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DENND6A DENN domain containing 6A [ Homo sapiens (human) ]

Gene ID: 201627, updated on 5-Mar-2024

Summary

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Official Symbol
DENND6Aprovided by HGNC
Official Full Name
DENN domain containing 6Aprovided by HGNC
Primary source
HGNC:HGNC:26635
See related
Ensembl:ENSG00000174839 MIM:620561; AllianceGenome:HGNC:26635
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
AFI1A; FAM116A
Summary
Enables guanyl-nucleotide exchange factor activity. Involved in positive regulation of cell-cell adhesion mediated by cadherin. Located in recycling endosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in ovary (RPKM 8.9), thyroid (RPKM 8.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
3p14.3
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (57625454..57693077, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (57665829..57733445, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (57611181..57678804, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene phosphodiesterase 12 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:57582608-57583807 Neighboring gene ARF4 antisense RNA 1 Neighboring gene RNA, U6atac small nuclear 26, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14481 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:57678132-57678632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14483 Neighboring gene DENND6A divergent transcript Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:57737311-57738510 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr3:57741142-57742044 and GRCh37_chr3:57742045-57742946 Neighboring gene MPRA-validated peak4671 silencer Neighboring gene sarcolemma associated protein Neighboring gene PDHA1 pseudogene 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. DENN domain proteins: regulators of Rab GTPases. Marat AL, et al. J Biol Chem, 2011 Apr 22. PMID 21330364, Free PMC Article
  2. Rab14 and its exchange factor FAM116 link endocytic recycling and adherens junction stability in migrating cells. Linford A, et al. Dev Cell, 2012 May 15. PMID 22595670, Free PMC Article
  3. BioID reveals an ATG9A interaction with ATG13-ATG101 in the degradation of p62/SQSTM1-ubiquitin clusters. Kannangara AR, et al. EMBO Rep, 2021 Oct 5. PMID 34369648, Free PMC Article
  4. Integrative analysis of kinase networks in TRAIL-induced apoptosis provides a source of potential targets for combination therapy. So J, et al. Sci Signal, 2015 Apr 7. PMID 25852190
  5. E3 ubiquitin ligase RNF123 targets lamin B1 and lamin-binding proteins. Khanna R, et al. FEBS J, 2018 Jun. PMID 29676528

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. FAM116 and Rab14 therefore define an endocytic recycling pathway needed for ADAM protease trafficking and regulation of cell-cell junctions.
    Title: Rab14 and its exchange factor FAM116 link endocytic recycling and adherens junction stability in migrating cells.
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

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

  • FLJ34969

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables guanyl-nucleotide exchange factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables guanyl-nucleotide exchange factor activity TAS
Traceable Author Statement
more info
  
Process Evidence Code Pubs
involved_in positive regulation of cell-cell adhesion mediated by cadherin IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
is_active_in recycling endosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in recycling endosome IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
protein DENND6A
Names
DENN domain-containing protein 6A
DENN/MADD domain containing 6A
family with sequence similarity 116, member A
protein FAM116A

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_152678.3 → NP_689891.1  protein DENND6A

    See identical proteins and their annotated locations for NP_689891.1

    Status: VALIDATED

    Source sequence(s)
    AA605125, AC114480, AK074156, BC040291
    Consensus CDS
    CCDS33773.1
    UniProtKB/Swiss-Prot
    Q7Z5T4, Q8IWF6, Q8N235, Q8TEG8
    Related
    ENSP00000311401.5, ENST00000311128.10
    Conserved Domains (3) summary
    cl11519
    Location:171 → 359
    DENN; DENN (AEX-3) domain
    cl40631
    Location:270 → 373
    SPA; Stabilization of polarity axis
    cl40632
    Location:64 → 201
    Avl9; Transport protein Avl9

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    57625454..57693077 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006713019.4 → XP_006713082.1  protein DENND6A isoform X1

    Conserved Domains (2) summary
    pfam08616
    Location:269 → 372
    SPA; Stabilization of polarity axis
    cl11519
    Location:170 → 358
    DENN; DENN (AEX-3) domain

  2. XM_047447670.1 → XP_047303626.1  protein DENND6A isoform X2

RNA

  1. XR_007095649.1 RNA Sequence

  2. XR_245100.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    57665829..57733445 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345650.1 → XP_054201625.1  protein DENND6A isoform X1

  2. XM_054345651.1 → XP_054201626.1  protein DENND6A isoform X2

RNA

  1. XR_008486678.1 RNA Sequence

  2. XR_008486677.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IWF6.1 GenPept UniProtKB/Swiss-Prot:Q8IWF6

Gene LinkOut

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