SMYD3
Basic information
Region (hg38): 1:245749342-246507312
Previous symbols: [ "ZNFN3A1", "ZMYND1" ]
Links
Phenotypes
GenCC
Source:
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 SMYD3 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 | 1 | |||||
| missense | 26 | 26 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 27 | 0 | 1 |
Variants in SMYD3
This is a list of pathogenic ClinVar variants found in the SMYD3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SMYD3 | protein_coding | protein_coding | ENST00000388985 | 12 | 757973 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.44e-7 | 0.956 | 125659 | 0 | 89 | 125748 | 0.000354 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.245 | 225 | 236 | 0.955 | 0.0000126 | 2815 |
| Missense in Polyphen | 63 | 65.148 | 0.96703 | 778 | ||
| Synonymous | -0.0406 | 87 | 86.5 | 1.01 | 0.00000469 | 777 |
| Loss of Function | 1.96 | 15 | 25.7 | 0.584 | 0.00000141 | 291 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000606 | 0.000606 |
| Ashkenazi Jewish | 0.00109 | 0.00109 |
| East Asian | 0.000166 | 0.000163 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000439 | 0.000422 |
| Middle Eastern | 0.000166 | 0.000163 |
| South Asian | 0.000264 | 0.000261 |
| Other | 0.000340 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Histone methyltransferase. Specifically methylates 'Lys- 4' of histone H3, inducing di- and tri-methylation, but not monomethylation (PubMed:15235609, PubMed:22419068). Also methylates 'Lys-5' of histone H4 (PubMed:22419068). Plays an important role in transcriptional activation as a member of an RNA polymerase complex (PubMed:15235609). Binds DNA containing 5'- CCCTCC-3' or 5'-GAGGGG-3' sequences (PubMed:15235609). {ECO:0000269|PubMed:15235609, ECO:0000269|PubMed:22419068}.;
- Pathway
- Histone Modifications;PKMTs methylate histone lysines;Chromatin modifying enzymes;Lysine metabolism;Chromatin organization
(Consensus)
Recessive Scores
- pRec
- 0.114
Intolerance Scores
- loftool
- 0.960
- rvis_EVS
- -0.31
- rvis_percentile_EVS
- 31.93
Haploinsufficiency Scores
- pHI
- 0.220
- hipred
- N
- hipred_score
- 0.322
- ghis
- 0.588
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.874
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Smyd3
- Phenotype
- normal phenotype;
Zebrafish Information Network
- Gene name
- smyd3
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- curved dorsal
Gene ontology
- Biological process
- nucleosome assembly;negative regulation of protein kinase activity;myotube cell development;positive regulation of peptidyl-serine phosphorylation;histone lysine methylation;establishment of protein localization;positive regulation of transcription by RNA polymerase II;cellular response to dexamethasone stimulus
- Cellular component
- nucleus;nucleoplasm;cytosol
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II complex binding;RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding;protein binding;histone-lysine N-methyltransferase activity;metal ion binding