WBP2NL

protein-coding

WBP2 N-terminal like, the group of GRAM domain containing

Gene summary

WBP2NL is a sperm-specific WW domain-binding protein that promotes meiotic resumption and pronuclear development during oocyte fertilization (Wu et al., 2007 [PubMed 17289678]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_152613.3

Inheritance

—

ClinVar variants

U:40B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr22:41,998,725-42,058,456

External References & Databases

Ensembl (ENSG00000183066)

Transcript & Mutation Effects

hg38 • Region Span ~59.7 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 WBP2NL variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 46

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152613.3. 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						0
missense			40 clinvar	7 clinvar		47
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	40	7	0	47

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152613.3	RefSeq	NP_689826.2	6	MANE Select
ENST00000328823.13	Ensembl	ENSP00000332983.9	6	MANE Select
ENST00000329620.9	Ensembl	ENSP00000328800.5	6	Standard
ENST00000412113.5	Ensembl	ENSP00000389598.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

egg activation
female pronucleus assembly
male pronucleus assembly
meiotic cell cycle
regulation of cytosolic calcium ion concentration

Molecular Function

transcription coactivator activity
chromatin DNA binding
WW domain binding

Cellular Component

nucleus
perinuclear theca
sperm flagellum
sperm head

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000328823
Coding exons: 6
Length: 59732
Individuals with no LoFs: 125700
Homozygous LoFs: 1
Heterozygous LoFs: 46
Defined: 125747
p: 0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.301	168	179	0.937	0.00000974	1918
Missense (PolyPhen)		52	57.192	0.90923		620
Synonymous	-0.580	75	68.9	1.09	0.00000425	683
Loss of Function	0.0632	11	11.2	0.980	6.48e-7	115

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00024	0.00023	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in meotic resumption and pronuclear formation, mediated by a WW domain-signaling pathway during fertilization. {ECO:0000250}.;

Recessive Scores

pRec: 0.0877

Intolerance Scores

LoFtool: 0.686
RVIS EVS: 1.35
RVIS percentile EVS: 94.35

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0188

Gene Damage Prediction

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