DPYSL3
Basic information
Region (hg38): 5:147390808-147510068
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (51 variants)
- not_provided (8 variants)
- Autism (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPYSL3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001197294.2. 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 | 4 | |||||
| missense | 51 | 52 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 51 | 3 | 2 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DPYSL3 | protein_coding | protein_coding | ENST00000343218 | 14 | 119246 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.00113 | 125587 | 0 | 3 | 125590 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.48 | 271 | 413 | 0.657 | 0.0000223 | 4499 |
| Missense in Polyphen | 108 | 205.42 | 0.52575 | 2237 | ||
| Synonymous | 0.734 | 151 | 163 | 0.927 | 0.00000919 | 1363 |
| Loss of Function | 4.60 | 2 | 28.5 | 0.0701 | 0.00000121 | 351 |
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) | 0.0000268 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Necessary for signaling by class 3 semaphorins and subsequent remodeling of the cytoskeleton. Plays a role in axon guidance, neuronal growth cone collapse and cell migration (By similarity). {ECO:0000250}.;
- Pathway
- Developmental Biology;Semaphorin interactions;Axon guidance;CRMPs in Sema3A signaling
(Consensus)
Recessive Scores
- pRec
- 0.147
Intolerance Scores
- loftool
- rvis_EVS
- -0.36
- rvis_percentile_EVS
- 29.16
Haploinsufficiency Scores
- pHI
- 0.891
- hipred
- Y
- hipred_score
- 0.765
- ghis
- 0.590
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.885
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dpysl3
- Phenotype
- cellular 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);
Zebrafish Information Network
- Gene name
- dpysl3
- Affected structure
- Rohon-Beard neuron
- Phenotype tag
- abnormal
- Phenotype quality
- displaced to
Gene ontology
- Biological process
- positive regulation of neuron projection development;negative regulation of neuron projection development;negative regulation of cell migration;neuron development;response to axon injury;actin filament bundle assembly;protein homooligomerization;positive regulation of filopodium assembly;actin crosslink formation;cellular response to cytokine stimulus
- Cellular component
- extracellular space;cytosol;lamellipodium;growth cone;filamentous actin;cell body;synapse;exocytic vesicle
- Molecular function
- protein binding;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds;SH3 domain binding;filamin binding;chondroitin sulfate binding