WFDC2

WAP four-disulfide core domain 2, the group of WAP four-disulfide core domain containing

Basic information

Region (hg38): 20:45469753-45481532

Links

ENSG00000101443 ∙ NCBI:10406 ∙ OMIM:617548 ∙ HGNC:15939 ∙ Uniprot:Q14508 ∙ 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 WFDC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WFDC2 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in WFDC2

This is a list of pathogenic ClinVar variants found in the WFDC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45469810-C-T		not specified	Uncertain significance (Feb 13, 2024)
20-45469825-T-A		not specified	Uncertain significance (Apr 28, 2023)
20-45470416-G-A		not specified	Uncertain significance (Nov 02, 2023)
20-45470466-A-C		not specified	Uncertain significance (Oct 29, 2021)
20-45470530-A-G		not specified	Uncertain significance (Dec 21, 2022)
20-45479989-G-A		not specified	Uncertain significance (Aug 16, 2021)
20-45480053-A-G		not specified	Uncertain significance (May 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WFDC2	protein_coding	protein_coding	ENST00000372676	3	11827

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.794	0.201	103484	0	1	103485	0.00000483

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0559	69	70.3	0.981	0.00000346	800
Missense in Polyphen		20	24.233	0.82533		295
Synonymous	0.286	27	29.0	0.932	0.00000136	240
Loss of Function	2.12	0	5.23	0.00	2.24e-7	60

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)	0.0000113	0.0000113
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Broad range protease inhibitor. {ECO:0000269|PubMed:23139753}.

Recessive Scores

• pRec: 0.176

Intolerance Scores

• loftool: 0.397
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.484
• hipred: N
• hipred_score: 0.203
• ghis: 0.570

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wfdc2

Gene ontology

• Biological process: proteolysis;spermatogenesis;negative regulation of endopeptidase activity
• Cellular component: extracellular space;extracellular exosome
• Molecular function: endopeptidase inhibitor activity;serine-type endopeptidase inhibitor activity;cysteine-type endopeptidase inhibitor activity;aspartic-type endopeptidase inhibitor activity