CSKMT citrate synthase lysine methyltransferase [Homo sapiens (human)] - Gene

Summary

Official Symbol: CSKMTprovided by HGNC
Official Full Name: citrate synthase lysine methyltransferaseprovided by HGNC
Primary source: HGNC:HGNC:33113
See related: Ensembl:ENSG00000214756 MIM:617897; AllianceGenome:HGNC:33113
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: U99HG; CS-KMT; METTL12
Summary: Enables protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine dimethylation; peptidyl-lysine monomethylation; and peptidyl-lysine trimethylation. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]
Expression: Ubiquitous expression in ovary (RPKM 1.7), endometrium (RPKM 1.6) and 25 other tissues See more
Orthologs: all
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Genomic context

Location:: 11q12.3

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2025_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (62665312..62668108)
RS_2025_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (62654726..62657526)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (62432784..62435580)

Chromosome 11 - NC_000011.10 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Data suggest that METTL12, localized in mitochondrial matrix, modifies/methylates Lys368 of citrate synthase in external surface region close to its catalytic site; addition/removal of methylation has no effect on citrate synthase activity; Lys368 occurs in highly conserved sequence of amino acid residues of citrate synthase.
Title: Human METTL12 is a mitochondrial methyltransferase that modifies citrate synthase.

Submit: New GeneRIF Correction

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

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

D8S2279 (e-PCR)
- UniSTS:473907

D10S16 (e-PCR)
- UniSTS:155756

Gene Ontology Provided by GOA

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

Process	Evidence Code	Pubs
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in peptidyl-lysine dimethylation	IDA Inferred from Direct Assay more info	PubMed
involved_in peptidyl-lysine monomethylation	IDA Inferred from Direct Assay more info	PubMed
involved_in peptidyl-lysine trimethylation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein methylation	IDA Inferred from Direct Assay more info	PubMed
involved_in tricarboxylic acid cycle	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
located_in mitochondrial matrix	TAS Traceable Author Statement more info
located_in mitochondrion	HTP more info	PubMed
located_in mitochondrion	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: citrate synthase-lysine N-methyltransferase CSKMT, mitochondrial

Names: methyltransferase like 12; methyltransferase-like protein 12, mitochondrial

NP_001036694.1

EC 2.1.1.-

XP_005274289.1

EC 2.1.1.-

XP_054225838.1

EC 2.1.1.-

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.

mRNA and Protein(s)

NM_001043229.2 → NP_001036694.1 citrate synthase-lysine N-methyltransferase CSKMT, mitochondrial precursor

See identical proteins and their annotated locations for NP_001036694.1

Status: VALIDATED

Source sequence(s)

AP001458, BG676615, BX348415, BY796224

Consensus CDS

CCDS41657.1

UniProtKB/Swiss-Prot

A8MUP2, B7Z4C1

Related

ENSP00000431287.1, ENST00000532971.2

Conserved Domains (1) summary

pfam13847
Location:75 → 196

Methyltransf_31; Methyltransferase domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

62665312..62668108

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005274232.6 → XP_005274289.1 citrate synthase-lysine N-methyltransferase CSKMT, mitochondrial isoform X1

Conserved Domains (1) summary

pfam13847
Location:198 → 319

Methyltransf_31; Methyltransferase domain