WFDC1

WAP four-disulfide core domain 1, the group of WAP four-disulfide core domain containing

Basic information

Region (hg38): 16:84294846-84329844

Links

ENSG00000103175 ∙ NCBI:58189 ∙ OMIM:605322 ∙ HGNC:15466 ∙ Uniprot:Q9HC57 ∙ 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 WFDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WFDC1 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				2		2
missense			19	2	3	24
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	5	3

Variants in WFDC1

This is a list of pathogenic ClinVar variants found in the WFDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-84294975-C-G		not specified	Uncertain significance (Oct 07, 2024)
16-84294984-G-A			Likely benign (Dec 14, 2018)
16-84294987-G-A		not specified	Uncertain significance (Oct 17, 2024)
16-84295003-G-A		not specified	Uncertain significance (Jun 12, 2023)
16-84295007-G-C		not specified	Uncertain significance (Mar 25, 2024)
16-84295024-C-T		not specified	Uncertain significance (Jun 29, 2023)
16-84295047-C-T		not specified	Uncertain significance (Aug 20, 2024)
16-84295052-C-T			Likely benign (Mar 29, 2018)
16-84295053-G-A		not specified	Uncertain significance (Jun 13, 2024)
16-84295056-G-A		not specified	Likely benign (Apr 03, 2023)
16-84295081-G-A		not specified	Uncertain significance (May 24, 2023)
16-84295090-C-T		not specified	Uncertain significance (Nov 03, 2022)
16-84295107-A-G		not specified	Uncertain significance (Aug 28, 2023)
16-84312984-C-A			Likely benign (Mar 01, 2018)
16-84312992-G-A		not specified	Uncertain significance (Oct 13, 2023)
16-84313001-G-A		not specified	Uncertain significance (Aug 28, 2024)
16-84313043-G-A		not specified	Uncertain significance (Dec 06, 2024)
16-84313072-G-A		not specified	Uncertain significance (Dec 15, 2022)
16-84313079-A-C		not specified	Uncertain significance (Jan 24, 2024)
16-84313082-G-T		not specified	Uncertain significance (Sep 30, 2024)
16-84313084-C-G		not specified	Uncertain significance (Mar 23, 2023)
16-84313093-C-T		not specified	Uncertain significance (Mar 25, 2024)
16-84313110-C-G		not specified	Uncertain significance (Mar 18, 2024)
16-84313148-C-A		not specified	Uncertain significance (Sep 16, 2021)
16-84318293-C-T		not specified	Uncertain significance (Jul 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WFDC1	protein_coding	protein_coding	ENST00000219454	6	35199

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.47e-11	0.0250	125598	0	150	125748	0.000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.71	155	105	1.47	0.00000636	1373
Missense in Polyphen		42	27.438	1.5307		368
Synonymous	-0.922	56	47.9	1.17	0.00000313	463
Loss of Function	-0.472	15	13.2	1.14	8.12e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00462	0.00463
Ashkenazi Jewish	0.00	0.00
East Asian	0.00141	0.00141
Finnish	0.00	0.00
European (Non-Finnish)	0.000282	0.000281
Middle Eastern	0.00141	0.00141
South Asian	0.000229	0.000229
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has growth inhibitory activity. {ECO:0000250}.

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.815
• rvis_EVS: 1.75
• rvis_percentile_EVS: 96.67

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.300

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.155

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wfdc1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; immune system phenotype

Gene ontology

• Biological process: regulation of cell growth;negative regulation of endopeptidase activity;negative regulation of cell growth;response to estradiol;response to drug;negative regulation of epithelial cell proliferation;negative regulation of inflammatory response;negative regulation of wound healing
• Cellular component: extracellular space
• Molecular function: molecular_function;serine-type endopeptidase inhibitor activity