SYNE3
Basic information
Region (hg38): 14:95407266-95516650
Previous symbols: [ "C14orf49", "LINC00341", "C14orf139", "NCRNA00341" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (170 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNE3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152592.6. 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 | 1 | |||||
missense | 158 | 12 | 170 | |||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 158 | 13 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SYNE3 | protein_coding | protein_coding | ENST00000334258 | 17 | 58343 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.76e-25 | 0.00894 | 125531 | 0 | 217 | 125748 | 0.000863 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.00387 | 577 | 577 | 1.00 | 0.0000366 | 6283 |
Missense in Polyphen | 119 | 108.82 | 1.0936 | 1402 | ||
Synonymous | -0.767 | 274 | 258 | 1.06 | 0.0000167 | 1983 |
Loss of Function | 1.08 | 43 | 51.4 | 0.837 | 0.00000254 | 530 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00294 | 0.00294 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00354 | 0.00354 |
Finnish | 0.0000950 | 0.0000924 |
European (Non-Finnish) | 0.000355 | 0.000352 |
Middle Eastern | 0.00354 | 0.00354 |
South Asian | 0.000819 | 0.000817 |
Other | 0.000652 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: As a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex involved in the connection between the nuclear lamina and the cytoskeleton. The nucleocytoplasmic interactions established by the LINC complex play an important role in the transmission of mechanical forces across the nuclear envelope and in nuclear movement and positioning. Probable anchoring protein which tethers the nucleus to the cytoskeleton by binding PLEC which can associate with the intermediate filament system. Plays a role in the regulation of aortic epithelial cell morphology, and is required for flow-induced centrosome polarization and directional migration in aortic endothelial cells. {ECO:0000269|PubMed:16330710, ECO:0000269|PubMed:18396275, ECO:0000269|PubMed:21937718}.;
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- loftool
- rvis_EVS
- 1.17
- rvis_percentile_EVS
- 92.66
Haploinsufficiency Scores
- pHI
- 0.123
- hipred
- N
- hipred_score
- 0.144
- ghis
- 0.448
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- gene_indispensability_score
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | High | Medium | High |
Mouse Genome Informatics
- Gene name
- Syne3
- Phenotype
Zebrafish Information Network
- Gene name
- syne3
- Affected structure
- epidermal cell
- Phenotype tag
- abnormal
- Phenotype quality
- spatial pattern
Gene ontology
- Biological process
- cytoskeleton organization;nuclear migration;regulation of cell shape;nucleus localization;establishment of protein localization to membrane;cytoskeletal anchoring at nuclear membrane
- Cellular component
- nuclear envelope;nuclear outer membrane;cytoplasm;rough endoplasmic reticulum;membrane;integral component of membrane;nuclear membrane;meiotic nuclear membrane microtubule tethering complex
- Molecular function
- protein binding;actin filament binding