SMYD4

SET and MYND domain containing 4, the group of SET domain containing|Zinc fingers MYND-type

Basic information

Region (hg38): 17:1779484-1830634

Links

ENSG00000186532 ∙ NCBI:114826 ∙ OMIM:619134 ∙ HGNC:21067 ∙ Uniprot:Q8IYR2 ∙ 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 SMYD4 gene.

• Inborn genetic diseases (32 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMYD4 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			27	7	1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	7	1

Variants in SMYD4

This is a list of pathogenic ClinVar variants found in the SMYD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-1781364-G-T		not specified	Uncertain significance (May 23, 2023)
17-1781371-G-C		not specified	Uncertain significance (Aug 08, 2022)
17-1783036-C-T		not specified	Uncertain significance (Jul 06, 2021)
17-1783096-C-T		not specified	Uncertain significance (Jul 05, 2023)
17-1783137-G-A		not specified	Uncertain significance (Jan 23, 2024)
17-1783378-G-A		not specified	Uncertain significance (Jan 17, 2023)
17-1783411-C-T		not specified	Likely benign (Dec 08, 2023)
17-1783461-C-T		not specified	Likely benign (Nov 13, 2023)
17-1783462-G-A		not specified	Uncertain significance (Mar 08, 2024)
17-1784337-T-A		not specified	Uncertain significance (Jun 29, 2022)
17-1784413-C-T			Likely benign (Oct 01, 2022)
17-1784425-C-T		not specified	Likely benign (Aug 05, 2023)
17-1786824-C-T		not specified	Likely benign (May 27, 2022)
17-1786902-C-T		not specified	Likely benign (Jan 09, 2023)
17-1786908-C-G		not specified	Uncertain significance (Jan 30, 2024)
17-1786911-A-G		not specified	Uncertain significance (Jan 19, 2024)
17-1786939-C-A		not specified	Uncertain significance (Aug 01, 2022)
17-1786944-C-T		not specified	Uncertain significance (Mar 13, 2023)
17-1786959-G-A			Likely benign (Oct 01, 2022)
17-1787457-C-T		not specified	Likely benign (Aug 31, 2022)
17-1787487-C-T		not specified	Uncertain significance (Oct 25, 2022)
17-1787507-G-T		not specified	Uncertain significance (Mar 01, 2024)
17-1787566-G-A		not specified	Uncertain significance (Oct 12, 2021)
17-1787581-C-T		not specified	Likely benign (Dec 16, 2023)
17-1799859-G-A		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMYD4	protein_coding	protein_coding	ENST00000305513	10	51150

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.78e-15	0.234	125476	0	272	125748	0.00108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00749	462	462	1.00	0.0000262	5239
Missense in Polyphen		110	134.23	0.8195		1586
Synonymous	0.227	183	187	0.979	0.0000118	1587
Loss of Function	1.21	26	33.5	0.775	0.00000160	405

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00123	0.00121
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00164	0.00163
Finnish	0.000304	0.000277
European (Non-Finnish)	0.00168	0.00164
Middle Eastern	0.00164	0.00163
South Asian	0.000524	0.000523
Other	0.000995	0.000978

dbNSFP

Source: dbNSFP

• Pathway: Histone Modifications (Consensus)

Intolerance Scores

• loftool: 0.920
• rvis_EVS: 1.41
• rvis_percentile_EVS: 94.8

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.146
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.335

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Smyd4
• Phenotype: endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype

Gene ontology

• Biological process: methylation
• Molecular function: methyltransferase activity;metal ion binding