SMYD1

SET and MYND domain containing 1, the group of Zinc fingers MYND-type|SET domain containing|Lysine methyltransferases

Basic information

Region (hg38): 2:88067825-88113384

Links

ENSG00000115593

∙ NCBI:150572 ∙ OMIM:606846 ∙ HGNC:20986 ∙ Uniprot:Q8NB12 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

hypertrophic cardiomyopathy (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SMYD1 gene.

not_specified (86 variants)
not_provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMYD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000198274.4. 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 clinvar	2 clinvar	3
missense			86 clinvar	1 clinvar	1 clinvar	88
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	86	2	3

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMYD1	protein_coding	protein_coding	ENST00000419482	10	45608

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.14e-7	0.894	125666	0	82	125748	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.250	310	298	1.04	0.0000178	3268
Missense in Polyphen		90	93.897	0.9585		977
Synonymous	-1.88	142	116	1.22	0.00000762	866
Loss of Function	1.66	14	22.5	0.622	9.55e-7	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000958	0.000958
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00103	0.00103
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.00103	0.00103
South Asian	0.000229	0.000229
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. Acts as a transcriptional repressor. Essential for cardiomyocyte differentiation and cardiac morphogenesis.;
Pathway: Heart Development;Histone Modifications (Consensus)

Recessive Scores

pRec: 0.0934

Intolerance Scores

loftool: 0.408
rvis_EVS: -0.2
rvis_percentile_EVS: 39.17

Haploinsufficiency Scores

pHI: 0.516
hipred: N
hipred_score: 0.329
ghis: 0.553

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.198

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Smyd1
Phenotype: growth/size/body region phenotype; cellular phenotype; muscle phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype;

Zebrafish Information Network

Gene name: smyd1b
Affected structure: cardiac muscle cell
Phenotype tag: abnormal
Phenotype quality: disorganized

Gene ontology

Biological process: chromatin remodeling;heart development;positive regulation of myotube differentiation;histone lysine methylation;skeletal muscle cell differentiation;positive regulation of myoblast differentiation;negative regulation of transcription, DNA-templated
Cellular component: nucleus;cytoplasm
Molecular function: DNA binding;transcription corepressor activity;protein binding;histone-lysine N-methyltransferase activity;metal ion binding