WDR17

protein-coding

WD repeat domain 17, the group of WD repeat domain containing

Gene summary

This gene encodes a WD repeat-containing protein. It is abundantly expressed in retina and testis, and is thought to be a candidate gene for retinal disease. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2009]

MANE transcript

NM_181265.4

Inheritance

—

ClinVar variants

U:173B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr4:176,065,841-176,182,818

External References & Databases

Ensembl (ENSG00000150627)

Transcript & Mutation Effects

hg38 • Region Span ~117.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to WDR17 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 182

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_181265.4. 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
missense			171 clinvar	8 clinvar		179
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	173	9	0	182

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_181265.4	RefSeq	NP_851782.3	28	MANE Select
ENST00000508596.6	Ensembl	ENSP00000422763.1	28	MANE Select
NM_001350727.2	RefSeq	NP_001337656.1	30	Standard
NM_001378103.1	RefSeq	NP_001365032.1	30	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000280190
Coding exons: 30
Length: 116994
Individuals with no LoFs: 125332
Homozygous LoFs: 0
Heterozygous LoFs: 416
Defined: 125748
p: 0.00166

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.486	648	684	0.948	0.0000333	8613
Missense (PolyPhen)		258	289.72	0.89053		3577
Synonymous	-0.0240	237	237	1.00	0.0000119	2495
Loss of Function	2.62	50	74.4	0.672	0.00000368	931

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00093	0.00092	rare
Latino/Admixed American	0.0032	0.0030	notable
Ashkenazi Jewish	0.0064	0.0062	notable
East Asian	0.00072	0.00071	rare
Finnish	0.00074	0.00074	rare
European (Non-Finnish)	0.0015	0.0015	notable
South Asian	0.0012	0.0011	notable
Other	0.0010	0.00098	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.994
RVIS EVS: 1.53
RVIS percentile EVS: 95.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.510

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High