WDFY1

WD repeat and FYVE domain containing 1, the group of Zinc fingers FYVE-type|WD repeat domain containing

Basic information

Region (hg38): 2:223855716-223945357

Links

ENSG00000085449 ∙ NCBI:57590 ∙ OMIM:618080 ∙ HGNC:20451 ∙ Uniprot:Q8IWB7 ∙ 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 WDFY1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDFY1 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			22			22
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	0	0

Variants in WDFY1

This is a list of pathogenic ClinVar variants found in the WDFY1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-223878693-G-A		not specified	Uncertain significance (Oct 26, 2022)
2-223880161-C-T		not specified	Uncertain significance (Dec 01, 2022)
2-223880195-T-C		not specified	Uncertain significance (May 26, 2024)
2-223882039-C-G		not specified	Uncertain significance (Oct 12, 2021)
2-223882039-C-T		not specified	Uncertain significance (Jul 12, 2022)
2-223894248-C-T		not specified	Uncertain significance (Mar 31, 2024)
2-223894272-C-T		not specified	Uncertain significance (Jun 29, 2023)
2-223894293-C-T		not specified	Uncertain significance (Feb 22, 2023)
2-223894325-G-A		not specified	Uncertain significance (Mar 04, 2024)
2-223895526-T-C		not specified	Uncertain significance (Jul 15, 2021)
2-223901220-C-T		not specified	Uncertain significance (May 06, 2022)
2-223901241-T-C		not specified	Uncertain significance (Nov 30, 2022)
2-223901250-A-G		not specified	Uncertain significance (May 30, 2024)
2-223901252-C-T		not specified	Uncertain significance (Nov 18, 2023)
2-223905957-C-A		not specified	Uncertain significance (Mar 07, 2024)
2-223905959-T-C		not specified	Uncertain significance (Feb 14, 2023)
2-223905995-G-A		not specified	Uncertain significance (Oct 30, 2023)
2-223912302-T-C		not specified	Uncertain significance (Nov 16, 2021)
2-223912308-G-A		not specified	Uncertain significance (Sep 20, 2023)
2-223917947-C-A		not specified	Uncertain significance (Sep 14, 2022)
2-223917985-C-T		not specified	Uncertain significance (Oct 06, 2023)
2-223918002-C-T		not specified	Uncertain significance (Aug 10, 2021)
2-223945191-G-C		not specified	Uncertain significance (Apr 25, 2022)
2-223945203-T-A		not specified	Uncertain significance (May 03, 2023)
2-223945265-G-C		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDFY1	protein_coding	protein_coding	ENST00000233055	12	89672

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000634	0.995	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.43	190	254	0.747	0.0000149	2729
Missense in Polyphen		56	89.523	0.62554		958
Synonymous	0.868	87	97.9	0.888	0.00000635	731
Loss of Function	2.49	11	24.2	0.454	0.00000103	275

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000294	0.000294
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000452	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.000175	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Positively regulates TLR3- and TLR4-mediated signaling pathways by bridging the interaction between TLR3 or TLR4 and TICAM1. Promotes TLR3/4 ligand-induced activation of transcription factors IRF3 and NF-kappa-B, as well as the production of IFN-beta and inflammatory cytokines (PubMed:25736436). {ECO:0000269|PubMed:25736436}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.689
• rvis_EVS: -0.85
• rvis_percentile_EVS: 11.06

Haploinsufficiency Scores

• pHI: 0.159
• hipred: N
• hipred_score: 0.450
• ghis: 0.646

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.375

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdfy1

Gene ontology

• Biological process: positive regulation of toll-like receptor 3 signaling pathway;positive regulation of toll-like receptor 4 signaling pathway
• Cellular component: nucleus;early endosome;cytosol
• Molecular function: protein binding;1-phosphatidylinositol binding;zinc ion binding