DENND3 DENN domain containing 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: DENND3provided by HGNC
Official Full Name: DENN domain containing 3provided by HGNC
Primary source: HGNC:HGNC:29134
See related: Ensembl:ENSG00000105339 MIM:617503; AllianceGenome:HGNC:29134
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 endosome to lysosome transport; protein catabolic process; and regulation of Rab protein signal transduction. Predicted to be located in cytosol. Predicted to be active in cytoplasmic vesicle. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in bone marrow (RPKM 17.0), lung (RPKM 14.2) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 8q24.3

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (141128589..141195804)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (142248713..142315919)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (142138688..142205903)

Chromosome 8 - NC_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

DENND3 p.L708V activating variant is involved in the pathogenesis of hereditary hemochromatosis via the RAB12/TFR2 signaling pathway.
Title: DENND3 p.L708V activating variant is involved in the pathogenesis of hereditary hemochromatosis via the RAB12/TFR2 signaling pathway.
show that DENND3 binds actin through a surface of positively charged residues on the PHenn domain of Ran12
Title: A PH-like domain of the Rab12 guanine nucleotide exchange factor DENND3 binds actin and is required for autophagy.
DENND3 is the exchange factor for the small GTPase Rab12 regulated through an intramolecular interaction
Title: Regulation of DENND3, the exchange factor for the small GTPase Rab12 through an intramolecular interaction.
a novel signaling pathway identified whereby starvation-induced activation of ULK leads to phosphorylation of endogenous DENND3, with subsequent activation of Rab12 and initiation of membrane trafficking events required for autophagy
Title: Phosphorylation of the exchange factor DENND3 by ULK in response to starvation activates Rab12 and induces autophagy.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Single-nucleotide polymorphisms in HLA- and non-HLA genes associated with the development of antibodies to interferon-&#x003b2; therapy in multiple sclerosis patients. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH16253 (e-PCR)
- UniSTS:41234

D8S2279 (e-PCR)
- UniSTS:473907

RH35806 (e-PCR)
- UniSTS:43069

D15S1477 (e-PCR)
- UniSTS:474482

RH16164 (e-PCR)
- UniSTS:13701

G29698 (e-PCR)
- UniSTS:20625

G44334 (e-PCR)
- UniSTS:95121

RH48089 (e-PCR)
- UniSTS:19147

SGC33849 (e-PCR)
- UniSTS:979

G09322 (e-PCR)
- UniSTS:41434

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 endosome to lysosome transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of Rab protein signal transduction	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytoplasmic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	TAS Traceable Author Statement more info

General protein information

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Preferred Names: DENN domain-containing protein 3

Names: DENN/MADD domain containing 3

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)

NM_001352890.3 → NP_001339819.2 DENN domain-containing protein 3 isoform 1

Status: VALIDATED

Source sequence(s)

AC040970, BC110827, BX331731, CA413644

Consensus CDS

CCDS87629.1

UniProtKB/TrEMBL

E9PF32, H0YAY3

Related

ENSP00000428714.1, ENST00000519811.6

Conserved Domains (5) summary

smart00801
Location:435 → 497

dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins

sd00039
Location:1028 → 1063

7WD40; WD40 repeat [structural motif]

pfam02141
Location:185 → 371

DENN; DENN (AEX-3) domain

cl04085
Location:122 → 158

uDENN; uDENN domain

cl25539
Location:1004 → 1276

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001352891.3 → NP_001339820.2 DENN domain-containing protein 3 isoform 3

Status: VALIDATED

Source sequence(s)

AC040970, AL544320, BC110827, BX331731

Related

ENSP00000430695.1, ENST00000518347.5

Conserved Domains (1) summary

cl04085
Location:122 → 158

uDENN; uDENN domain
NM_001362798.2 → NP_001349727.1 DENN domain-containing protein 3 isoform 4

Status: VALIDATED

Source sequence(s)

AA760923, AC040970

UniProtKB/TrEMBL

H0YAY3

Conserved Domains (5) summary

smart00801
Location:435 → 497

dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins

sd00039
Location:1028 → 1063

7WD40; WD40 repeat [structural motif]

pfam02141
Location:185 → 371

DENN; DENN (AEX-3) domain

cl04085
Location:122 → 158

uDENN; uDENN domain

cl25539
Location:1019 → 1120

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_014957.5 → NP_055772.3 DENN domain-containing protein 3 isoform 2

Status: VALIDATED

Source sequence(s)

AC040970, BX331731, CB989310

Consensus CDS

CCDS34947.1

UniProtKB/Swiss-Prot

A2RUS2, B7ZM28, O94947, Q2TAM7, Q6ZMS6, Q96DK3

Related

ENSP00000262585.2, ENST00000262585.6

Conserved Domains (5) summary

smart00801
Location:368 → 430

dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins

sd00039
Location:961 → 996

7WD40; WD40 repeat [structural motif]

pfam02141
Location:118 → 304

DENN; DENN (AEX-3) domain

cl04085
Location:55 → 91

uDENN; uDENN domain

cl25539
Location:937 → 1209

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RNA

NR_148197.3 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC040970, BC110827, BX331731, CA413644

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000008.11 Reference GRCh38.p14 Primary Assembly

Range

141128589..141195804

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011516933.3 → XP_011515235.2 DENN domain-containing protein 3 isoform X1

UniProtKB/TrEMBL

H0YAY3

Conserved Domains (5) summary

smart00801
Location:435 → 497

dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins

sd00039
Location:1028 → 1063

7WD40; WD40 repeat [structural motif]

pfam02141
Location:185 → 371

DENN; DENN (AEX-3) domain

cl04085
Location:122 → 158

uDENN; uDENN domain

cl25539
Location:1019 → 1120

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_011516934.4 → XP_011515236.2 DENN domain-containing protein 3 isoform X6

UniProtKB/TrEMBL

H0YAY3

Conserved Domains (5) summary

smart00801
Location:435 → 497

dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins

sd00039
Location:1028 → 1063

7WD40; WD40 repeat [structural motif]

pfam02141
Location:185 → 371

DENN; DENN (AEX-3) domain

cl04085
Location:122 → 158

uDENN; uDENN domain

cl25539
Location:1019 → 1120

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_047421591.1 → XP_047277547.1 DENN domain-containing protein 3 isoform X3
XM_047421595.1 → XP_047277551.1 DENN domain-containing protein 3 isoform X10
XM_005250841.5 → XP_005250898.3 DENN domain-containing protein 3 isoform X4

UniProtKB/TrEMBL

H0YAY3

Related

ENSP00000428276.1, ENST00000518668.5

Conserved Domains (5) summary

smart00801
Location:393 → 445

dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins

sd00039
Location:976 → 1011

7WD40; WD40 repeat [structural motif]

pfam02141
Location:185 → 371

DENN; DENN (AEX-3) domain

cl04085
Location:122 → 158

uDENN; uDENN domain

cl25539
Location:952 → 1224

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_047421592.1 → XP_047277548.1 DENN domain-containing protein 3 isoform X7
XM_047421598.1 → XP_047277554.1 DENN domain-containing protein 3 isoform X13
XM_047421593.1 → XP_047277549.1 DENN domain-containing protein 3 isoform X8
XM_047421597.1 → XP_047277553.1 DENN domain-containing protein 3 isoform X12
XM_005250840.6 → XP_005250897.3 DENN domain-containing protein 3 isoform X2

UniProtKB/TrEMBL

H0YAY3

Conserved Domains (5) summary

smart00801
Location:393 → 445

dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins

sd00039
Location:976 → 1011

7WD40; WD40 repeat [structural motif]

pfam02141
Location:185 → 371

DENN; DENN (AEX-3) domain

cl04085
Location:122 → 158

uDENN; uDENN domain

cl25539
Location:967 → 1068

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_005250842.5 → XP_005250899.1 DENN domain-containing protein 3 isoform X5

UniProtKB/TrEMBL

H0YAY3

Conserved Domains (6) summary

smart00801
Location:357 → 419

dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins

COG2319
Location:919 → 1108

WD40; WD40 repeat [General function prediction only]

sd00039
Location:950 → 985

7WD40; WD40 repeat [structural motif]

cl02567
Location:941 → 1042

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

cl04085
Location:122 → 158

uDENN; uDENN domain

cl11519
Location:170 → 293

DENN; DENN (AEX-3) domain
XM_047421594.1 → XP_047277550.1 DENN domain-containing protein 3 isoform X9
XM_047421596.1 → XP_047277552.1 DENN domain-containing protein 3 isoform X11
XM_047421599.1 → XP_047277555.1 DENN domain-containing protein 3 isoform X14
XM_011516937.3 → XP_011515239.2 DENN domain-containing protein 3 isoform X16

Conserved Domains (3) summary

smart00801
Location:435 → 497

dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins

pfam02141
Location:185 → 371

DENN; DENN (AEX-3) domain

cl04085
Location:122 → 158

uDENN; uDENN domain
XM_017013242.2 → XP_016868731.1 DENN domain-containing protein 3 isoform X15

UniProtKB/Swiss-Prot

A2RUS2, B7ZM28, O94947, Q2TAM7, Q6ZMS6, Q96DK3

Conserved Domains (5) summary

smart00801
Location:187 → 249

dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins

COG2319
Location:749 → 938

WD40; WD40 repeat [General function prediction only]

sd00039
Location:780 → 815

7WD40; WD40 repeat [structural motif]

cl02567
Location:771 → 872

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

cl11519
Location:6 → 123

DENN; DENN (AEX-3) domain
XM_047421600.1 → XP_047277556.1 DENN domain-containing protein 3 isoform X18
XM_011516938.4 → XP_011515240.1 DENN domain-containing protein 3 isoform X17

Conserved Domains (4) summary

smart00801
Location:91 → 153

dDENN; Domain always found downstream of DENN domain, found in a variety of signalling proteins

COG2319
Location:653 → 842

WD40; WD40 repeat [General function prediction only]

sd00039
Location:684 → 719

7WD40; WD40 repeat [structural motif]

cl02567
Location:675 → 776

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_047421601.1 → XP_047277557.1 DENN domain-containing protein 3 isoform X20
XM_011516939.4 → XP_011515241.1 DENN domain-containing protein 3 isoform X19

See identical proteins and their annotated locations for XP_011515241.1

Conserved Domains (3) summary

COG2319
Location:496 → 685

WD40; WD40 repeat [General function prediction only]

sd00039
Location:527 → 562

7WD40; WD40 repeat [structural motif]

cl02567
Location:518 → 619

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_011516940.3 → XP_011515242.1 DENN domain-containing protein 3 isoform X19

See identical proteins and their annotated locations for XP_011515242.1

Conserved Domains (3) summary

COG2319
Location:496 → 685

WD40; WD40 repeat [General function prediction only]

sd00039
Location:527 → 562

7WD40; WD40 repeat [structural motif]

cl02567
Location:518 → 619

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...