WNT2B
Wnt family member 2B, the group of Wnt family
Basic information
Region (hg38): 1:112466541-112530165
Previous symbols: [ "WNT13" ]
Links
Phenotypes
GenCC
Source:
- diarrhea 9 (Strong), mode of inheritance: AR
- diarrhea 9 (Limited), mode of inheritance: AR
- diarrhea 9 (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Diarrhea 9 | AR | Gastrointestinal | The condition can involve severe and early-onset diarrhea, and awareness may help with management (eg, via parenteral nutrition, which has been described as necessary) | Gastrointestinal | 29909964 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (142 variants)
- not_specified (53 variants)
- WNT2B-related_disorder (6 variants)
- Diarrhea_9 (6 variants)
- Failure_to_thrive_in_infancy (1 variants)
- Chronic_diarrhea (1 variants)
- Impaired_feeding_ability (1 variants)
- Diarrhea (1 variants)
- Failure_to_thrive (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the WNT2B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024494.3. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 64 | 67 | ||||
| missense | 86 | 90 | ||||
| nonsense | 4 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 2 | 3 | 87 | 65 | 5 |
Highest pathogenic variant AF is 0.0000065770437
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| WNT2B | protein_coding | protein_coding | ENST00000369684 | 5 | 63625 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0383 | 0.960 | 125735 | 0 | 13 | 125748 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.51 | 198 | 267 | 0.741 | 0.0000185 | 2492 |
| Missense in Polyphen | 60 | 115.19 | 0.52087 | 1074 | ||
| Synonymous | -0.0268 | 98 | 97.7 | 1.00 | 0.00000529 | 836 |
| Loss of Function | 2.82 | 6 | 19.4 | 0.309 | 0.00000154 | 170 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000152 | 0.000152 |
| Ashkenazi Jewish | 0.000210 | 0.000198 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000529 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Ligand for members of the frizzled family of seven transmembrane receptors. Functions in the canonical Wnt/beta- catenin signaling pathway. Plays a redundant role in embryonic lung development. {ECO:0000250|UniProtKB:O70283}.;
- Pathway
- Gastric cancer - Homo sapiens (human);mTOR signaling pathway - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Breast cancer - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Basal cell carcinoma - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);Melanogenesis - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Differentiation Pathway;ESC Pluripotency Pathways;Wnt Signaling Pathway and Pluripotency;Wnt Signaling in Kidney Disease;EMT transition in Colorectal Cancer;Wnt Signaling Pathway;DNA Damage Response (only ATM dependent);Signaling by GPCR;Signaling by WNT;Signal Transduction;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Class B/2 (Secretin family receptors);GPCR ligand binding;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;WNT ligand biogenesis and trafficking;GPCR signaling-G alpha i;Wnt Canonical;Wnt Mammals
(Consensus)
Recessive Scores
- pRec
- 0.223
Intolerance Scores
- loftool
- 0.851
- rvis_EVS
- -0.54
- rvis_percentile_EVS
- 20.54
Haploinsufficiency Scores
- pHI
- 0.0424
- hipred
- Y
- hipred_score
- 0.735
- ghis
- 0.550
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.379
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Wnt2b
- Phenotype
- respiratory system phenotype; normal phenotype;
Zebrafish Information Network
- Gene name
- wnt2bb
- Affected structure
- extrahepatic duct
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- chondrocyte differentiation;lens development in camera-type eye;male gonad development;cellular response to starvation;Wnt signaling pathway;forebrain regionalization;neuron differentiation;cell fate commitment;canonical Wnt signaling pathway;lung induction;mesenchymal-epithelial cell signaling;iris morphogenesis;cornea development in camera-type eye;hematopoietic stem cell proliferation;positive regulation of branching involved in ureteric bud morphogenesis
- Cellular component
- extracellular region;extracellular space;intracellular membrane-bounded organelle
- Molecular function
- frizzled binding