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.

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.

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	2	3
missense			38		1	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	1	3

Variants in SMYD1

This is a list of pathogenic ClinVar variants found in the SMYD1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-88067896-T-A		not specified	Uncertain significance (Jan 31, 2024)
2-88067910-G-A		not specified	Uncertain significance (Sep 26, 2023)
2-88067913-A-C		not specified	Uncertain significance (Feb 07, 2023)
2-88067959-T-C		not specified	Uncertain significance (Jan 09, 2024)
2-88067978-T-A			Likely benign (Jan 11, 2018)
2-88084318-T-G		not specified	Uncertain significance (Jul 26, 2024)
2-88084369-G-A		not specified	Uncertain significance (Mar 19, 2024)
2-88084392-C-T		not specified	Uncertain significance (May 28, 2024)
2-88084401-G-A		not specified	Uncertain significance (Dec 18, 2023)
2-88084408-C-T		not specified	Uncertain significance (Jan 16, 2024)
2-88084422-G-A		not specified	Uncertain significance (Dec 04, 2024)
2-88084423-C-T		not specified	Uncertain significance (Aug 16, 2022)
2-88084473-G-A		not specified	Uncertain significance (Sep 11, 2024)
2-88084480-A-G		not specified	Uncertain significance (Oct 12, 2021)
2-88087867-C-T		not specified	Uncertain significance (Feb 28, 2023)
2-88087872-C-T		not specified	Uncertain significance (Nov 12, 2021)
2-88087873-G-A		not specified	Uncertain significance (Jun 18, 2021)
2-88087878-A-C		not specified	Uncertain significance (May 24, 2024)
2-88087879-T-C		not specified	Uncertain significance (Aug 28, 2024)
2-88087929-T-C		not specified	Uncertain significance (Mar 07, 2023)
2-88087989-C-A			Benign (May 09, 2018)
2-88087990-G-T		not specified	Uncertain significance (Oct 24, 2023)
2-88087999-T-C		not specified	Uncertain significance (Sep 30, 2024)
2-88088032-G-A		not specified	Uncertain significance (Dec 10, 2024)
2-88088064-A-G		not specified	Uncertain significance (Feb 02, 2022)

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