WFDC13

protein-coding

WAP four-disulfide core domain 13, the group of WAP four-disulfide core domain containing

Gene summary

This gene encodes a member of the WAP-type four-disulfide core (WFDC) domain family. The WFDC domain, or WAP signature motif, contains eight cysteines forming four disulfide bonds at the core of the protein, and functions as a protease inhibitor. Most WFDC gene members are localized to chromosome 20q12-q13 in two clusters: centromeric and telomeric. This gene belongs to the telomeric cluster. [provided by RefSeq, Jul 2008]

Previous symbols:

C20orf138

MANE transcript

NM_172005.2

Inheritance

—

ClinVar variants

U:11B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr20:45,702,038-45,708,817

External References & Databases

Ensembl (ENSG00000168634)

Transcript & Mutation Effects

hg38 • Region Span ~6.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to WFDC13 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 15

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_172005.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			11 clinvar	1 clinvar		12
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	11	1	1	13

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_172005.2	RefSeq	NP_742002.1	3	MANE Select
ENST00000305479.3	Ensembl	ENSP00000302938.2	3	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of endopeptidase activity

Molecular Function

serine-type endopeptidase inhibitor activity

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000305479
Coding exons: 3
Length: 6802
Individuals with no LoFs: 125712
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125725
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.268	44	49.3	0.893	0.00000241	596
Missense (PolyPhen)		9	10.852	0.82936		132
Synonymous	1.08	12	17.8	0.674	8.52e-7	177
Loss of Function	0.741	3	4.74	0.633	1.98e-7	65

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative acid-stable proteinase inhibitor. {ECO:0000250}.;

Recessive Scores

pRec: 0.0441

Intolerance Scores

LoFtool: 0.694
RVIS EVS: 0.24
RVIS percentile EVS: 68.72

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0911

Gene Damage Prediction

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