WDR74

WD repeat domain 74, the group of WD repeat domain containing

Basic information

Region (hg38): 11:62832342-62841809

Links

ENSG00000133316 ∙ NCBI:54663 ∙ OMIM:617947 ∙ HGNC:25529 ∙ Uniprot:Q6RFH5 ∙ 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 WDR74 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR74 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			27	1	2	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	27	1	3

Variants in WDR74

This is a list of pathogenic ClinVar variants found in the WDR74 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62833013-G-A			Benign (Dec 31, 2019)
11-62833026-C-G		not specified	Uncertain significance (May 22, 2023)
11-62833629-C-G		not specified	Uncertain significance (Jan 03, 2024)
11-62833806-C-T		not specified	Uncertain significance (Jul 05, 2022)
11-62833809-G-A		not specified	Uncertain significance (Aug 14, 2023)
11-62833868-G-C		not specified	Uncertain significance (Apr 08, 2022)
11-62833896-G-A		not specified	Uncertain significance (May 09, 2023)
11-62833934-C-T		not specified	Uncertain significance (Aug 14, 2023)
11-62833935-G-A		not specified	Uncertain significance (Oct 04, 2022)
11-62834282-G-A		not specified	Uncertain significance (Sep 15, 2021)
11-62834436-G-C		not specified	Uncertain significance (Jan 17, 2024)
11-62834436-G-T		not specified	Uncertain significance (Sep 22, 2022)
11-62834479-T-C		not specified	Likely benign (Nov 10, 2022)
11-62834497-G-A		not specified	Uncertain significance (Mar 14, 2023)
11-62834523-C-T		not specified	Uncertain significance (Jan 29, 2024)
11-62835460-T-C		not specified	Uncertain significance (Mar 07, 2023)
11-62835487-C-A		not specified	Uncertain significance (May 27, 2022)
11-62835508-G-A		not specified	Uncertain significance (Mar 23, 2023)
11-62835529-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-62835718-C-T		not specified	Uncertain significance (Dec 03, 2021)
11-62835723-G-A		not specified	Uncertain significance (Mar 01, 2023)
11-62835802-G-A		not specified	Uncertain significance (Nov 17, 2022)
11-62835992-T-C		not specified	Uncertain significance (Jun 13, 2023)
11-62839122-C-G		not specified	Uncertain significance (Dec 28, 2022)
11-62839202-G-T		not specified	Uncertain significance (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR74	protein_coding	protein_coding	ENST00000525239	11	9468

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.43e-9	0.534	124522	0	120	124642	0.000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.923	185	224	0.826	0.0000119	2445
Missense in Polyphen		40	62.952	0.6354		656
Synonymous	1.19	72	86.0	0.837	0.00000399	789
Loss of Function	1.13	16	21.7	0.739	0.00000103	234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000946	0.000940
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.000167	0.000167
Finnish	0.00225	0.00218
European (Non-Finnish)	0.000373	0.000363
Middle Eastern	0.000167	0.000167
South Asian	0.000174	0.000163
Other	0.000358	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory protein of the MTREX-exosome complex involved in the synthesis of the 60S ribosomal subunit (PubMed:26456651). Participates in an early cleavage of the pre-rRNA processing pathway in cooperation with NVL (PubMed:29107693). Required for blastocyst formation, is necessary for RNA transcription, processing and/or stability during preimplantation development (By similarity). {ECO:0000250|UniProtKB:Q8VCG3, ECO:0000269|PubMed:26456651, ECO:0000269|PubMed:29107693}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.648
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• pHI: 0.259
• hipred: Y
• hipred_score: 0.510
• ghis: 0.575

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr74

Gene ontology

• Biological process: blastocyst formation;rRNA processing;RNA metabolic process;ribosomal large subunit biogenesis
• Cellular component: nuclear exosome (RNase complex);nucleus;nucleolus;preribosome, large subunit precursor
• Molecular function: protein binding