WDFY4

WDFY family member 4, the group of BEACH domain containing |WD repeat domain containing|Armadillo like helical domain containing

Basic information

Region (hg38): 10:48684872-48982956

Previous symbols: [ "C10orf64" ]

Links

ENSG00000128815 ∙ NCBI:57705 ∙ OMIM:613316 ∙ HGNC:29323 ∙ Uniprot:Q6ZS81 ∙ 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 WDFY4 gene.

• Inborn genetic diseases (177 variants)
• not provided (11 variants)
• WDFY4-related condition (6 variants)
• not specified (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDFY4 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	3	4
missense			154	12	5	171
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					3	3
non coding			16	1		17
Total	0	0	170	14	8

Variants in WDFY4

This is a list of pathogenic ClinVar variants found in the WDFY4 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-48709791-A-G		not specified	Likely benign (Jul 20, 2022)
10-48709925-C-T		not specified	Uncertain significance (Apr 13, 2023)
10-48709926-G-A		not specified	Likely benign (Oct 18, 2021)
10-48720030-G-T		not specified	Uncertain significance (Mar 12, 2024)
10-48720071-G-A		not specified	Uncertain significance (Aug 15, 2023)
10-48720105-C-T		not specified	Uncertain significance (Jul 26, 2022)
10-48721269-C-T		not specified	Uncertain significance (Sep 25, 2023)
10-48721308-G-A		not specified	Likely benign (Jul 25, 2023)
10-48721312-A-T		not specified	Uncertain significance (Aug 10, 2023)
10-48721318-A-G		not specified	Uncertain significance (Dec 21, 2023)
10-48721356-G-A		not specified	Uncertain significance (May 25, 2022)
10-48723437-C-T		not specified	Uncertain significance (Sep 28, 2022)
10-48723467-C-T		not specified	Uncertain significance (Jan 09, 2024)
10-48723473-T-A		not specified	Uncertain significance (Aug 02, 2023)
10-48723473-T-G		not specified	Uncertain significance (Jun 21, 2023)
10-48723482-A-G		not specified	Uncertain significance (May 09, 2022)
10-48723508-C-A		not specified	Uncertain significance (Mar 24, 2023)
10-48723557-T-C		not specified	Uncertain significance (May 16, 2023)
10-48723570-G-A			Benign (Dec 31, 2019)
10-48725920-G-C		not specified	Uncertain significance (Nov 07, 2022)
10-48725926-C-T		not specified	Uncertain significance (Aug 08, 2023)
10-48726016-G-C		not specified	Uncertain significance (Sep 16, 2021)
10-48726029-T-C		not specified	Uncertain significance (Jan 16, 2024)
10-48727472-A-G		not specified	Uncertain significance (Apr 26, 2023)
10-48727498-G-C		not specified	Uncertain significance (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDFY4	protein_coding	protein_coding	ENST00000325239	61	298081

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.340	0.660	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.12	1319	1.68e+3	0.785	0.0000931	20668
Missense in Polyphen		321	503.31	0.63778		6515
Synonymous	1.90	643	707	0.909	0.0000422	6405
Loss of Function	8.63	33	145	0.227	0.00000679	1766

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0993

Intolerance Scores

• rvis_EVS: 4.26
• rvis_percentile_EVS: 99.72

Haploinsufficiency Scores

• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.185

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdfy4

Gene ontology

• Cellular component: integral component of membrane