WDR76

WD repeat domain 76, the group of WD repeat domain containing

Basic information

Region (hg38): 15:43826980-43868412

Links

ENSG00000092470 ∙ NCBI:79968 ∙ OMIM:620302 ∙ HGNC:25773 ∙ Uniprot:Q9H967 ∙ 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 WDR76 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR76 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						0
missense			31	3		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	3	0

Variants in WDR76

This is a list of pathogenic ClinVar variants found in the WDR76 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-43827054-G-A		not specified	Uncertain significance (Dec 07, 2024)
15-43827995-G-T		not specified	Uncertain significance (Aug 12, 2024)
15-43828016-G-T		not specified	Uncertain significance (Aug 08, 2023)
15-43828058-G-T		not specified	Uncertain significance (Jul 13, 2021)
15-43828121-A-G		not specified	Uncertain significance (Mar 18, 2024)
15-43828150-G-C		not specified	Uncertain significance (May 02, 2024)
15-43828155-C-G		not specified	Uncertain significance (Oct 08, 2024)
15-43828165-G-T		not specified	Uncertain significance (Nov 21, 2023)
15-43828211-T-G		not specified	Uncertain significance (Jul 05, 2024)
15-43828250-G-A		not specified	Uncertain significance (Jul 17, 2024)
15-43828256-A-G		not specified	Uncertain significance (Oct 06, 2021)
15-43835106-A-G		not specified	Uncertain significance (Sep 26, 2024)
15-43835107-T-C		not specified	Uncertain significance (May 09, 2023)
15-43835123-C-G		not specified	Uncertain significance (May 24, 2024)
15-43836176-C-T		not specified	Uncertain significance (Jan 19, 2024)
15-43839644-G-T		not specified	Uncertain significance (Aug 28, 2024)
15-43839648-A-G		not specified	Uncertain significance (Feb 05, 2024)
15-43839681-T-A		not specified	Uncertain significance (Oct 06, 2021)
15-43839700-C-T		not specified	Uncertain significance (Sep 25, 2024)
15-43839713-A-T		not specified	Uncertain significance (Oct 17, 2024)
15-43842439-G-A		not specified	Uncertain significance (Dec 03, 2024)
15-43842446-C-T		not specified	Likely benign (Jul 02, 2024)
15-43842470-A-G		not specified	Likely benign (Sep 22, 2023)
15-43842482-A-G		not specified	Uncertain significance (Mar 24, 2023)
15-43842484-G-C		not specified	Uncertain significance (Feb 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR76	protein_coding	protein_coding	ENST00000263795	13	41457

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.77e-9	0.977	125668	0	79	125747	0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.462	320	344	0.930	0.0000177	4098
Missense in Polyphen		47	67.942	0.69177		710
Synonymous	-0.208	131	128	1.02	0.00000718	1201
Loss of Function	2.22	19	32.7	0.581	0.00000183	393

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000892	0.000892
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000327	0.000325
Middle Eastern	0.000327	0.000326
South Asian	0.000261	0.000261
Other	0.000658	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically binds 5-hydroxymethylcytosine (5hmC), suggesting that it acts as a specific reader of 5hmC. {ECO:0000250}.

Recessive Scores

• pRec: 0.0932

Intolerance Scores

• loftool: 0.244
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.31

Haploinsufficiency Scores

• pHI: 0.619
• hipred: N
• hipred_score: 0.313
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.932

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr76

Gene ontology

• Biological process: cellular response to DNA damage stimulus;regulation of DNA damage checkpoint
• Cellular component: heterochromatin;nucleus;site of DNA damage
• Molecular function: DNA binding;protein binding;enzyme binding