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
dJ1156J9.1
Summary
Enables guanyl-nucleotide exchange factor activity. Predicted to be involved in regulation of catalytic activity. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in esophagus (RPKM 11.0), skin (RPKM 6.6) and 10 other tissues See more
Orthologs
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Genomic context

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Location:
1p13.2
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (114582850..114670049, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (114594305..114681497, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (115125471..115212670, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene pyruvate kinase M1/2 pseudogene 1 Neighboring gene uncharacterized LOC105378914 Neighboring gene BCAS2 pre-mRNA processing factor Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:115142450-115143649 Neighboring gene MPRA-validated peak379 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1221 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1547 Neighboring gene uncharacterized LOC124904354 Neighboring gene adenosine monophosphate deaminase 1

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. Common genetic variants on 1p13.2 associate with risk of autism. Xia K, et al. Mol Psychiatry, 2014 Nov. PMID 24189344
  2. Protein interaction discovery using parallel analysis of translated ORFs (PLATO). Zhu J, et al. Nat Biotechnol, 2013 Apr. PMID 23503679, Free PMC Article
  3. Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. Yoshimura S, et al. J Cell Biol, 2010 Oct 18. PMID 20937701, Free PMC Article
  4. Proximity interactions of the ubiquitin ligase Mind bomb 1 reveal a role in regulation of epithelial polarity complex proteins. Dho SE, et al. Sci Rep, 2019 Aug 28. PMID 31462741, Free PMC Article
  5. Matrix-screening reveals a vast potential for direct protein-protein interactions among RNA binding proteins. Lang B, et al. Nucleic Acids Res, 2021 Jul 9. PMID 34133714, Free PMC Article

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

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
Common genetic variants on 1p13.2 associate with risk of autism.
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

Potential readthrough

Included gene: BCAS2

Potential readthrough

Included gene: AMPD1

Homology

Clone Names

  • FLJ37099, DKFZp686G0351, DKFZp686N1631, DKFZp779P1149

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
DENN domain-containing protein 2C
Names
DENN/MADD domain containing 2C
RP5-1156J9.1

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_001256404.2 → NP_001243333.1  DENN domain-containing protein 2C isoform 1

    See identical proteins and their annotated locations for NP_001243333.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer variant and it encodes the longer protein (isoform 1).
    Source sequence(s)
    AL096773, AL133382, AL390241, BX647950
    Consensus CDS
    CCDS58018.1
    UniProtKB/Swiss-Prot
    B1AL26, Q5TCX6, Q68D51, Q6P3R3
    Related
    ENSP00000376955.1, ENST00000393274.6
    Conserved Domains (3) summary
    smart00801
    Location:815 → 881
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:487 → 576
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:586 → 770
    DENN; DENN (AEX-3) domain

  2. NM_198459.4 → NP_940861.3  DENN domain-containing protein 2C isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks several exons in the 5' UTR and in the coding region, compared to variant 1. The resulting protein (isoform 2) is shorter when it is compared to isoform 1.
    Source sequence(s)
    AL133382, AL390241, BC063894, BX647950, DB071246
    Consensus CDS
    CCDS875.1
    UniProtKB/Swiss-Prot
    Q68D51
    Related
    ENSP00000376957.3, ENST00000393276.7
    Conserved Domains (3) summary
    smart00801
    Location:758 → 824
    dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
    smart00800
    Location:430 → 519
    uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
    pfam02141
    Location:529 → 713
    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
    114582850..114670049 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    114594305..114681497 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q68D51.2 GenPept UniProtKB/Swiss-Prot:Q68D51

Gene LinkOut

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

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