KMT5C

lysine methyltransferase 5C, the group of Lysine methyltransferases|SET domain containing

Basic information

Region (hg38): 19:55339852-55348121

Previous symbols: [ "SUV420H2" ]

Links

ENSG00000133247 ∙ NCBI:84787 ∙ OMIM:613198 ∙ HGNC:28405 ∙ Uniprot:Q86Y97 ∙ 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 KMT5C gene.

• Inborn genetic diseases (5 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KMT5C 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					3	3
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1			1
Total	0	0	5	0	3

Variants in KMT5C

This is a list of pathogenic ClinVar variants found in the KMT5C region.

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

Position	Type	Phenotype	Significance	ClinVar
19-55342024-C-T		not specified	Uncertain significance (Jun 18, 2021)
19-55342738-C-A			Likely benign (Mar 01, 2023)
19-55346308-C-T			Benign (May 24, 2018)
19-55346318-A-T		not specified	Uncertain significance (Jun 11, 2021)
19-55346619-G-A		not specified	Uncertain significance (Jun 11, 2021)
19-55347043-C-A		not specified	Uncertain significance (Oct 12, 2021)
19-55347117-C-T		not specified	Uncertain significance (Oct 06, 2021)
19-55347206-C-A			Benign (Dec 31, 2019)
19-55347431-C-T			Benign (May 24, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KMT5C	protein_coding	protein_coding	ENST00000255613	8	8268

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.547	0.453	125628	0	19	125647	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	225	308	0.732	0.0000221	2847
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000196	0.000183
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000573	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000974	0.0000880
Middle Eastern	0.0000573	0.0000544
South Asian	0.0000661	0.0000653
Other	0.000177	0.000163

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Lysine degradation - Homo sapiens (human);Histone Modifications;PKMTs methylate histone lysines;Chromatin modifying enzymes;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.115

Haploinsufficiency Scores

• pHI: 0.240
• hipred: Y
• hipred_score: 0.701
• ghis: 0.695

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Kmt5c
• Phenotype: immune system phenotype; hematopoietic 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); normal phenotype; respiratory system phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: histone H4-K20 trimethylation
• Cellular component: condensed nuclear chromosome, centromeric region;nucleoplasm;nuclear heterochromatin;pericentric heterochromatin
• Molecular function: protein binding;histone-lysine N-methyltransferase activity;histone methyltransferase activity (H4-K20 specific)