WIPI2 WD repeat domain, phosphoinositide interacting 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: WIPI2provided by HGNC
Official Full Name: WD repeat domain, phosphoinositide interacting 2provided by HGNC
Primary source: HGNC:HGNC:32225
See related: Ensembl:ENSG00000157954 MIM:609225; AllianceGenome:HGNC:32225
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: Atg21; ATG18B; CGI-50; IDDSSA; WIPI-2
Summary: WD40 repeat proteins are key components of many essential biologic functions. They regulate the assembly of multiprotein complexes by presenting a beta-propeller platform for simultaneous and reversible protein-protein interactions. Members of the WIPI subfamily of WD40 repeat proteins, such as WIPI2, have a 7-bladed propeller structure and contain a conserved motif for interaction with phospholipids (Proikas-Cezanne et al., 2004 [PubMed 15602573]).[supplied by OMIM, Mar 2008]
Expression: Ubiquitous expression in testis (RPKM 20.8), brain (RPKM 12.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7p22.1

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (5190233..5233855)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (5307988..5351615)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (5229864..5273486)

Chromosome 7 - NC_000007.14 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?

STING directly recruits WIPI2 for autophagosome formation during STING-induced autophagy.
Title: STING directly recruits WIPI2 for autophagosome formation during STING-induced autophagy.
Structural basis for membrane recruitment of ATG16L1 by WIPI2 in autophagy.
Title: Structural basis for membrane recruitment of ATG16L1 by WIPI2 in autophagy.
A PI3K-WIPI2 positive feedback loop allosterically activates LC3 lipidation in autophagy.
Title: A PI3K-WIPI2 positive feedback loop allosterically activates LC3 lipidation in autophagy.
WIPI2 depletion inhibits the growth of hepatocellular carcinoma cells through the AMPK signaling pathway.
Title: WIPI2 depletion inhibits the growth of hepatocellular carcinoma cells through the AMPK signaling pathway.
A mutation in a highly conserved region of WIPI2 is an essential requirement for autophagy to proceed and is found in a large pedigree with global developmental abnormalities.
Title: A mutation in the major autophagy gene, WIPI2, associated with global developmental abnormalities.
Regulation of the intracellular WIPI2 protein level by mTORC1 and HUWE1 is a key determinant of autophagy flux.
Title: mTORC1-Regulated and HUWE1-Mediated WIPI2 Degradation Controls Autophagy Flux.
Results suggest that Optn potentiates LC3-II production and maturation of the phagophore into the autophagosome, by facilitating the recruitment of the Atg12-5-16L1 complex to Wipi2-positive phagophores.
Title: Optineurin promotes autophagosome formation by recruiting the autophagy-related Atg12-5-16L1 complex to phagophores containing the Wipi2 protein.
Data suggest that, in patients with diabetic kidney disease, urinary excretion of mRNAs for MAP1LC3A, WIPI2, and RB1CC1 is down-regulated as compared to healthy control subjects; these transcripts may serve as urinary autophagy biomarkers. (MAP1LC3A = microtubule associated protein 1 light chain 3; WIPI2 = WD repeat domain phosphoinositide-interacting protein 2; RB1CC1 = RB1 inducible coiled-coil 1)
Title: Evaluation of urinary autophagy transcripts expression in diabetic kidney disease.
Here the authors show that recruitment of WIPI2, itself essential for anti-bacterial autophagy, is dependent on the localization of catalytically active TBK1 to the vicinity of cytosolic bacteria.
Title: Recruitment of TBK1 to cytosol-invading Salmonella induces WIPI2-dependent antibacterial autophagy.
The specific autophagosomal localization of both WIPI1 and WIPI2 (refered to as WIPI puncta) has been employed to assess autophagy using fluorescence microscopy methods, such as confocal and live-cell video microscopy
Title: Fluorescence-based imaging of autophagy progression by human WIPI protein detection.

Submit: New GeneRIF Correction See all GeneRIFs (17)

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

Associated conditions

Description	Tests
Intellectual developmental disorder with short stature and variable skeletal anomalies MedGen: C5193105 OMIM: 618453 GeneReviews: Not available	not available

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

RH93080 (e-PCR)
- UniSTS:90899

RH45406 (e-PCR)
- UniSTS:67391

A003P36 (e-PCR)
- UniSTS:43630

RH12207 (e-PCR)
- UniSTS:13228

WI-20761 (e-PCR)
- UniSTS:14538

WI-17069 (e-PCR)
- UniSTS:32477

Clone Names

FLJ12979, FLJ14217, FLJ42984, DKFZp434J154, DKFZp686P02188

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables phosphatidylinositol-3,5-bisphosphate binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol-3,5-bisphosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol-3-phosphate binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol-3-phosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in autophagosome assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in autophagosome assembly	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in autophagosome maturation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in autophagy of mitochondrion	IBA Inferred from Biological aspect of Ancestor more info
involved_in autophagy of peroxisome	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to starvation	IDA Inferred from Direct Assay more info	PubMed
involved_in glycophagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in nucleophagy	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein lipidation	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein localization to phagophore assembly site	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein localization to phagophore assembly site	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in xenophagy	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
NOT colocalizes_with autophagosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
is_active_in extrinsic component of membrane	IBA Inferred from Biological aspect of Ancestor more info
colocalizes_with membrane	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in phagophore assembly site	IDA Inferred from Direct Assay more info	PubMed
is_active_in phagophore assembly site membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in phagophore assembly site membrane	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: WD repeat domain phosphoinositide-interacting protein 2

Names: WD40 repeat protein interacting with phosphoinositides 2; WIPI49-like protein 2

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_001033518.2 → NP_001028690.1 WD repeat domain phosphoinositide-interacting protein 2 isoform c

See identical proteins and their annotated locations for NP_001028690.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice junction in a 3' exon compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AC093376, AL080155

Consensus CDS

CCDS47531.1

UniProtKB/TrEMBL

B3KMZ0

Related

ENSP00000385297.3, ENST00000404704.7

Conserved Domains (3) summary

COG2319
Location:37 → 290

WD40; WD40 repeat [General function prediction only]

sd00039
Location:161 → 200

7WD40; WD40 repeat [structural motif]

cl02567
Location:184 → 363

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_001033519.2 → NP_001028691.1 WD repeat domain phosphoinositide-interacting protein 2 isoform d

See identical proteins and their annotated locations for NP_001028691.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks an alternate in-frame 5' exon and uses an alternate in-frame splice junction in a 3' exon compared to variant 1. The resulting isoform (d) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AC093376, AL080155

Consensus CDS

CCDS47532.1

UniProtKB/TrEMBL

B3KMZ0

Related

ENSP00000371821.2, ENST00000382384.6

Conserved Domains (2) summary

COG2319
Location:21 → 272

WD40; WD40 repeat [General function prediction only]

sd00039
Location:143 → 182

7WD40; WD40 repeat [structural motif]
NM_001033520.1 → NP_001028692.1 WD repeat domain phosphoinositide-interacting protein 2 isoform e

See identical proteins and their annotated locations for NP_001028692.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction in a 3' exon compared to variant 1. The resulting isoform (e) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform a.

Source sequence(s)

AC093376, AY691426, BC016912

Consensus CDS

CCDS47533.1

UniProtKB/TrEMBL

B3KMZ0

Related

ENSP00000429654.1, ENST00000484262.1

Conserved Domains (3) summary

COG2319
Location:9 → 231

WD40; WD40 repeat [General function prediction only]

sd00039
Location:102 → 141

7WD40; WD40 repeat [structural motif]

cl02567
Location:125 → 304

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_001278299.2 → NP_001265228.1 WD repeat domain phosphoinositide-interacting protein 2 isoform f

See identical proteins and their annotated locations for NP_001265228.1

Status: VALIDATED

Description

Transcript Variant: This variant (6) uses an alternate splice junction in a 5' exon compared to variant 1. This difference causes translation initiation at a downstream AUG and results in an isoform (f) with a shorter N-terminus, compared to isoform a.

Source sequence(s)

AC093376, AI074985, AK315468, AL080155

UniProtKB/Swiss-Prot

Q9Y4P8

Conserved Domains (3) summary

COG2319
Location:2 → 216

WD40; WD40 repeat [General function prediction only]

sd00039
Location:17 → 56

7WD40; WD40 repeat [structural motif]

cl02567
Location:40 → 219

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_015610.4 → NP_056425.1 WD repeat domain phosphoinositide-interacting protein 2 isoform a

See identical proteins and their annotated locations for NP_056425.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (a).

Source sequence(s)

AC093376, AL080155

Consensus CDS

CCDS5339.1

UniProtKB/Swiss-Prot

B3KNC2, Q5MNZ8, Q6FI96, Q75L50, Q96IE4, Q9Y364, Q9Y4P8

UniProtKB/TrEMBL

B3KMZ0

Related

ENSP00000288828.4, ENST00000288828.9

Conserved Domains (3) summary

COG2319
Location:37 → 290

WD40; WD40 repeat [General function prediction only]

sd00039
Location:161 → 200

7WD40; WD40 repeat [structural motif]

cl02567
Location:184 → 363

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_016003.4 → NP_057087.2 WD repeat domain phosphoinositide-interacting protein 2 isoform b

See identical proteins and their annotated locations for NP_057087.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame 5' exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AC093376, AK024279

Consensus CDS

CCDS34593.1

UniProtKB/TrEMBL

B3KMZ0

Related

ENSP00000384945.3, ENST00000401525.7

Conserved Domains (2) summary

COG2319
Location:21 → 272

WD40; WD40 repeat [General function prediction only]

sd00039
Location:143 → 182

7WD40; WD40 repeat [structural motif]

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_000007.14 Reference GRCh38.p14 Primary Assembly

Range

5190233..5233855

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006715685.2 → XP_006715748.1 WD repeat domain phosphoinositide-interacting protein 2 isoform X1

See identical proteins and their annotated locations for XP_006715748.1

Conserved Domains (3) summary

COG2319
Location:2 → 216

WD40; WD40 repeat [General function prediction only]

sd00039
Location:17 → 56

7WD40; WD40 repeat [structural motif]

cl02567
Location:40 → 219

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 ...