GeneBe

WBP2

WW domain binding protein 2, the group of GRAM domain containing

Basic information

Region (hg38): 17:75845699-75856507

Links

ENSG00000132471 ∙ NCBI:23558 ∙ OMIM:606962 ∙ HGNC:12738 ∙ Uniprot:Q969T9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • hearing loss, autosomal recessive 107 (Moderate), mode of inheritance: AR
  • hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
  • hearing loss, autosomal recessive 107 (Limited), mode of inheritance: Unknown
  • hearing loss, autosomal recessive (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Deafness, autosomal recessive 107ARAudiologic/OtolaryngologicEarly recognition and treatment of hearing impairment may improve outcomes, including speech and language developmentAudiologic/Otolaryngologic26881968

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WBP2 gene.

  • not_provided (78 variants)
  • not_specified (36 variants)
  • WBP2-related_disorder (6 variants)
  • Hearing_loss,_autosomal_recessive_107 (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WBP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012478.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
16
clinvar
3
clinvar
 19
missense
1
clinvar
58
clinvar
3
clinvar
 62
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 1 58 19 3

Highest pathogenic variant AF is 6.84856e-7

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
WBP2protein_codingprotein_codingENST00000591399 810809
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.3490.648125743041257470.0000159
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2961511620.9340.000009091687
Missense in Polyphen4246.8470.89653544
Synonymous-0.2146764.81.030.00000438495
Loss of Function2.59313.10.2295.53e-7166

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006150.0000615
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00004650.0000462
European (Non-Finnish)0.000.00
Middle Eastern0.00005440.0000544
South Asian0.00003400.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Acts as transcriptional coactivator of estrogen and progesterone receptors (ESR1 and PGR) upon hormone activation (PubMed:16772533). In presence of estrogen, binds to ESR1- responsive promoters (PubMed:16772533). Required for YAP1 coactivation function on PGR activity (PubMed:16772533). Synergizes with WBP2 in enhancing PGR activity (PubMed:16772533). Modulates expression of post-synaptic scaffolding proteins via regulation of ESR1, ESR2 and PGR (By similarity). {ECO:0000250|UniProtKB:P97765, ECO:0000269|PubMed:16772533}.;
Disease
DISEASE: Deafness, autosomal recessive, 107 (DFNB107) [MIM:617639]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:26881968}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
EGFR1 (Consensus)

Recessive Scores

pRec
0.130

Intolerance Scores

loftool
0.350
rvis_EVS
-0.03
rvis_percentile_EVS
51.66

Haploinsufficiency Scores

pHI
0.460
hipred
Y
hipred_score
0.744
ghis
0.527

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.988

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Wbp2
Phenotype
immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype;

Gene ontology

Biological process
response to progesterone;positive regulation of intracellular estrogen receptor signaling pathway;response to estrogen;establishment of protein localization;positive regulation of gene expression, epigenetic;positive regulation of transcription by RNA polymerase II;progesterone receptor signaling pathway;cellular response to estrogen stimulus;positive regulation of histone H3-K14 acetylation
Cellular component
nuclear chromatin;nucleus;cytoplasm
Molecular function
RNA polymerase II proximal promoter sequence-specific DNA binding;transcription coactivator activity;protein binding;estrogen receptor binding;chromatin DNA binding