KMT5C
protein-codinglysine methyltransferase 5C, the group of Lysine methyltransferases|SET domain containing
Gene summary
SUV420H2 and the related enzyme SUV420H1 (MIM 610881) function as histone methyltransferases that specifically trimethylate nucleosomal histone H4 (see MIM 602822) on lysine-20 (K20) (Schotta et al., 2004 [PubMed 15145825]).[supplied by OMIM, Dec 2009]
- SUV420H2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to KMT5C variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032701.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 3 | 6 | |||
| missense | 7 | 7 | ||||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 13 | 0 | 3 | 16 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_116090.2 | 8 | MANE Select | |
| Ensembl | ENSP00000255613.3 | 8 | MANE Select | |
| RefSeq | NP_001425877.1 | 8 | Standard | |
| RefSeq | NP_001425878.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Lysine degradation - Homo sapiens (human)
- Histone Modifications
- PKMTs methylate histone lysines
- Chromatin modifying enzymes
- Chromatin organization
Biological Process
- histone H4-K20 trimethylation
Molecular Function
- protein binding
- histone-lysine N-methyltransferase activity
- histone methyltransferase activity (H4-K20 specific)
Cellular Component
- condensed nuclear chromosome, centromeric region
- nucleoplasm
- nuclear heterochromatin
- pericentric heterochromatin
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000255613
- Coding exons
- 8
- Length
- 8268
- Individuals with no LoFs
- 125628
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 19
- Defined
- 125647
- p
- 0.0000756
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.67 | 225 | 308 | 0.732 | 0.0000221 | 2847 |
| Missense (PolyPhen) | 52 | 110.94 | 0.46872 | 1092 | ||
| Synonymous | -1.44 | 149 | 128 | 1.16 | 0.00000841 | 1021 |
| Loss of Function | 3.61 | 5 | 24.1 | 0.207 | 0.00000166 | 205 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000075 | 0.000062 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000057 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000097 | 0.000088 | rare |
| South Asian | 0.000066 | 0.000065 | rare |
| Other | 0.00018 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Histone methyltransferase that specifically trimethylates 'Lys-20' of histone H4. H4 'Lys-20' trimethylation represents a specific tag for epigenetic transcriptional repression. Mainly functions in pericentric heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin in these regions. KMT5C is targeted to histone H3 via its interaction with RB1 family proteins (RB1, RBL1 and RBL2) (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.115
Essentials
- Essential (gene trap)
- N