WBP2NL

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

Basic information

Region (hg38): 22:41998724-42058456

Links

ENSG00000183066 ∙ NCBI:164684 ∙ OMIM:610981 ∙ HGNC:28389 ∙ Uniprot:Q6ICG8 ∙ 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 WBP2NL gene.

• Inborn genetic diseases (17 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WBP2NL 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			12	5		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	5	0

Variants in WBP2NL

This is a list of pathogenic ClinVar variants found in the WBP2NL region.

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

Position	Type	Phenotype	Significance	ClinVar
22-41998832-A-T		not specified	Uncertain significance (Oct 06, 2021)
22-42019322-G-A		not specified	Likely benign (May 16, 2022)
22-42019337-A-G		not specified	Uncertain significance (Dec 15, 2023)
22-42019339-C-T		not specified	Uncertain significance (May 05, 2023)
22-42019686-A-G		not specified	Likely benign (Aug 14, 2023)
22-42019705-C-A		not specified	Uncertain significance (Jan 19, 2024)
22-42019732-C-T		not specified	Uncertain significance (Jun 07, 2023)
22-42020072-T-G		not specified	Uncertain significance (Jan 08, 2024)
22-42022252-C-T		not specified	Uncertain significance (Apr 25, 2023)
22-42022331-G-A		not specified	Likely benign (Mar 21, 2023)
22-42026775-A-G		not specified	Uncertain significance (Nov 07, 2023)
22-42026852-G-A		not specified	Uncertain significance (Dec 18, 2023)
22-42026945-G-A		not specified	Uncertain significance (Sep 12, 2023)
22-42026951-C-T		not specified	Uncertain significance (Jun 29, 2023)
22-42027018-C-T		not specified	Uncertain significance (Oct 03, 2022)
22-42027042-C-T		not specified	Uncertain significance (Jan 04, 2024)
22-42027054-G-C		not specified	Likely benign (Dec 05, 2022)
22-42027057-C-T		not specified	Likely benign (Oct 04, 2022)
22-42027071-A-G		not specified	Uncertain significance (Jul 15, 2021)
22-42027111-C-T		not specified	Uncertain significance (Feb 23, 2023)
22-42027137-G-A		not specified	Uncertain significance (Dec 06, 2022)
22-42027140-G-C		not specified	Uncertain significance (Aug 02, 2021)
22-42027176-T-G		not specified	Uncertain significance (Sep 14, 2022)
22-42058349-C-T		Alpha-N-acetylgalactosaminidase deficiency type 1 • Alpha-N-acetylgalactosaminidase deficiency type 2	Likely benign (Jan 12, 2018)
22-42058350-G-A		Alpha-N-acetylgalactosaminidase deficiency type 2 • Alpha-N-acetylgalactosaminidase deficiency type 1	Benign (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WBP2NL	protein_coding	protein_coding	ENST00000328823	6	59732

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.18e-8	0.166	125700	1	46	125747	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.301	168	179	0.937	0.00000974	1918
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000447	0.000447
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000238	0.000229
Middle Eastern	0.000219	0.000217
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0684
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0188

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wbp2nl

Gene ontology

• Biological process: egg activation;female pronucleus assembly;male pronucleus assembly;meiotic cell cycle;regulation of cytosolic calcium ion concentration;positive regulation of nucleic acid-templated transcription
• Cellular component: nucleus;perinuclear theca;sperm flagellum;sperm head
• Molecular function: transcription coactivator activity;chromatin DNA binding;WW domain binding