SMYD2
SET and MYND domain containing 2, the group of SET domain containing|Zinc fingers MYND-type|Lysine methyltransferases
Basic information
Region (hg38): 1:214281102-214337131
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 SMYD2 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 | 21 | 21 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 21 | 0 | 0 |
Variants in SMYD2
This is a list of pathogenic ClinVar variants found in the SMYD2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-214281283-A-T | not specified | Uncertain significance (Nov 29, 2021) | ||
| 1-214281286-G-C | not specified | Uncertain significance (Feb 27, 2024) | ||
| 1-214281370-A-G | not specified | Uncertain significance (Nov 15, 2021) | ||
| 1-214281396-C-T | not specified | Uncertain significance (Jun 09, 2022) | ||
| 1-214314777-A-G | not specified | Uncertain significance (May 26, 2023) | ||
| 1-214314817-A-G | not specified | Uncertain significance (Aug 16, 2021) | ||
| 1-214314819-A-C | not specified | Uncertain significance (Dec 22, 2023) | ||
| 1-214314829-C-T | not specified | Uncertain significance (Jun 18, 2024) | ||
| 1-214318137-C-T | not specified | Uncertain significance (Jan 03, 2024) | ||
| 1-214318945-T-A | not specified | Uncertain significance (Jan 18, 2022) | ||
| 1-214318963-C-T | not specified | Uncertain significance (Jun 16, 2024) | ||
| 1-214324674-G-A | not specified | Uncertain significance (Jul 09, 2021) | ||
| 1-214324696-C-T | not specified | Uncertain significance (Mar 20, 2023) | ||
| 1-214327638-C-G | not specified | Uncertain significance (Oct 06, 2021) | ||
| 1-214327714-C-G | not specified | Uncertain significance (Feb 15, 2023) | ||
| 1-214330983-G-A | not specified | Uncertain significance (Oct 04, 2022) | ||
| 1-214331008-G-A | not specified | Uncertain significance (Sep 01, 2021) | ||
| 1-214331059-A-G | not specified | Uncertain significance (Jan 04, 2024) | ||
| 1-214332044-G-A | not specified | Uncertain significance (Sep 29, 2022) | ||
| 1-214334215-G-C | not specified | Uncertain significance (Dec 21, 2023) | ||
| 1-214336747-A-C | not specified | Uncertain significance (Oct 13, 2023) | ||
| 1-214336755-G-A | not specified | Uncertain significance (Apr 18, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SMYD2 | protein_coding | protein_coding | ENST00000366957 | 12 | 56030 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000246 | 0.980 | 125725 | 0 | 23 | 125748 | 0.0000915 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.28 | 179 | 234 | 0.765 | 0.0000120 | 2870 |
| Missense in Polyphen | 52 | 76.406 | 0.68057 | 960 | ||
| Synonymous | -0.311 | 93 | 89.3 | 1.04 | 0.00000501 | 760 |
| Loss of Function | 2.14 | 13 | 24.4 | 0.533 | 0.00000121 | 305 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000885 | 0.0000885 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000218 | 0.000217 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000792 | 0.0000791 |
| Middle Eastern | 0.000218 | 0.000217 |
| South Asian | 0.000166 | 0.000163 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Protein-lysine N-methyltransferase that methylates both histones and non-histone proteins, including p53/TP53 and RB1. Specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). Shows even higher methyltransferase activity on p53/TP53. Monomethylates 'Lys-370' of p53/TP53, leading to decreased DNA-binding activity and subsequent transcriptional regulation activity of p53/TP53. Monomethylates RB1 at 'Lys-860'. {ECO:0000269|PubMed:17108971, ECO:0000269|PubMed:17805299, ECO:0000269|PubMed:18065756, ECO:0000269|PubMed:20870719, ECO:0000269|PubMed:21782458, ECO:0000269|PubMed:21880715}.;
- Pathway
- Histone Modifications;Gene expression (Transcription);Generic Transcription Pathway;PKMTs methylate histone lysines;RNA Polymerase II Transcription;Chromatin modifying enzymes;Chromatin organization;Regulation of TP53 Activity through Methylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;p53 pathway
(Consensus)
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- 0.369
- rvis_EVS
- 0.35
- rvis_percentile_EVS
- 74.49
Haploinsufficiency Scores
- pHI
- 0.234
- hipred
- Y
- hipred_score
- 0.765
- ghis
- 0.505
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.973
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Smyd2
- Phenotype
- homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- smyd2a
- Affected structure
- skeletal muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- disorganized
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;heart development;negative regulation of cell population proliferation;histone H3-K36 methylation;peptidyl-lysine monomethylation;peptidyl-lysine dimethylation;regulation of DNA damage response, signal transduction by p53 class mediator;regulation of signal transduction by p53 class mediator
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol
- Molecular function
- RNA polymerase II complex binding;p53 binding;protein binding;lysine N-methyltransferase activity;protein-lysine N-methyltransferase activity;histone-lysine N-methyltransferase activity;metal ion binding;histone methyltransferase activity (H3-K36 specific)