SMYD5

SMYD family member 5, the group of Zinc fingers MYND-type|SET domain containing

Basic information

Region (hg38): 2:73214221-73227221

Previous symbols: [ "RAI15" ]

Links

ENSG00000135632 ∙ NCBI:10322 ∙ OMIM:619114 ∙ HGNC:16258 ∙ Uniprot:Q6GMV2 ∙ 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 SMYD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMYD5 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	1
missense			22		1	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	2

Variants in SMYD5

This is a list of pathogenic ClinVar variants found in the SMYD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-73214280-T-G		not specified	Uncertain significance (Jan 26, 2022)
2-73214283-G-A		not specified	Uncertain significance (Oct 03, 2022)
2-73214293-C-A		not specified	Uncertain significance (May 03, 2023)
2-73214297-T-C		not specified	Uncertain significance (Jun 18, 2024)
2-73214327-G-A		not specified	Uncertain significance (Apr 15, 2024)
2-73214352-G-A		not specified	Uncertain significance (Jul 09, 2021)
2-73218919-G-A		not specified	Uncertain significance (Dec 20, 2023)
2-73220059-C-T		not specified	Uncertain significance (Oct 26, 2021)
2-73220082-G-T		not specified	Uncertain significance (Feb 16, 2023)
2-73220183-A-G		not specified	Uncertain significance (Oct 22, 2021)
2-73220746-C-A		not specified	Uncertain significance (Feb 05, 2024)
2-73220775-G-A			Benign (Mar 29, 2018)
2-73221842-G-C		not specified	Uncertain significance (Jul 12, 2023)
2-73221862-C-A		not specified	Uncertain significance (May 31, 2023)
2-73221873-C-T			Benign (Mar 29, 2018)
2-73221881-C-T		not specified	Uncertain significance (Jul 09, 2021)
2-73221884-A-G		not specified	Uncertain significance (Apr 28, 2022)
2-73223057-C-T		not specified	Uncertain significance (Nov 09, 2021)
2-73223099-G-A		not specified	Uncertain significance (Nov 06, 2023)
2-73223445-C-A		not specified	Uncertain significance (Dec 27, 2022)
2-73223451-T-G		not specified	Uncertain significance (Oct 06, 2021)
2-73225640-A-G		not specified	Uncertain significance (Dec 09, 2023)
2-73225655-T-G		not specified	Uncertain significance (Aug 04, 2022)
2-73225667-G-A		not specified	Uncertain significance (Mar 14, 2023)
2-73225676-C-T		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMYD5	protein_coding	protein_coding	ENST00000389501	13	13016

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0131	0.987	125692	0	56	125748	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.19	192	244	0.786	0.0000132	2766
Missense in Polyphen		83	93.079	0.89172		1105
Synonymous	-1.15	101	87.3	1.16	0.00000421	770
Loss of Function	3.18	8	25.3	0.317	0.00000116	291

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000701	0.000701
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000217	0.000217
South Asian	0.000196	0.000196
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Pathway: Histone Modifications (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.518
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

• pHI: 0.285
• hipred: N
• hipred_score: 0.488
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.915

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smyd5
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: biological_process;methylation
• Cellular component: cellular_component
• Molecular function: molecular_function;methyltransferase activity;metal ion binding