WDR70

WD repeat domain 70, the group of WD repeat domain containing

Basic information

Region (hg38): 5:37379284-37753435

Links

ENSG00000082068 ∙ NCBI:55100 ∙ OMIM:617233 ∙ HGNC:25495 ∙ Uniprot:Q9NW82 ∙ 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 WDR70 gene.

• Inborn genetic diseases (23 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR70 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					2	2
missense			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	2

Variants in WDR70

This is a list of pathogenic ClinVar variants found in the WDR70 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-37379383-C-A		not specified	Uncertain significance (May 31, 2022)
5-37381613-C-T		not specified	Uncertain significance (Dec 01, 2022)
5-37392067-G-T		not specified	Uncertain significance (Oct 26, 2021)
5-37392100-T-G		not specified	Uncertain significance (Mar 06, 2023)
5-37396434-G-A		not specified	Uncertain significance (Oct 14, 2021)
5-37396540-G-T		not specified	Likely benign (Jul 12, 2023)
5-37443299-G-A		not specified	Uncertain significance (Aug 18, 2021)
5-37479867-A-C			Benign (May 15, 2018)
5-37479873-C-G		not specified	Uncertain significance (Aug 09, 2021)
5-37516565-G-A		not specified	Uncertain significance (Feb 02, 2022)
5-37605113-T-A		not specified	Uncertain significance (Aug 12, 2021)
5-37605146-A-G		not specified	Uncertain significance (Aug 30, 2022)
5-37605152-A-G		not specified	Uncertain significance (May 04, 2023)
5-37605156-C-T		not specified	Uncertain significance (May 15, 2023)
5-37605234-T-C		not specified	Uncertain significance (Jan 29, 2024)
5-37697712-G-A		not specified	Uncertain significance (Jun 29, 2023)
5-37697725-A-G		not specified	Uncertain significance (Aug 13, 2021)
5-37697748-C-T		not specified	Uncertain significance (Aug 17, 2022)
5-37697749-G-A		not specified	Uncertain significance (Oct 22, 2021)
5-37701062-C-T			Benign (May 15, 2018)
5-37701063-G-A		not specified	Uncertain significance (Apr 27, 2023)
5-37701121-G-T		not specified	Uncertain significance (Dec 21, 2022)
5-37703044-G-A		not specified	Uncertain significance (Nov 23, 2022)
5-37724970-G-A		not specified	Uncertain significance (Aug 10, 2021)
5-37726954-A-C		not specified	Uncertain significance (Nov 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR70	protein_coding	protein_coding	ENST00000265107	18	374224

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.58e-9	0.998	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.21	259	380	0.681	0.0000207	4322
Missense in Polyphen		52	114.77	0.45307		1272
Synonymous	-1.34	145	126	1.15	0.00000662	1199
Loss of Function	2.78	21	40.0	0.525	0.00000219	465

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000297	0.000297
Ashkenazi Jewish	0.000207	0.000198
East Asian	0.000163	0.000163
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.000163	0.000163
South Asian	0.000230	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.525
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.3

Haploinsufficiency Scores

• pHI: 0.223
• hipred: Y
• hipred_score: 0.639
• ghis: 0.631

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.937

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr70

Gene ontology

• Biological process: regulation of DNA double-strand break processing;regulation of histone H2B conserved C-terminal lysine ubiquitination
• Cellular component: nucleus;site of double-strand break
• Molecular function: enzyme binding