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

ENSG00000143499 ∙ NCBI:56950 ∙ OMIM:610663 ∙ HGNC:20982 ∙ Uniprot:Q9NRG4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SMYD2 gene.

• not_specified (49 variants)

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. These statistics are base on transcript: NM_000020197.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			48	1		49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	1	0

GnomAD

Source: gnomAD

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: dbNSFP

• 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)