WFDC9

WAP four-disulfide core domain 9, the group of WAP four-disulfide core domain containing

Basic information

Region (hg38): 20:45607939-45631284

Links

ENSG00000180205 ∙ NCBI:259240 ∙ ∙ HGNC:20380 ∙ Uniprot:Q8NEX5 ∙ 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 WFDC9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WFDC9 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			1	1		2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8	1		9
Total	0	0	9	2	0

Variants in WFDC9

This is a list of pathogenic ClinVar variants found in the WFDC9 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45608124-T-C		not specified	Uncertain significance (Aug 20, 2024)
20-45608697-A-T		not specified	Uncertain significance (Mar 18, 2024)
20-45608798-A-G		not specified	Uncertain significance (Aug 13, 2021)
20-45608802-T-A		not specified	Likely benign (Dec 14, 2021)
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)
20-45630977-T-C		not specified	Uncertain significance (Nov 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WFDC9	protein_coding	protein_coding	ENST00000326000	3	23330

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00977	0.616	125692	0	11	125703	0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.350	41	47.8	0.858	0.00000228	586
Missense in Polyphen		13	12.741	1.0203		162
Synonymous	-0.0911	15	14.6	1.03	6.91e-7	151
Loss of Function	0.336	3	3.70	0.811	1.56e-7	45

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000888	0.0000888
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000894	0.00000880
Middle Eastern	0.000109	0.000109
South Asian	0.000134	0.000131
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.672
• rvis_EVS: 0.72
• rvis_percentile_EVS: 85.92

Haploinsufficiency Scores

• pHI: 0.0262
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: 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

Mouse Genome Informatics

• Gene name: Wfdc9

Gene ontology

• Cellular component: extracellular region
• Molecular function: protein binding