DENND1A DENN domain containing 1A [Homo sapiens (human)] - Gene

Summary

Official Symbol: DENND1Aprovided by HGNC
Official Full Name: DENN domain containing 1Aprovided by HGNC
Primary source: HGNC:HGNC:29324
See related: Ensembl:ENSG00000119522 MIM:613633; AllianceGenome:HGNC:29324
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: FAM31A; KIAA1608
Summary: Clathrin (see MIM 118955)-mediated endocytosis is a major mechanism for internalization of proteins and lipids. Members of the connecdenn family, such as DENND1A, function as guanine nucleotide exchange factors (GEFs) for the early endosomal small GTPase RAB35 (MIM 604199) and bind to clathrin and clathrin adaptor protein-2 (AP2; see MIM 601024). Thus, connecdenns link RAB35 activation with the clathrin machinery (Marat and McPherson, 2010 [PubMed 20154091]).[supplied by OMIM, Nov 2010]
Expression: Ubiquitous expression in spleen (RPKM 4.6), kidney (RPKM 4.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q33.3

Exon count:: 32

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (123379658..123930126, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (135577391..136128012, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (126141937..126692405, complement)

Chromosome 9 - NC_000009.12 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
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?

Association of FSHR and DENND1A polymorphisms with polycystic ovary syndrome: a meta-analysis.
Title: Association of FSHR and DENND1A polymorphisms with polycystic ovary syndrome: a meta-analysis.
A Multi-center Genome-wide Association Study of Cervical Dystonia.
Title: A Multi-center Genome-wide Association Study of Cervical Dystonia.
The tagging SNPs rs2479106 and rs2468819 in the DENND1A gene are associated with polycystic ovary syndrome (PCOS) in the Chinese population, whereas rs2670139, rs2536951 and rs2479102 are not correlated with PCOS in the same population
Title: Association analysis between the tag single nucleotide polymorphisms of DENND1A and the risk of polycystic ovary syndrome in Chinese Han women.
Genetic variants of PCOS (rs13405728 in LHCGR gene; rs13429458 in THADA gene and rs2479106 in DENND1A gene) may not be involved in the development of preeclampsia in Han Chinese women.
Title: Association study between variants in LHCGR DENND1A and THADA with preeclampsia risk in Han Chinese populations.
decreased miR-130b-3p expression in PCOS theca cells, which was correlated with increased DENND1A.V2, cytochrome P450 17alpha-hydroxylase (CYP17A1) mRNA and androgen biosynthesis.
Title: miRNA Profiling Reveals miRNA-130b-3p Mediates DENND1A Variant 2 Expression and Androgen Biosynthesis.
we evaluated the frequencies of CYP19A1 rs2414096 and DENND1A rs10818854 polymorphisms in overweight and normal individuals and didn't find any significant difference between these groups which demonstrates a lack of association between obesity risk and these SNPs
Title: The role of DENND1A and CYP19A1 gene variants in individual susceptibility to obesity in Turkish population-a preliminary study.
The association of DENND1A rs10818854 and rs10986105 variants with PCOS in Tunisian but not Bahraini women confirms the dependence of this association on the ethnic/racial origin of study subjects.
Title: Differential association of DENND1A genetic variants with polycystic ovary syndrome in Tunisian but not Bahraini Arab women.
Genome-wide association studies have identified DENND1A as a candidate gene for polycystic ovary syndrome (PCOS). PCOS theca cells are shown to overexpress DENND1A splice variant 2 (V2), but not V1. Also, the genetic variation 330 bp upstream of exon 20A is not associated with VE variant expression.
Title: Alternative splicing of DENND1A, a PCOS candidate gene, generates variant 2.
DENND1A gene variant is likely to have influence on PCOS risk.
Title: The association of DENND1A gene polymorphisms and polycystic ovary syndrome risk: a systematic review and meta-analysis.
This meta-analysis suggested that rs2479106 and rs10818854 polymorphisms in the DENND1A gene were associated with increased risk of polycystic ovary syndrome
Title: Association of DENND1A Gene Polymorphisms with Polycystic Ovary Syndrome: A Meta-Analysis.

Submit: New GeneRIF Correction See all GeneRIFs (21)

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
A genome-wide association study of chemotherapy-induced alopecia in breast cancer patients. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study of Cloninger's temperament scales: implications for the evolutionary genetics of personality. EBI GWAS Catalog EBI GWAS CatalogPubMed
A genome-wide association study provides evidence for association of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in the French Population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association of body fat distribution in African ancestry populations suggests new loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies eight new risk loci for polycystic ovary syndrome. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies susceptibility loci for polycystic ovary syndrome on chromosome 2p16.3, 2p21 and 9q33.3. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of body mass index in 23 000 individuals with and without asthma. 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

SHGC-173239 (e-PCR)
- UniSTS:185346

SHGC-83135 (e-PCR)
- UniSTS:101126

RH94250 (e-PCR)
- UniSTS:86802

D9S2029 (e-PCR)
- UniSTS:11542

RH45219 (e-PCR)
- UniSTS:71191

SHGC-106899 (e-PCR)
- UniSTS:184867

SHGC-68745 (e-PCR)
- UniSTS:95529

RH76528 (e-PCR)
- UniSTS:86588

RH104311 (e-PCR)
- UniSTS:98636

RH45992 (e-PCR)
- UniSTS:43100

RH94094 (e-PCR)
- UniSTS:85127

AFMb277xd5 (e-PCR)
- UniSTS:71305

G59691 (e-PCR)
- UniSTS:136845

SHGC-33874 (e-PCR)
- UniSTS:75700

RH78231 (e-PCR)
- UniSTS:31169

RH36501 (e-PCR)
- UniSTS:45257

SHGC-52447 (e-PCR)
- UniSTS:10218

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 phosphatidylinositol phosphate binding	ISS Inferred from Sequence or Structural Similarity more info
enables phosphatidylinositol-3-phosphate binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in endocytic recycling	IBA Inferred from Biological aspect of Ancestor more info
involved_in endocytic recycling	ISS Inferred from Sequence or Structural Similarity more info
involved_in endocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of Rab protein signal transduction	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cell projection	IEA Inferred from Electronic Annotation more info
is_active_in clathrin-coated vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in clathrin-coated vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in clathrin-coated vesicle membrane	ISS Inferred from Sequence or Structural Similarity 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
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in presynaptic membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: DENN domain-containing protein 1A

Names: DENN/MADD domain containing 1A; connecdenn 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)

NM_001352964.2 → NP_001339893.1 DENN domain-containing protein 1A isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).

Source sequence(s)

AC006450, AL161790, AL390774, AL445489

Consensus CDS

CCDS94479.1

UniProtKB/TrEMBL

A0A0A0MS48

Related

ENSP00000377763.4, ENST00000394215.7

Conserved Domains (4) summary

smart00801
Location:305 → 371

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

smart00799
Location:95 → 273

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:9 → 91

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

cl26464
Location:705 → 1056

Atrophin-1; Atrophin-1 family
NM_001352965.2 → NP_001339894.1 DENN domain-containing protein 1A isoform 4

Status: VALIDATED

Source sequence(s)

AC006450, AL161790, AL390774, AL445489

UniProtKB/TrEMBL

Q9HCG4

Conserved Domains (4) summary

smart00801
Location:273 → 339

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

smart00799
Location:63 → 241

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:10 → 59

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

cl26464
Location:655 → 1006

Atrophin-1; Atrophin-1 family
NM_001352966.2 → NP_001339895.1 DENN domain-containing protein 1A isoform 5

Status: VALIDATED

Source sequence(s)

AC006450, AL161790, AL390774, AL445489

Conserved Domains (3) summary

smart00801
Location:275 → 341

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

smart00799
Location:65 → 243

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:14 → 61

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
NM_001352967.2 → NP_001339896.1 DENN domain-containing protein 1A isoform 6

Status: VALIDATED

Source sequence(s)

AC006450, AL161790, AL390774, AL445489

Conserved Domains (3) summary

smart00801
Location:273 → 339

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

smart00799
Location:63 → 241

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:26 → 59

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
NM_001352968.2 → NP_001339897.1 DENN domain-containing protein 1A isoform 7

Status: VALIDATED

Source sequence(s)

AC006450, AL161790, AL390774, AL445489

Consensus CDS

CCDS87687.1

Related

ENSP00000362720.1, ENST00000373618.1

Conserved Domains (3) summary

smart00801
Location:273 → 339

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

smart00799
Location:63 → 241

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

cl04085
Location:26 → 59

uDENN; uDENN domain
NM_001393654.1 → NP_001380583.1 DENN domain-containing protein 1A isoform 8

Status: VALIDATED

Source sequence(s)

AC006450, AL161790, AL390774, AL445489

UniProtKB/TrEMBL

Q9HCG4

Conserved Domains (4) summary

smart00801
Location:305 → 371

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

smart00799
Location:95 → 273

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:9 → 91

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

PHA03247
Location:687 → 1038

PHA03247; large tegument protein UL36; Provisional
NM_001400446.1 → NP_001387375.1 DENN domain-containing protein 1A isoform 9

Status: VALIDATED

Source sequence(s)

AC006450, AL161790, AL390774, AL445489
NM_001400449.1 → NP_001387378.1 DENN domain-containing protein 1A isoform 10

Status: VALIDATED

Source sequence(s)

AC006450, AL161790, AL390774, AL445489
NM_020946.2 → NP_065997.1 DENN domain-containing protein 1A isoform 1

See identical proteins and their annotated locations for NP_065997.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

AC006450, AL161790, AL390774, AL445489

Consensus CDS

CCDS35133.1

UniProtKB/Swiss-Prot

A8MZA3, B1AM80, B7Z3C8, B7Z669, D3PFD3, Q05C88, Q5VWF0, Q6PJZ5, Q8IVD6, Q8TEH3, Q9H796

UniProtKB/TrEMBL

Q9HCG4

Related

ENSP00000362727.2, ENST00000373624.6

Conserved Domains (3) summary

smart00801
Location:305 → 371

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

smart00799
Location:95 → 273

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:9 → 91

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
NM_024820.3 → NP_079096.2 DENN domain-containing protein 1A isoform 2

See identical proteins and their annotated locations for NP_079096.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 3' UTR and coding region compared to variant 1, that causes a frameshift. The resulting isoform (2) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AL445489, BC009616, BC028061, BC039703

Consensus CDS

CCDS35134.1

UniProtKB/Swiss-Prot

Q8TEH3

Related

ENSP00000362722.3, ENST00000373620.7

Conserved Domains (3) summary

smart00801
Location:305 → 371

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

smart00799
Location:95 → 273

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:9 → 91

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

RNA

NR_148208.2 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC006450, AL161790, AL390774, AL445489

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

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

123379658..123930126 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047423624.1 → XP_047279580.1 DENN domain-containing protein 1A isoform X18
XM_047423622.1 → XP_047279578.1 DENN domain-containing protein 1A isoform X16
XM_024447622.2 → XP_024303390.1 DENN domain-containing protein 1A isoform X9

UniProtKB/TrEMBL

Q9HCG4

Conserved Domains (4) summary

smart00801
Location:275 → 341

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

smart00799
Location:65 → 243

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:14 → 61

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

cl26464
Location:675 → 1026

Atrophin-1; Atrophin-1 family
XM_047423625.1 → XP_047279581.1 DENN domain-containing protein 1A isoform X19
XM_047423623.1 → XP_047279579.1 DENN domain-containing protein 1A isoform X17
XM_024447621.2 → XP_024303389.1 DENN domain-containing protein 1A isoform X10

UniProtKB/TrEMBL

Q9HCG4

Conserved Domains (4) summary

smart00801
Location:273 → 339

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

smart00799
Location:63 → 241

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:26 → 59

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins

cl26464
Location:673 → 1024

Atrophin-1; Atrophin-1 family
XM_047423621.1 → XP_047279577.1 DENN domain-containing protein 1A isoform X15
XM_047423618.1 → XP_047279574.1 DENN domain-containing protein 1A isoform X11
XM_011518882.4 → XP_011517184.1 DENN domain-containing protein 1A isoform X2

Conserved Domains (3) summary

smart00801
Location:320 → 386

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

smart00799
Location:110 → 288

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:24 → 106

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
XM_006717195.5 → XP_006717258.1 DENN domain-containing protein 1A isoform X5

Conserved Domains (3) summary

smart00801
Location:320 → 386

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

smart00799
Location:110 → 288

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:24 → 106

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
XM_011518886.4 → XP_011517188.1 DENN domain-containing protein 1A isoform X8

Conserved Domains (3) summary

smart00801
Location:320 → 386

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

smart00799
Location:110 → 288

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:24 → 106

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
XM_005252111.5 → XP_005252168.1 DENN domain-containing protein 1A isoform X13

Conserved Domains (3) summary

smart00801
Location:320 → 386

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

smart00799
Location:110 → 288

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:24 → 106

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
XM_011518885.4 → XP_011517187.1 DENN domain-containing protein 1A isoform X6

UniProtKB/TrEMBL

Q9HCG4

Related

ENST00000473039.5

Conserved Domains (3) summary

smart00801
Location:284 → 350

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

smart00799
Location:74 → 252

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:9 → 70

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
XM_047423615.1 → XP_047279571.1 DENN domain-containing protein 1A isoform X4
XM_047423613.1 → XP_047279569.1 DENN domain-containing protein 1A isoform X1
XM_047423620.1 → XP_047279576.1 DENN domain-containing protein 1A isoform X14
XM_047423614.1 → XP_047279570.1 DENN domain-containing protein 1A isoform X3
XM_047423616.1 → XP_047279572.1 DENN domain-containing protein 1A isoform X7
XM_047423619.1 → XP_047279575.1 DENN domain-containing protein 1A isoform X12
XM_024447623.2 → XP_024303391.1 DENN domain-containing protein 1A isoform X20

UniProtKB/TrEMBL

Q9HCG4

Conserved Domains (3) summary

smart00801
Location:109 → 175

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

smart00799
Location:4 → 77

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

cl26464
Location:509 → 860

Atrophin-1; Atrophin-1 family
XM_047423630.1 → XP_047279586.1 DENN domain-containing protein 1A isoform X26
XM_047423631.1 → XP_047279587.1 DENN domain-containing protein 1A isoform X27
XM_047423627.1 → XP_047279583.1 DENN domain-containing protein 1A isoform X22
XM_005252113.6 → XP_005252170.1 DENN domain-containing protein 1A isoform X24

Conserved Domains (3) summary

smart00801
Location:320 → 386

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

smart00799
Location:110 → 288

DENN; Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN

smart00800
Location:24 → 106

uDENN; Domain always found upstream of DENN domain, found in a variety of signalling proteins
XM_047423626.1 → XP_047279582.1 DENN domain-containing protein 1A isoform X21
XM_047423629.1 → XP_047279585.1 DENN domain-containing protein 1A isoform X25
XM_047423628.1 → XP_047279584.1 DENN domain-containing protein 1A isoform X23
XM_047423633.1 → XP_047279589.1 DENN domain-containing protein 1A isoform X29
XM_047423632.1 → XP_047279588.1 DENN domain-containing protein 1A isoform X28