WFDC3

WAP four-disulfide core domain 3, the group of WAP four-disulfide core domain containing

Basic information

Region (hg38): 20:45747944-45791932

Links

ENSG00000124116 ∙ NCBI:140686 ∙ ∙ HGNC:15957 ∙ Uniprot:Q8IUB2 ∙ 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 WFDC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WFDC3 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in WFDC3

This is a list of pathogenic ClinVar variants found in the WFDC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45775539-T-C		not specified	Uncertain significance (Sep 27, 2022)
20-45775558-C-T		not specified	Uncertain significance (Aug 02, 2021)
20-45777087-C-T		not specified	Uncertain significance (Nov 03, 2023)
20-45777101-C-A		not specified	Uncertain significance (Nov 01, 2022)
20-45777113-G-T		not specified	Uncertain significance (Aug 08, 2022)
20-45777135-G-C		not specified	Uncertain significance (Nov 17, 2022)
20-45777146-G-T		not specified	Uncertain significance (Sep 16, 2021)
20-45777173-G-A		not specified	Uncertain significance (Jul 05, 2023)
20-45777177-G-T		not specified	Uncertain significance (Dec 07, 2021)
20-45777186-C-T		not specified	Uncertain significance (Aug 28, 2023)
20-45777197-C-T		not specified	Uncertain significance (Feb 13, 2024)
20-45787852-G-C		not specified	Uncertain significance (May 23, 2023)
20-45787868-C-T		not specified	Uncertain significance (Jan 06, 2023)
20-45787901-A-G		not specified	Uncertain significance (Jun 10, 2024)
20-45787902-C-A		not specified	Uncertain significance (May 06, 2022)
20-45787911-A-G		not specified	Uncertain significance (Oct 05, 2022)
20-45787940-C-T		not specified	Uncertain significance (Dec 19, 2023)
20-45788955-G-A		not specified	Uncertain significance (Sep 14, 2022)
20-45788963-C-G		not specified	Uncertain significance (Sep 12, 2023)
20-45788981-T-C		not specified	Uncertain significance (Jun 22, 2021)
20-45789024-A-G		not specified	Uncertain significance (Oct 26, 2021)
20-45789041-G-A		not specified	Uncertain significance (Dec 20, 2021)
20-45789953-A-C		not specified	Uncertain significance (May 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WFDC3	protein_coding	protein_coding	ENST00000243938	6	43989

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.08e-8	0.175	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.405	119	132	0.901	0.00000710	1495
Missense in Polyphen		40	47.889	0.83527		535
Synonymous	-0.0866	50	49.2	1.02	0.00000270	439
Loss of Function	0.0977	11	11.4	0.969	5.60e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.000329	0.000326
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000329	0.000326
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0908

Intolerance Scores

• loftool: 0.476
• rvis_EVS: 0.95
• rvis_percentile_EVS: 90.01

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.337

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wfdc3

Gene ontology

• Biological process: negative regulation of endopeptidase activity
• Cellular component: extracellular region
• Molecular function: serine-type endopeptidase inhibitor activity