WFDC10A

WAP four-disulfide core domain 10A, the group of WAP four-disulfide core domain containing

Basic information

Region (hg38): 20:45629738-45631196

Previous symbols: [ "C20orf146" ]

Links

ENSG00000180305 ∙ NCBI:140832 ∙ ∙ HGNC:16139 ∙ Uniprot:Q9H1F0 ∙ 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 WFDC10A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WFDC10A 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			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in WFDC10A

This is a list of pathogenic ClinVar variants found in the WFDC10A region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45629826-A-G		Inborn genetic diseases	Likely benign (Aug 16, 2021)
20-45629868-G-T		not specified	Uncertain significance (Mar 24, 2023)
20-45629886-G-A		not specified	Uncertain significance (Mar 07, 2023)
20-45629891-G-C		not specified	Uncertain significance (Dec 28, 2022)
20-45629894-G-C		not specified	Uncertain significance (Jan 06, 2023)
20-45630895-A-C		not specified	Uncertain significance (Mar 31, 2024)
20-45630897-T-A		not specified	Uncertain significance (Jan 23, 2024)
20-45630933-A-T		not specified	Uncertain significance (Feb 23, 2023)
20-45630963-C-A		not specified	Uncertain significance (Mar 20, 2024)
20-45630971-A-G		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WFDC10A	protein_coding	protein_coding	ENST00000372643	2	1671

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0144	0.462	115274	0	1	115275	0.00000434

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0496	40	39.1	1.02	0.00000191	500
Missense in Polyphen		4	7.9213	0.50497		100
Synonymous	-0.909	20	15.5	1.29	6.69e-7	155
Loss of Function	-0.795	2	1.10	1.82	4.64e-8	14

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)	0.00000940	0.00000940
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.602
• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.0620
• hipred: N
• hipred_score: 0.123
• ghis: 0.384

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.445

Gene Damage Prediction

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

Gene ontology

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