DVL3
Basic information
Region (hg38): 3:184155377-184173614
Links
Phenotypes
GenCC
Source:
- autosomal dominant Robinow syndrome 2 (Definitive), mode of inheritance: AD
- autosomal dominant Robinow syndrome 3 (Strong), mode of inheritance: AD
- autosomal dominant Robinow syndrome (Supportive), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Robinow syndrome, autosomal dominant 3 | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Genitourinary | 26924530 |
ClinVar
This is a list of variants' phenotypes submitted to
- Autosomal dominant Robinow syndrome 3 (6 variants)
- Autosomal dominant Robinow syndrome 1 (5 variants)
- Autosomal dominant Robinow syndrome 2 (4 variants)
- not provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DVL3 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 | 76 | 82 | ||||
missense | 116 | 17 | 12 | 145 | ||
nonsense | 2 | |||||
start loss | 1 | |||||
frameshift | 16 | |||||
inframe indel | 5 | |||||
splice donor/acceptor (+/-2bp) | 5 | |||||
splice region | 5 | 9 | 14 | |||
non coding | 23 | 34 | ||||
Total | 8 | 5 | 132 | 119 | 26 |
Variants in DVL3
This is a list of pathogenic ClinVar variants found in the DVL3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-184155630-A-G | Uncertain significance (Jul 01, 2022) | |||
3-184155638-G-T | Uncertain significance (Mar 18, 2023) | |||
3-184155640-G-C | Uncertain significance (Oct 05, 2023) | |||
3-184155641-C-G | Likely benign (Jun 12, 2023) | |||
3-184155641-C-T | Likely benign (Mar 18, 2023) | |||
3-184155662-C-T | Likely benign (Aug 10, 2023) | |||
3-184155676-A-G | Inborn genetic diseases | Uncertain significance (Mar 24, 2023) | ||
3-184155689-T-C | Likely benign (Nov 29, 2022) | |||
3-184155701-C-T | Likely benign (Aug 30, 2022) | |||
3-184155715-G-T | Likely benign (Aug 04, 2023) | |||
3-184155729-G-A | Uncertain significance (Oct 26, 2022) | |||
3-184155755-C-T | Likely benign (Sep 19, 2021) | |||
3-184155757-G-A | Uncertain significance (Sep 05, 2023) | |||
3-184155780-A-G | Uncertain significance (Jun 04, 2022) | |||
3-184155787-A-G | Uncertain significance (Jul 16, 2023) | |||
3-184155788-C-T | DVL3-related disorder | Likely benign (Mar 12, 2023) | ||
3-184155963-C-T | Benign (Nov 16, 2018) | |||
3-184163446-G-A | Benign (Dec 01, 2018) | |||
3-184163454-A-G | Likely benign (Sep 13, 2019) | |||
3-184163640-T-A | Likely benign (Oct 03, 2021) | |||
3-184163641-C-G | Likely benign (Oct 03, 2023) | |||
3-184163659-T-C | Likely benign (Aug 23, 2022) | |||
3-184163666-G-A | Likely benign (Apr 12, 2021) | |||
3-184163677-C-T | Uncertain significance (Dec 27, 2019) | |||
3-184163681-TG-T | Uncertain significance (May 11, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
DVL3 | protein_coding | protein_coding | ENST00000313143 | 15 | 18223 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.385 | 0.615 | 125735 | 0 | 13 | 125748 | 0.0000517 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.32 | 345 | 489 | 0.705 | 0.0000325 | 4683 |
Missense in Polyphen | 97 | 180.18 | 0.53835 | 1755 | ||
Synonymous | 0.596 | 189 | 200 | 0.946 | 0.0000142 | 1440 |
Loss of Function | 4.01 | 7 | 31.2 | 0.225 | 0.00000159 | 345 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000117 | 0.000117 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000352 | 0.0000352 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.0000653 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the signal transduction pathway mediated by multiple Wnt genes. {ECO:0000250|UniProtKB:Q61062}.;
- Disease
- DISEASE: Robinow syndrome, autosomal dominant 3 (DRS3) [MIM:616894]: A form of Robinow syndrome, a rare skeletal dysplasia syndrome characterized by dysmorphic features resembling a fetal face, mesomelic limb shortening, genital hypoplasia, renal anomalies, and costovertebral segmentation defects. {ECO:0000269|PubMed:26924530}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- 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);EGF-Core;WNT-Core;Neural Crest Differentiation;Notch Signaling Pathway;Wnt Signaling Pathway;ESC Pluripotency Pathways;Wnt Signaling Pathway and Pluripotency;Wnt Signaling in Kidney Disease;Notch Signaling Pathway;Wnt Signaling Pathway;DNA Damage Response (only ATM dependent);Signaling by WNT;Signal Transduction;RHO GTPases Activate Formins;Disassembly of the destruction complex and recruitment of AXIN to the membrane;RHO GTPase Effectors;Signaling by Rho GTPases;PCP/CE pathway;Beta-catenin independent WNT signaling;Noncanonical Wnt signaling pathway;Negative regulation of TCF-dependent signaling by DVL-interacting proteins;Degradation of DVL;Wnt;Wnt Canonical;WNT mediated activation of DVL;Regulation of nuclear beta catenin signaling and target gene transcription;Degradation of beta catenin;TCF dependent signaling in response to WNT;Canonical Wnt signaling pathway;Wnt Mammals
(Consensus)
Recessive Scores
- pRec
- 0.177
Intolerance Scores
- loftool
- 0.282
- rvis_EVS
- -0.96
- rvis_percentile_EVS
- 9.17
Haploinsufficiency Scores
- pHI
- 0.632
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.629
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.985
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dvl3
- Phenotype
- growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; vision/eye phenotype; hematopoietic system 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); embryo phenotype; respiratory system phenotype; immune system phenotype; skeleton phenotype; renal/urinary 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; limbs/digits/tail phenotype;
Gene ontology
- Biological process
- positive regulation of protein phosphorylation;intracellular signal transduction;non-canonical Wnt signaling pathway;non-canonical Wnt signaling pathway via JNK cascade;positive regulation of JUN kinase activity;positive regulation of GTPase activity;positive regulation of transcription, DNA-templated;protein stabilization;canonical Wnt signaling pathway;Wnt signaling pathway, planar cell polarity pathway;negative regulation of canonical Wnt signaling pathway;planar cell polarity pathway involved in neural tube closure;positive regulation of neuron projection arborization;regulation of cellular protein localization;beta-catenin destruction complex disassembly
- Cellular component
- nuclear chromatin;cytosol
- Molecular function
- protease binding;signaling receptor binding;frizzled binding;protein binding;beta-catenin binding;protein heterodimerization activity;Rac GTPase binding