SUV39H2

SUV39H2 histone lysine methyltransferase, the group of Lysine methyltransferases|SET domain containing

Basic information

Region (hg38): 10:14878819-14904315

Links

ENSG00000152455 ∙ NCBI:79723 ∙ OMIM:606503 ∙ HGNC:17287 ∙ Uniprot:Q9H5I1 ∙ 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 SUV39H2 gene.

• Inborn genetic diseases (6 variants)
• not provided (3 variants)
• not specified (2 variants)
• Histiocytic medullary reticulosis (1 variants)
• Severe combined immunodeficiency due to DCLRE1C deficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUV39H2 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			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				2	2	4
Total	0	0	5	3	2

Variants in SUV39H2

This is a list of pathogenic ClinVar variants found in the SUV39H2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-14881511-C-A		not specified	Uncertain significance (Feb 23, 2023)
10-14897157-G-T		not specified	Uncertain significance (Jul 25, 2023)
10-14897194-A-C		not specified	Uncertain significance (Aug 23, 2021)
10-14897282-A-C		not specified	Uncertain significance (Dec 05, 2022)
10-14897449-C-T		not specified	Likely benign (Jul 21, 2021)
10-14899056-T-G		not specified	Benign (Jan 24, 2024)
10-14899187-G-A			Likely benign (Oct 01, 2023)
10-14899206-G-C			Likely benign (Nov 01, 2023)
10-14899234-C-T		Severe combined immunodeficiency due to DCLRE1C deficiency • Histiocytic medullary reticulosis • not specified	Benign (Jan 24, 2024)
10-14899244-C-G		SUV39H2-related disorder	Likely benign (Jun 05, 2019)
10-14899283-G-A		DCLRE1C-related disorder	Likely benign (Jun 20, 2019)
10-14899533-G-C			Benign (Mar 29, 2018)
10-14899588-A-G		not specified	Uncertain significance (Sep 12, 2023)
10-14902438-C-G		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUV39H2	protein_coding	protein_coding	ENST00000354919	6	25496

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.929	0.0708	125729	0	3	125732	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.28	76	210	0.362	0.0000102	2686
Missense in Polyphen		14	91.911	0.15232		1219
Synonymous	0.359	70	73.9	0.947	0.00000379	746
Loss of Function	3.72	3	21.7	0.138	0.00000133	253

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)	0.0000264	0.0000264
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. 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 cell cycle regulation, transcriptional repression and regulation of telomere length. May participate in regulation of higher-order chromatin organization during spermatogenesis. 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}.
• Pathway: Lysine degradation - Homo sapiens (human);Histone Modifications;PKMTs methylate histone lysines;Chromatin modifying enzymes;Lysine metabolism;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.0916

Intolerance Scores

• loftool: 0.103
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.301
• hipred: Y
• hipred_score: 0.633
• ghis: 0.701

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Suv39h2
• 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; growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin assembly or disassembly;chromatin remodeling;cell cycle;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;chromatin;nucleoplasm
• Molecular function: transcription regulatory region sequence-specific DNA binding;protein binding;zinc ion binding;histone-lysine N-methyltransferase activity;histone methyltransferase activity (H3-K9 specific);S-adenosyl-L-methionine binding