SUV39H1

SUV39H1 histone lysine methyltransferase, the group of SET domain containing|eNoSC complex|Lysine methyltransferases

Basic information

Region (hg38): X:48695553-48709016

Previous symbols: [ "SUV39H" ]

Links

ENSG00000101945 ∙ NCBI:6839 ∙ OMIM:300254 ∙ HGNC:11479 ∙ Uniprot:O43463 ∙ 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 SUV39H1 gene.

• Inborn genetic diseases (3 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUV39H1 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	2
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	1

Variants in SUV39H1

This is a list of pathogenic ClinVar variants found in the SUV39H1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-48695823-G-A			Likely benign (Dec 01, 2022)
X-48700221-G-A		not specified	Uncertain significance (Jul 06, 2021)
X-48700223-C-G		not specified	Uncertain significance (Sep 12, 2023)
X-48700340-C-T		Ependymoma	Uncertain significance (Dec 29, 2017)
X-48700687-T-C			Benign (Feb 26, 2018)
X-48700705-C-T			Likely benign (Nov 01, 2022)
X-48706311-G-A		not specified	Uncertain significance (Feb 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUV39H1	protein_coding	protein_coding	ENST00000376687	6	13459

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.990	0.0104	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.49	65	206	0.316	0.0000199	2686
Missense in Polyphen		10	63.008	0.15871		881
Synonymous	0.642	70	77.2	0.907	0.00000693	807
Loss of Function	3.43	0	13.7	0.00	0.00000107	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3 using monomethylated H3 'Lys- 9' as substrate. Also weakly methylates histone H1 (in vitro). H3 'Lys-9' trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions. H3 'Lys-9' trimethylation is also required to direct DNA methylation at pericentric repeats. SUV39H1 is targeted to histone H3 via its interaction with RB1 and is involved in many processes, such as repression of MYOD1-stimulated differentiation, regulation of the control switch for exiting the cell cycle and entering differentiation, repression by the PML-RARA fusion protein, BMP-induced repression, repression of switch recombination to IgA and regulation of telomere length. Component of the eNoSC (energy-dependent nucleolar silencing) complex, a complex that mediates silencing of rDNA in response to intracellular energy status and acts by recruiting histone- modifying enzymes. The eNoSC complex is able to sense the energy status of cell: upon glucose starvation, elevation of NAD(+)/NADP(+) ratio activates SIRT1, leading to histone H3 deacetylation followed by dimethylation of H3 at 'Lys-9' (H3K9me2) by SUV39H1 and the formation of silent chromatin in the rDNA locus. Recruited by the large PER complex to the E-box elements of the circadian target genes such as PER2 itself or PER1, contributes to the conversion of local chromatin to a heterochromatin-like repressive state through H3 'Lys-9' trimethylation. {ECO:0000269|PubMed:14765126, ECO:0000269|PubMed:16449642, ECO:0000269|PubMed:16818776, ECO:0000269|PubMed:16858404, ECO:0000269|PubMed:18004385, ECO:0000269|PubMed:18485871}.
• Pathway: Lysine degradation - Homo sapiens (human);Histone Modifications;Retinoblastoma (RB) in Cancer;Simplified Interaction Map Between LOXL4 and Oxidative Stress Pathway;SIRT1 negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);PKMTs methylate histone lysines;Chromatin modifying enzymes;Lysine metabolism;Chromatin organization;Regulation of retinoblastoma protein (Consensus)

Recessive Scores

• pRec: 0.221

Intolerance Scores

• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.597
• hipred: Y
• hipred_score: 0.714
• ghis: 0.570

Essentials

• essential_gene_CRISPR: E
• 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: Suv39h1
• Phenotype: hematopoietic system phenotype; reproductive system phenotype; 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); neoplasm; embryo phenotype; immune system phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: suv39h1a
• Affected structure: exocrine pancreas
• Phenotype tag: abnormal
• Phenotype quality: undifferentiated

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin silencing at rDNA;chromatin organization;rRNA processing;cellular response to DNA damage stimulus;cell cycle;viral process;cell differentiation;histone H3-K9 dimethylation;histone H3-K9 trimethylation;negative regulation of circadian rhythm;negative regulation of transcription, DNA-templated;rhythmic process;cellular response to hypoxia
• Cellular component: chromosome, centromeric region;heterochromatin;condensed nuclear chromosome;nucleus;nuclear lamina;nucleoplasm;chromatin silencing complex;rDNA heterochromatin
• Molecular function: transcription regulatory region sequence-specific DNA binding;chromatin binding;protein binding;zinc ion binding;S-adenosylmethionine-dependent methyltransferase activity;histone-lysine N-methyltransferase activity;histone methyltransferase activity;histone methyltransferase activity (H3-K9 specific);protein N-terminus binding