DAND5
DAN domain BMP antagonist family member 5, the group of DAN family
Basic information
Region (hg38): 19:12965159-12974760
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DAND5 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 | 0 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 2 | 0 |
Variants in DAND5
This is a list of pathogenic ClinVar variants found in the DAND5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-12969623-GGACA-G | Benign (Sep 01, 2024) | |||
| 19-12969707-C-T | not specified | Uncertain significance (Mar 07, 2024) | ||
| 19-12969728-G-C | not specified | Uncertain significance (Sep 26, 2024) | ||
| 19-12969757-T-C | not specified | Likely benign (Jul 17, 2024) | ||
| 19-12969856-CT-C | Heterotaxy | Uncertain significance (Aug 01, 2022) | ||
| 19-12969877-G-T | not specified | Uncertain significance (Apr 20, 2024) | ||
| 19-12969895-C-T | not specified | Uncertain significance (Nov 08, 2022) | ||
| 19-12969916-G-T | not specified | Uncertain significance (Mar 20, 2024) | ||
| 19-12969944-A-G | not specified | Uncertain significance (Sep 29, 2022) | ||
| 19-12969973-C-T | not specified | Uncertain significance (Dec 28, 2022) | ||
| 19-12973398-C-T | not specified | Uncertain significance (Nov 11, 2024) | ||
| 19-12973410-T-G | not specified | Uncertain significance (Jun 16, 2024) | ||
| 19-12973419-C-T | not specified | Uncertain significance (Nov 08, 2024) | ||
| 19-12973453-C-CCT | Heterotaxy | Conflicting classifications of pathogenicity (Aug 14, 2023) | ||
| 19-12973471-G-T | not specified | Uncertain significance (Oct 05, 2023) | ||
| 19-12973483-C-T | not specified | Uncertain significance (Jul 30, 2024) | ||
| 19-12973525-G-A | not specified | Likely benign (Feb 14, 2023) | ||
| 19-12973596-A-G | not specified | Likely benign (May 25, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DAND5 | protein_coding | protein_coding | ENST00000317060 | 2 | 9595 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00204 | 0.521 | 125109 | 0 | 1 | 125110 | 0.00000400 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.356 | 128 | 117 | 1.09 | 0.00000686 | 1181 |
| Missense in Polyphen | 36 | 31.857 | 1.1301 | 356 | ||
| Synonymous | 0.336 | 45 | 48.0 | 0.938 | 0.00000264 | 445 |
| Loss of Function | 0.164 | 4 | 4.37 | 0.915 | 2.33e-7 | 34 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Seems to play a role in the correct specification of the left-right axis. May antagonize NODAL and BMP4 signaling. Cystine knot-containing proteins play important roles during development, organogenesis, tissue growth and differentiation (By similarity). {ECO:0000250}.;
- Pathway
- Developmental Biology;Regulation of signaling by NODAL;Signaling by NODAL
(Consensus)
Recessive Scores
- pRec
- 0.203
Intolerance Scores
- loftool
- 0.808
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.4
Haploinsufficiency Scores
- pHI
- 0.107
- hipred
- N
- hipred_score
- 0.123
- ghis
- 0.462
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0545
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dand5
- Phenotype
- embryo phenotype; respiratory system phenotype; 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); 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); growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- dand5
- Affected structure
- determination of left/right symmetry
- Phenotype tag
- abnormal
- Phenotype quality
- disrupted
Gene ontology
- Biological process
- determination of left/right asymmetry in lateral mesoderm;ventricular septum development;atrial septum development;regulation of signaling receptor activity;signal transduction involved in regulation of gene expression;negative regulation of transforming growth factor beta receptor signaling pathway;negative regulation of BMP signaling pathway;sequestering of BMP in extracellular matrix;sequestering of nodal from receptor via nodal binding;determination of heart left/right asymmetry;negative regulation of nodal signaling pathway;negative regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry
- Cellular component
- extracellular region;extracellular space
- Molecular function
- morphogen activity