WFDC10B

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

Basic information

Region (hg38): 20:45684651-45705019

Links

ENSG00000182931 ∙ NCBI:280664 ∙ ∙ HGNC:20479 ∙ Uniprot:Q8IUB3 ∙ 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 WFDC10B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WFDC10B 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			4		1	5
Total	0	0	7	0	1

Variants in WFDC10B

This is a list of pathogenic ClinVar variants found in the WFDC10B region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45684928-C-A		not specified	Uncertain significance (Oct 06, 2024)
20-45684949-A-G		not specified	Uncertain significance (Sep 22, 2023)
20-45702137-T-G		not specified	Uncertain significance (Aug 07, 2024)
20-45702202-C-T		not specified	Uncertain significance (Dec 21, 2023)
20-45702203-G-A		not specified	Likely benign (Aug 01, 2024)
20-45702205-G-A		not specified	Uncertain significance (Dec 20, 2023)
20-45704450-T-A		not specified	Uncertain significance (Jul 27, 2022)
20-45704466-C-T			Benign (Mar 29, 2018)
20-45704560-G-A		not specified	Uncertain significance (Jan 02, 2024)
20-45704921-C-T		not specified	Uncertain significance (Mar 24, 2023)
20-45704966-C-T		not specified	Uncertain significance (Oct 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WFDC10B	protein_coding	protein_coding	ENST00000335769	3	20367

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0362	0.647	124697	32	984	125713	0.00405

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.162	44	47.1	0.933	0.00000222	587
Missense in Polyphen		11	6.3148	1.7419		83
Synonymous	0.913	11	15.6	0.706	6.72e-7	154
Loss of Function	0.377	2	2.66	0.751	1.12e-7	33

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0608	0.0605
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000704	0.0000704
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00130	0.00130

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.606
• rvis_EVS: 0.39
• rvis_percentile_EVS: 75.87

Haploinsufficiency Scores

• pHI: 0.0447
• hipred: N
• hipred_score: 0.123
• ghis: 0.377

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

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 peptidase activity
• Cellular component: extracellular region
• Molecular function: peptidase inhibitor activity