DKK2
Basic information
Region (hg38): 4:106921802-107283806
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (22 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DKK2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014421.3. 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 | 0 | |||||
missense | 22 | 22 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 22 | 0 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
DKK2 | protein_coding | protein_coding | ENST00000285311 | 4 | 362005 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.753 | 0.246 | 125730 | 0 | 3 | 125733 | 0.0000119 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.415 | 139 | 153 | 0.906 | 0.00000836 | 1689 |
Missense in Polyphen | 58 | 69.617 | 0.83313 | 752 | ||
Synonymous | 0.215 | 56 | 58.1 | 0.964 | 0.00000296 | 503 |
Loss of Function | 2.88 | 2 | 13.4 | 0.150 | 8.22e-7 | 140 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000123 | 0.000123 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Antagonizes canonical Wnt signaling by inhibiting LRP5/6 interaction with Wnt and by forming a ternary complex with the transmembrane protein KREMEN that promotes internalization of LRP5/6. DKKs play an important role in vertebrate development, where they locally inhibit Wnt regulated processes such as antero- posterior axial patterning, limb development, somitogenesis and eye formation. In the adult, Dkks are implicated in bone formation and bone disease, cancer and Alzheimer disease (By similarity). {ECO:0000250}.;
- Pathway
- Wnt signaling pathway - Homo sapiens (human);BMP Signaling Pathway in Eyelid Development;Wnt Signaling Pathway;Signaling by WNT;Signal Transduction;wnt signaling pathway;segmentation clock;multi-step regulation of transcription by pitx2;wnt lrp6 signalling;inactivation of gsk3 by akt causes accumulation of b-catenin in alveolar macrophages;Negative regulation of TCF-dependent signaling by WNT ligand antagonists;Wnt Canonical;TCF dependent signaling in response to WNT;Wnt Mammals;Presenilin action in Notch and Wnt signaling
(Consensus)
Recessive Scores
- pRec
- 0.144
Intolerance Scores
- loftool
- 0.167
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 60.09
Haploinsufficiency Scores
- pHI
- 0.450
- hipred
- Y
- hipred_score
- 0.776
- ghis
- 0.502
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.161
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dkk2
- Phenotype
- immune system phenotype; skeleton phenotype; vision/eye phenotype; hematopoietic system phenotype; cellular phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- dkk2
- Affected structure
- neuromast
- Phenotype tag
- abnormal
- Phenotype quality
- increased area
Gene ontology
- Biological process
- multicellular organism development;Wnt signaling pathway;negative regulation of canonical Wnt signaling pathway;positive regulation of canonical Wnt signaling pathway;extracellular negative regulation of signal transduction
- Cellular component
- extracellular space
- Molecular function
- co-receptor binding;receptor antagonist activity