DVL2
dishevelled segment polarity protein 2, the group of PDZ domain containing|Dishevelled segment polarity proteins
Basic information
Region (hg38): 17:7225342-7234517
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (95 variants)
- DVL2-related_disorder (10 variants)
- not_provided (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DVL2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004422.3. 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 | 5 | |||||
| missense | 93 | 99 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 93 | 8 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DVL2 | protein_coding | protein_coding | ENST00000005340 | 15 | 9205 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000136 | 1.00 | 125723 | 0 | 25 | 125748 | 0.0000994 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.322 | 447 | 467 | 0.958 | 0.0000280 | 4747 |
| Missense in Polyphen | 170 | 212.54 | 0.79984 | 2129 | ||
| Synonymous | -1.14 | 209 | 189 | 1.11 | 0.0000121 | 1541 |
| Loss of Function | 3.10 | 14 | 33.3 | 0.420 | 0.00000184 | 354 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000248 | 0.000248 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.0000464 | 0.0000462 |
| European (Non-Finnish) | 0.000104 | 0.0000967 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.0000981 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in the signal transduction pathways mediated by multiple Wnt genes. Participates both in canonical and non-canonical Wnt signaling by binding to the cytoplasmic C- terminus of frizzled family members and transducing the Wnt signal to down-stream effectors. Promotes internalization and degradation of frizzled proteins upon Wnt signaling. {ECO:0000250|UniProtKB:Q60838, ECO:0000269|PubMed:19252499}.;
- 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);Pathways in cancer - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);Notch signaling pathway - Homo sapiens (human);Melanogenesis - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);WNT-Core;Neural Crest Differentiation;Notch Signaling Pathway;Wnt Signaling Pathway;Regulation of Wnt-B-catenin Signaling by Small Molecule Compounds;ESC Pluripotency Pathways;Wnt Signaling Pathway and Pluripotency;Wnt Signaling in Kidney Disease;Type 2 papillary renal cell carcinoma;Notch Signaling Pathway;Wnt Signaling Pathway;DNA Damage Response (only ATM dependent);Signaling by WNT;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;RHO GTPases Activate Formins;Disassembly of the destruction complex and recruitment of AXIN to the membrane;RHO GTPase Effectors;Signaling by Rho GTPases;Clathrin-mediated endocytosis;Asymmetric localization of PCP proteins;WNT5A-dependent internalization of FZD4;PCP/CE pathway;Beta-catenin independent WNT signaling;Noncanonical Wnt signaling pathway;Cargo recognition for clathrin-mediated endocytosis;Negative regulation of TCF-dependent signaling by DVL-interacting proteins;Degradation of DVL;Signaling by Hippo;Wnt;Wnt Canonical;WNT mediated activation of DVL;Degradation of beta catenin;TCF dependent signaling in response to WNT;Canonical Wnt signaling pathway;Wnt Mammals
(Consensus)
Recessive Scores
- pRec
- 0.214
Intolerance Scores
- loftool
- 0.650
- rvis_EVS
- -1.21
- rvis_percentile_EVS
- 5.69
Haploinsufficiency Scores
- pHI
- 0.920
- hipred
- Y
- hipred_score
- 0.765
- ghis
- 0.595
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.995
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dvl2
- Phenotype
- embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; hearing/vestibular/ear 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); limbs/digits/tail phenotype; skeleton phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; craniofacial phenotype;
Zebrafish Information Network
- Gene name
- dvl2
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- neural tube closure;positive regulation of protein phosphorylation;outflow tract morphogenesis;transcription by RNA polymerase II;segment specification;heart development;convergent extension involved in neural plate elongation;cellular protein localization;hippo signaling;non-canonical Wnt signaling pathway;positive regulation of JUN kinase activity;positive regulation of GTPase activity;canonical Wnt signaling pathway involved in regulation of cell proliferation;positive regulation of transcription, DNA-templated;positive regulation of DNA-binding transcription factor activity;protein complex oligomerization;canonical Wnt signaling pathway;Wnt signaling pathway, planar cell polarity pathway;membrane organization;positive regulation of protein tyrosine kinase activity;negative regulation of canonical Wnt signaling pathway;cochlea morphogenesis;planar cell polarity pathway involved in neural tube closure;positive regulation of neuron projection arborization;beta-catenin destruction complex disassembly
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol;aggresome;lateral plasma membrane;nuclear body;cytoplasmic vesicle;apical part of cell;clathrin-coated endocytic vesicle
- Molecular function
- frizzled binding;protein binding;protein kinase binding;protein domain specific binding;protein binding, bridging;identical protein binding;protein self-association;Rac GTPase binding