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    DENND1C DENN domain containing 1C [ Homo sapiens (human) ]

    Gene ID: 79958, updated on 5-Mar-2024

    Summary

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    Official Symbol
    DENND1Cprovided by HGNC
    Official Full Name
    DENN domain containing 1Cprovided by HGNC
    Primary source
    HGNC:HGNC:26225
    See related
    Ensembl:ENSG00000205744 MIM:613634; AllianceGenome:HGNC:26225
    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
    FAM31C
    Summary
    The protein encoded by this gene functions as a guanine nucleotide exchange factor for the early endosomal small GTPase RAB35, which regulates endosomal membrane trafficking and is involved in actin polymerization. The encoded protein activates RAB35 by promoting the exchange of RAB35-bound GDP for GTP. This gene may play a role in linking RAB35 activation with the clathrin machinery. [provided by RefSeq, May 2017]
    Expression
    Broad expression in lymph node (RPKM 22.3), spleen (RPKM 19.6) and 19 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    19p13.3
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (6467207..6481787, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (6456694..6471589, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (6467218..6481798, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene microRNA 3940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13824 Neighboring gene KH-type splicing regulatory protein Neighboring gene solute carrier family 25 member 41 Neighboring gene solute carrier family 25 member 23 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9951 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:6464149-6464690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6475606-6476345 Neighboring gene crumbs cell polarity complex component 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6479893-6480392 Neighboring gene Sharpr-MPRA regulatory region 5032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13825 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9954 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9955 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9956 Neighboring gene tubulin beta 4A class IVa Neighboring gene CRISPRi-validated cis-regulatory element chr19.1358 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:6506805-6507716 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:6516143-6516683 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13828 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13831 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6532416-6532916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6532917-6533417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13833 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13834 Neighboring gene TNF superfamily member 9

    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. Connecdenn 3/DENND1C binds actin linking Rab35 activation to the actin cytoskeleton. Marat AL, et al. Mol Biol Cell, 2012 Jan. PMID 22072793, Free PMC Article
    2. The connecdenn family, Rab35 guanine nucleotide exchange factors interfacing with the clathrin machinery. Marat AL, et al. J Biol Chem, 2010 Apr 2. PMID 20154091, 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. USP9X controls translation efficiency via deubiquitination of eukaryotic translation initiation factor 4A1. Li Z, et al. Nucleic Acids Res, 2018 Jan 25. PMID 29228324, Free PMC Article
    5. Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan. Low SK, et al. Cancer Sci, 2013 Aug. PMID 23648065, Free PMC Article

    See all (15) 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
    Genome-wide association study of chemotherapeutic agent-induced severe neutropenia/leucopenia for patients in Biobank Japan.
    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

    • FLJ22757

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables guanyl-nucleotide exchange factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol phosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endocytic recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		  
    located_in clathrin-coated vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in intracellular membrane-bounded organelle 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 1C
    Names
    DENN/MADD domain containing 1C
    connecdenn 3
    family with sequence similarity 31, member C

    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.

    Genomic

    1. NG_054762.1 RefSeqGene

      Range
      5022..19602
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001290331.2 → NP_001277260.1  DENN domain-containing protein 1C isoform 2

      See identical proteins and their annotated locations for NP_001277260.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 2, which has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK303226, BC033437, BE674790
      Consensus CDS
      CCDS77225.1
      UniProtKB/Swiss-Prot
      Q8IV53
      Related
      ENSP00000437805.1, ENST00000543576.5
      Conserved Domains (3) summary
      smart00801
      Location:281 → 347
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:49 → 249
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      smart00800
      Location:1 → 43
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

    2. NM_024898.4 → NP_079174.2  DENN domain-containing protein 1C isoform 1

      See identical proteins and their annotated locations for NP_079174.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      BC033437, BE674790, DC378383
      Consensus CDS
      CCDS45938.1
      UniProtKB/Swiss-Prot
      B4E051, D3PFD4, Q8IV53, Q8NDB1, Q9H5Z2
      Related
      ENSP00000370889.1, ENST00000381480.7
      Conserved Domains (3) summary
      smart00801
      Location:325 → 391
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:93 → 293
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      smart00800
      Location:13 → 87
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      6467207..6481787 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011528318.3 → XP_011526620.1  DENN domain-containing protein 1C isoform X4

      See identical proteins and their annotated locations for XP_011526620.1

      UniProtKB/Swiss-Prot
      Q8IV53
      Conserved Domains (3) summary
      smart00801
      Location:281 → 347
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:49 → 249
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      smart00800
      Location:1 → 43
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

    2. XM_006722906.4 → XP_006722969.1  DENN domain-containing protein 1C isoform X4

      See identical proteins and their annotated locations for XP_006722969.1

      UniProtKB/Swiss-Prot
      Q8IV53
      Conserved Domains (3) summary
      smart00801
      Location:281 → 347
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:49 → 249
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      smart00800
      Location:1 → 43
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

    3. XM_047439458.1 → XP_047295414.1  DENN domain-containing protein 1C isoform X3

    4. XM_006722905.4 → XP_006722968.3  DENN domain-containing protein 1C isoform X2

      Conserved Domains (4) summary
      smart00799
      Location:230 → 430
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      smart00800
      Location:150 → 224
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      pfam03455
      Location:452 → 503
      dDENN; dDENN domain
      pfam11702
      Location:706 → 888
      DUF3295; Protein of unknown function (DUF3295)

    5. XM_024451727.2 → XP_024307495.1  DENN domain-containing protein 1C isoform X1

      Conserved Domains (4) summary
      smart00801
      Location:462 → 528
      dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins
      smart00799
      Location:230 → 430
      DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN
      smart00800
      Location:150 → 224
      uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
      pfam11702
      Location:748 → 930
      DUF3295; Protein of unknown function (DUF3295)

    6. XM_047439459.1 → XP_047295415.1  DENN domain-containing protein 1C isoform X5

      Related
      ENST00000590818.5

    7. XM_047439460.1 → XP_047295416.1  DENN domain-containing protein 1C isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      6456694..6471589 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322208.1 → XP_054178183.1  DENN domain-containing protein 1C isoform X7

    2. XM_054322209.1 → XP_054178184.1  DENN domain-containing protein 1C isoform X8

    3. XM_054322211.1 → XP_054178186.1  DENN domain-containing protein 1C isoform X4

    4. XM_054322212.1 → XP_054178187.1  DENN domain-containing protein 1C isoform X4

    5. XM_054322210.1 → XP_054178185.1  DENN domain-containing protein 1C isoform X3

    6. XM_054322213.1 → XP_054178188.1  DENN domain-containing protein 1C isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IV53.1 GenPept UniProtKB/Swiss-Prot:Q8IV53

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