WDR44

protein-coding

WD repeat domain 44, the group of WD repeat domain containing|MicroRNA protein coding host genes

Gene summary

This gene encodes a protein that interacts with the small GTPase rab11. A similar protein in rat binds the GTP-containing active form of rab11. This protein may play a role in endosome recycling. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2010]

MANE transcript

NM_019045.5

Inheritance

ClinVar variants

P:1U:283B:6

Top phenotype

ciliopathy

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chrX:118,346,073-118,449,961

External References & Databases

Ensembl (ENSG00000131725)

Transcript & Mutation Effects

hg38 • Region Span ~103.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

ciliopathySTRONG

Inheritance Pattern: XL

Disease ID:MONDO:0005308

Submitter: PanelApp Australia

ciliopathyMODERATE

Inheritance Pattern: XL

Disease ID:MONDO:0005308

Submitter: G2P

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to WDR44 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 51

not providedTotal: 29

CiliopathyTotal: 1

WDR44-related neurodevelopmental disorderTotal: 1

WDR44-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_019045.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			36 clinvar	3 clinvar		39
missense		1 clinvar	179 clinvar	3 clinvar		183
nonsense			18 clinvar			18
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			49 clinvar			49
Total	0	1	283	6	0	290

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_019045.5	RefSeq	NP_061918.3	20	MANE Select
ENST00000254029.8	Ensembl	ENSP00000254029.3	20	MANE Select
NM_001184965.2	RefSeq	NP_001171894.1	20	Standard
NM_001184966.1	RefSeq	NP_001171895.1	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ectoderm Differentiation

Molecular Function

Rab GTPase binding

Cellular Component

Golgi apparatus
cytosol
endosome membrane
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000254029
Coding exons: 20
Length: 103889
Individuals with no LoFs: 125389
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125391
p: 0.00000798

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.95	174	323	0.538	0.0000232	6002
Missense (PolyPhen)		17	86.198	0.19722		1592
Synonymous	1.04	101	115	0.877	0.00000842	1725
Loss of Function	4.93	2	32.2	0.0621	0.00000244	605

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000012	0.0000088	rare
South Asian	0.000068	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Downstream effector for RAB11. May be involved in vesicle recycling (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.100

Intolerance Scores

LoFtool: 0.0984
RVIS EVS: -0.16
RVIS percentile EVS: 41.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.502

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium