KMT5A lysine methyltransferase 5A [Homo sapiens (human)] - Gene

Summary

Official Symbol: KMT5Aprovided by HGNC
Official Full Name: lysine methyltransferase 5Aprovided by HGNC
Primary source: HGNC:HGNC:29489
See related: Ensembl:ENSG00000183955 MIM:607240; AllianceGenome:HGNC:29489
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SET8; SET07; SETD8; PR-Set7; PR/SET07
Summary: The protein encoded by this gene is a protein-lysine N-methyltransferase that can monomethylate Lys-20 of histone H4 to effect transcriptional repression of some genes. The encoded protein is required for cell proliferation and plays a role in chromatin condensation. [provided by RefSeq, May 2016]
Expression: Ubiquitous expression in prostate (RPKM 17.6), esophagus (RPKM 16.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q24.31

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (123384132..123409353)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (123380646..123405922)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (123868679..123893900)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Inhibition of FBP1 expression by KMT5A through TWIST1 methylation is one of the mechanisms leading to chemoresistance in breast cancer.
Title: Inhibition of FBP1 expression by KMT5A through TWIST1 methylation is one of the mechanisms leading to chemoresistance in breast cancer.
Lysine Methyltransferase 5A Promotes the Progression of Growth Hormone Pituitary Neuroendocrine Tumors through the Wnt/beta-Catenin Signaling Pathway.
Title: Lysine Methyltransferase 5A Promotes the Progression of Growth Hormone Pituitary Neuroendocrine Tumors through the Wnt/β-Catenin Signaling Pathway.
Interaction of Sp1 and Setd8 promotes vascular smooth muscle cells apoptosis by activating Mark4 in vascular calcification.
Title: Interaction of Sp1 and Setd8 promotes vascular smooth muscle cells apoptosis by activating Mark4 in vascular calcification.
SETD8 promotes glycolysis in colorectal cancer via regulating HIF1alpha/HK2 axis.
Title: SETD8 promotes glycolysis in colorectal cancer via regulating HIF1α/HK2 axis.
KMT5A Knockdown Suppresses Osteosarcoma Cell Proliferation and Metastasis Through -Catenin Signalling.
Title: KMT5A Knockdown Suppresses Osteosarcoma Cell Proliferation and Metastasis Through Ꞵ-Catenin Signalling.
KMT5A-methylated SNIP1 promotes triple-negative breast cancer metastasis by activating YAP signaling.
Title: KMT5A-methylated SNIP1 promotes triple-negative breast cancer metastasis by activating YAP signaling.
SET8, a novel regulator to ameliorate vascular calcification via activating PI3K/Akt mediated anti-apoptotic effects.
Title: SET8, a novel regulator to ameliorate vascular calcification via activating PI3K/Akt mediated anti-apoptotic effects.
SETD8 induces stemness and epithelial-mesenchymal transition of pancreatic cancer cells by regulating ROR1 expression.
Title: SETD8 induces stemness and epithelial-mesenchymal transition of pancreatic cancer cells by regulating ROR1 expression.
Integrative bioinformatics analysis the clinical value of KMT5A in different subtypes of lung cancer.
Title: Integrative bioinformatics analysis the clinical value of KMT5A in different subtypes of lung cancer.
ets1 associates with KMT5A to participate in high glucose-mediated EndMT via upregulation of PFN2 expression in diabetic nephropathy.
Title: ets1 associates with KMT5A to participate in high glucose-mediated EndMT via upregulation of PFN2 expression in diabetic nephropathy.

Submit: New GeneRIF Correction See all GeneRIFs (86)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis identifies 13 new risk loci for schizophrenia. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH102980 (e-PCR)
- UniSTS:97314

RH70202 (e-PCR)
- UniSTS:88758

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables histone H4 methyltransferase activity	TAS Traceable Author Statement more info
enables histone H4K20 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H4K20 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H4K20 methyltransferase activity	TAS Traceable Author Statement more info
enables histone H4K20 monomethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables lysine N-methyltransferase activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-lysine N-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in mitotic chromosome condensation	TAS Traceable Author Statement more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of double-strand break repair via homologous recombination	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in peptidyl-lysine monomethylation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA damage response, signal transduction by p53 class mediator	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of DNA damage response, signal transduction by p53 class mediator	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of signal transduction by p53 class mediator	TAS Traceable Author Statement more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in polytene chromosome	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: N-lysine methyltransferase KMT5A

Names: H4-K20-HMTase KMT5A; H4-K20-HMTase SETD8; H4-K20-specific histone methyltransferase; N-lysine methyltransferase SETD8; PR/SET domain containing protein 8; PR/SET domain-containing protein 07; SET domain containing (lysine methyltransferase) 8; SET domain-containing protein 8; histone-lysine N-methyltransferase KMT5A; histone-lysine N-methyltransferase SETD8; lysine (K)-specific methyltransferase 5A; lysine N-methyltransferase 5A; lysine-specific methylase 5A

NP_001311433.1

EC 2.1.1.361

NP_001311434.1

EC 2.1.1.361

NP_001311435.1

EC 2.1.1.361

NP_001354315.1

EC 2.1.1.361

NP_001354317.1

EC 2.1.1.361

NP_001354318.1

EC 2.1.1.361

NP_065115.3

EC 2.1.1.361

XP_047284792.1

EC 2.1.1.361

XP_047284793.1

EC 2.1.1.361

XP_054228016.1

EC 2.1.1.361

XP_054228017.1

EC 2.1.1.361

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_050615.2 RefSeqGene

Range

5002..30223

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001324504.2 → NP_001311433.1 N-lysine methyltransferase KMT5A isoform 2

Status: REVIEWED

Source sequence(s)

AC137767, AC145423

UniProtKB/Swiss-Prot

A8K9D0, Q86W83, Q8TD09, Q9NQR1

UniProtKB/TrEMBL

E3VVS3

Conserved Domains (1) summary

smart00317
Location:194 → 311

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
NM_001324505.2 → NP_001311434.1 N-lysine methyltransferase KMT5A isoform 3

Status: REVIEWED

Source sequence(s)

AC137767, AC145423

UniProtKB/TrEMBL

C9JKQ0

Conserved Domains (1) summary

smart00317
Location:167 → 284

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
NM_001324506.2 → NP_001311435.1 N-lysine methyltransferase KMT5A isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4), as well as variant 8, encodes isoform 4.

Source sequence(s)

AC137767, AC145423

UniProtKB/Swiss-Prot

Q9NQR1

Conserved Domains (1) summary

smart00317
Location:116 → 233

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
NM_001367386.2 → NP_001354315.1 N-lysine methyltransferase KMT5A isoform 5

Status: REVIEWED

Source sequence(s)

AC137767, AC145423

UniProtKB/Swiss-Prot

A8K9D0, Q86W83, Q8TD09, Q9NQR1
NM_001367388.2 → NP_001354317.1 N-lysine methyltransferase KMT5A isoform 6

Status: REVIEWED

Source sequence(s)

AC137767, AC145423

UniProtKB/TrEMBL

C9JKQ0
NM_001367389.2 → NP_001354318.1 N-lysine methyltransferase KMT5A isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (8), as well as variant 4, encodes isoform 4.

Source sequence(s)

AC137767, AC145423
NM_020382.7 → NP_065115.3 N-lysine methyltransferase KMT5A isoform 1

See identical proteins and their annotated locations for NP_065115.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AC137767, AC145423

Consensus CDS

CCDS9247.1

UniProtKB/Swiss-Prot

A8K9D0, Q86W83, Q8TD09, Q9NQR1

Related

ENSP00000384629.3, ENST00000402868.8

Conserved Domains (1) summary

cd10528
Location:200 → 339

SET_SETD8; SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins

RNA

NR_136910.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC137767, AC145423

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

123384132..123409353

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047428836.1 → XP_047284792.1 N-lysine methyltransferase KMT5A isoform X1

UniProtKB/Swiss-Prot

A8K9D0, Q86W83, Q8TD09, Q9NQR1
XM_047428837.1 → XP_047284793.1 N-lysine methyltransferase KMT5A isoform X2

UniProtKB/TrEMBL

C9JKQ0

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

123380646..123405922

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054372041.1 → XP_054228016.1 N-lysine methyltransferase KMT5A isoform X3

UniProtKB/Swiss-Prot

A8K9D0, Q86W83, Q8TD09, Q9NQR1
XM_054372042.1 → XP_054228017.1 N-lysine methyltransferase KMT5A isoform X2

UniProtKB/TrEMBL

C9JKQ0