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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
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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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