WDR17

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

Basic information

Region (hg38): 4:176065841-176182818

Links

ENSG00000150627 ∙ NCBI:116966 ∙ OMIM:609005 ∙ HGNC:16661 ∙ Uniprot:Q8IZU2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WDR17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR17 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			68	5		73
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	68	6	0

Variants in WDR17

This is a list of pathogenic ClinVar variants found in the WDR17 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-176096572-A-G		not specified	Uncertain significance (Sep 25, 2023)
4-176111618-G-A		not specified	Uncertain significance (Mar 19, 2024)
4-176111639-A-T		not specified	Uncertain significance (Jun 18, 2024)
4-176111695-A-G		not specified	Likely benign (Sep 17, 2021)
4-176115829-G-A		not specified	Uncertain significance (Jun 29, 2022)
4-176115901-A-G		not specified	Uncertain significance (Feb 21, 2024)
4-176115913-G-A		not specified	Uncertain significance (Apr 17, 2024)
4-176115964-C-T		not specified	Uncertain significance (Jul 21, 2021)
4-176119875-G-A		not specified	Uncertain significance (May 24, 2023)
4-176119893-T-C		not specified	Uncertain significance (Jan 10, 2022)
4-176119921-T-A		not specified	Uncertain significance (Jan 03, 2024)
4-176119945-T-A		not specified	Uncertain significance (Jun 07, 2023)
4-176120035-C-T		not specified	Uncertain significance (Mar 28, 2023)
4-176120055-G-A		not specified	Uncertain significance (Sep 22, 2023)
4-176125121-C-T		not specified	Uncertain significance (Jun 06, 2023)
4-176125122-A-G		not specified	Uncertain significance (Aug 02, 2021)
4-176125238-C-T		not specified	Uncertain significance (Jan 04, 2024)
4-176125281-A-C		not specified	Uncertain significance (Feb 22, 2023)
4-176125295-G-T		not specified	Uncertain significance (Jul 06, 2021)
4-176125296-C-A		not specified	Uncertain significance (Aug 30, 2022)
4-176125301-T-C		not specified	Uncertain significance (Dec 27, 2022)
4-176125304-G-A		not specified	Uncertain significance (Jul 06, 2021)
4-176125308-A-G		not specified	Uncertain significance (Dec 06, 2023)
4-176128758-C-T		not specified	Uncertain significance (Sep 16, 2021)
4-176131619-A-G		not specified	Uncertain significance (Nov 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR17	protein_coding	protein_coding	ENST00000280190	30	116994

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.65e-25	0.908	125332	0	416	125748	0.00166

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.486	648	684	0.948	0.0000333	8613
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00411	0.00410
Ashkenazi Jewish	0.00641	0.00617
East Asian	0.000716	0.000707
Finnish	0.000743	0.000739
European (Non-Finnish)	0.00150	0.00145
Middle Eastern	0.000716	0.000707
South Asian	0.00122	0.00114
Other	0.00102	0.000978

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.994
• rvis_EVS: 1.53
• rvis_percentile_EVS: 95.49

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.492
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.510

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr17