WDR45B WD repeat domain 45B [Homo sapiens (human)] - Gene

Summary

Official Symbol: WDR45Bprovided by HGNC
Official Full Name: WD repeat domain 45Bprovided by HGNC
Primary source: HGNC:HGNC:25072
See related: Ensembl:ENSG00000141580 MIM:609226; AllianceGenome:HGNC:25072
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: WIPI3; WDR45L; WIPI-3; NEDSBAS
Summary: This gene encodes a member of the WIPI or SVP1 family of WD40 repeat-containing proteins. The protein contains seven WD40 repeats that are thought to fold into a beta-propeller structure that mediates protein-protein interactions, and a conserved motif for interaction with phospholipids. The human genome contains several pseudogenes of this gene. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 30.3), esophagus (RPKM 20.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q25.3

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (82614562..82648444, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (83488501..83522749, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (80572438..80606320, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

A homozygous variant of WDR45B results in global developmental delay: Additional case and literature review.
Title: A homozygous variant of WDR45B results in global developmental delay: Additional case and literature review.
Multi-site-mediated entwining of the linear WIR-motif around WIPI beta-propellers for autophagy.
Title: Multi-site-mediated entwining of the linear WIR-motif around WIPI β-propellers for autophagy.
WDR45B has been identified as a potential intellectual disability gene through genomic sequencing of 2 large cohorts of affected individuals. In this report we present 6 individuals from 3 unrelated families with homozygous pathogenic variants in WDR45B: c.799C>T (p.Q267*) in 1 family and c.673C>T (p.R225*) in 2 families
Title: WDR45B-related intellectual disability, spastic quadriplegia, epilepsy, and cerebral hypoplasia: A consistent neurodevelopmental syndrome.
WIPI3 and WIPI4 beta-propellers have roles as scaffolds for LKB1-AMPK-TSC signalling circuits in the control of autophagy
Title: WIPI3 and WIPI4 β-propellers are scaffolds for LKB1-AMPK-TSC signalling circuits in the control of autophagy.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures MedGen: C4693816 OMIM: 617977 GeneReviews: El-Hattab-Alkuraya Syndrome	Compare labs

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

Bda09c07 (e-PCR)
- UniSTS:19476

SHGC-82391 (e-PCR)
- UniSTS:104537

RH79180 (e-PCR)
- UniSTS:46733

RH65862 (e-PCR)
- UniSTS:17295

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables TSC1-TSC2 complex binding	IDA Inferred from Direct Assay more info	PubMed
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	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 involved in autophagosome assembly	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

Component	Evidence Code	Pubs
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
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

General protein information

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Preferred Names: WD repeat domain phosphoinositide-interacting protein 3

Names: WD repeat protein 45-like; WD repeat-containing protein 45-like; WD repeat-containing protein 45B; WDR45-like protein; WIPI3 long; WIPI49-like protein

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

NG_046895.1 RefSeqGene

Range

5092..38974

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_019613.4 → NP_062559.2 WD repeat domain phosphoinositide-interacting protein 3

See identical proteins and their annotated locations for NP_062559.2

Status: REVIEWED

Source sequence(s)

AA861045, AC124283, AM182326, CN262716

Consensus CDS

CCDS11815.2

UniProtKB/Swiss-Prot

A0A024R8U4, A0A218N098, O95328, Q2MCP6, Q5MNZ6, Q6IBN2

Related

ENSP00000376139.4, ENST00000392325.9

Conserved Domains (2) summary

sd00039
Location:145 → 183

7WD40; WD40 repeat [structural motif]

cl29593
Location:25 → 258

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 ...

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_000017.11 Reference GRCh38.p14 Primary Assembly

Range

82614562..82648444 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005256377.6 → XP_005256434.1 WD repeat domain phosphoinositide-interacting protein 3 isoform X1

See identical proteins and their annotated locations for XP_005256434.1

Conserved Domains (2) summary

sd00039
Location:111 → 149

7WD40; WD40 repeat [structural motif]

cl29593
Location:46 → 223

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_047436412.1 → XP_047292368.1 WD repeat domain phosphoinositide-interacting protein 3 isoform X2
XM_047436413.1 → XP_047292369.1 WD repeat domain phosphoinositide-interacting protein 3 isoform X3
XM_047436414.1 → XP_047292370.1 WD repeat domain phosphoinositide-interacting protein 3 isoform X4

UniProtKB/TrEMBL

I3L4S6

Related

ENSP00000461488.1, ENST00000572583.5

Alternate T2T-CHM13v2.0

Genomic

NC_060941.1 Alternate T2T-CHM13v2.0

Range

83488501..83522749 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054316690.1 → XP_054172665.1 WD repeat domain phosphoinositide-interacting protein 3 isoform X1
XM_054316691.1 → XP_054172666.1 WD repeat domain phosphoinositide-interacting protein 3 isoform X3
XM_054316692.1 → XP_054172667.1 WD repeat domain phosphoinositide-interacting protein 3 isoform X4

UniProtKB/TrEMBL

I3L4S6