WDR47

protein-coding

WD repeat domain 47, the group of WD repeat domain containing

Gene summary

Predicted to act upstream of or within several processes, including detection of hot stimulus involved in thermoception; neuronal stem cell population maintenance; and telencephalon development. Located in cytoplasm and microtubule. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001142551.2

Inheritance

AR, AD

ClinVar variants

P:2U:81B:2

Top phenotype

complex neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr1:108,970,214-109,042,113

External References & Databases

Ensembl (ENSG00000085433)

Transcript & Mutation Effects

hg38 • Region Span ~71.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complex neurodevelopmental disorderSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0100038

Submitter: PanelApp Australia

congenital heart diseaseLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0005453

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to WDR47 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 73

not providedTotal: 1

Neurodevelopmental disorderTotal: 1

Complex neurodevelopmental disorderTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001142551.2. 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			1 clinvar	1 clinvar		2
missense		2 clinvar	77 clinvar	1 clinvar		80
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	2	81	2	0	85

Highest pathogenic variant AF is 0.000002478241

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001142551.2	RefSeq	NP_001136023.1	14	MANE Select
ENST00000369962.8	Ensembl	ENSP00000358979.3	14	MANE Select
NM_001142550.2	RefSeq	NP_001136022.1	14	Standard
NM_014969.6	RefSeq	NP_055784.3	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

multicellular organism development

Molecular Function

protein binding

Cellular Component

cytoplasm
microtubule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000400794
Coding exons: 14
Length: 72015
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125747
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.75	317	488	0.649	0.0000246	6100
Missense (PolyPhen)		77	187.62	0.4104		2301
Synonymous	-0.125	173	171	1.01	0.00000893	1754
Loss of Function	4.69	10	43.3	0.231	0.00000215	546

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000040	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00012	0.00011	rare
Finnish	0.000052	0.000046	rare
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.266
RVIS EVS: -0.76
RVIS percentile EVS: 13.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.862

Gene Damage Prediction

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