CSKMT

Summary

CSKMT (citrate synthase lysine methyltransferase, HGNC:33113) is a protein-coding gene on chromosome 11q12.3, encoding Citrate synthase-lysine N-methyltransferase CSKMT, mitochondrial (A8MUP2). Protein-lysine methyltransferase that selectively trimethylates citrate synthase (CS) in mitochondria.

Enables protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine dimethylation; peptidyl-lysine monomethylation; and peptidyl-lysine trimethylation. Located in mitochondrion.

Source: NCBI Gene 751071 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 62 total
• GTEx eGene: eQTL in 29 tissues, sQTL in 0 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.86 (unconstrained)
• MANE Select transcript: NM_001043229
• Notable: 62 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33113
Approved symbol	CSKMT
Name	citrate synthase lysine methyltransferase
Location	11q12.3
Locus type	gene with protein product
Status	Approved
Aliases	U99HG, CS-KMT
Ensembl gene	ENSG00000214756
Ensembl biotype	protein_coding
OMIM	617897
Entrez	751071

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 2 protein_coding_CDS_not_defined, 2 protein_coding, 1 retained_intron

MANE Select: ENST00000532971

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 1, TSL 4: 1

ENST00000532971, ENST00000398922, ENST00000529868, ENST00000594728, ENST00000913097

RefSeq mRNA: 1 — MANE Select: NM_001043229 NM_001043229

CCDS: CCDS41657

Canonical transcript exons

ENST00000532971 — 3 exons

Exon	Start	End
ENSE00002162029	62666396	62668108
ENSE00003675691	62665647	62665946
ENSE00003849012	62665312	62665332

Expression profiles

Bgee: expression breadth ubiquitous, 167 present calls, max score 99.42.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.2052 / max 856.5251, expressed in 1753 samples.

Highest expression (Bgee): colonic epithelium, bone marrow cell, granulocyte, lower esophagus mucosa, pancreatic ductal cell.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CSKMT is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 29 tissues and its splicing (sQTL) in 0 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 29 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Artery Tibial	eqtl	4.9e-25	-1.53	11:62665312:C:T
Skin Sun Exposed Lower leg	eqtl	2.7e-23	-1.41	11:62665312:C:T
Muscle Skeletal	eqtl	3.6e-15	-1.01	11:62665312:C:T
Cells EBV-transformed lymphocytes	eqtl	1.7e-13	-1.13	11:62644682:G:A
Cells Cultured fibroblasts	eqtl	3.2e-13	-0.94	11:62665312:C:T
Esophagus Mucosa	eqtl	1.5e-12	-1.23	11:62665312:C:T
Adipose Subcutaneous	eqtl	2.8e-12	-1.20	11:62495981:G:A
Whole Blood	eqtl	9.9e-12	-1.21	11:62495981:G:A
Esophagus Muscularis	eqtl	8.4e-10	-1.26	11:62665312:C:T
Nerve Tibial	eqtl	1.3e-09	-1.06	11:62665312:C:T
Skin Not Sun Exposed Suprapubic	eqtl	2.1e-09	-1.21	11:62791235:C:T
Artery Aorta	eqtl	2.9e-09	-1.54	11:62644682:G:A
Colon Sigmoid	eqtl	4.4e-08	-1.28	11:62644682:G:A
Esophagus Gastroesophageal Junction	eqtl	3.2e-06	-1.66	11:62665312:C:T
Lung	eqtl	5.7e-06	-1.26	11:62665312:C:T
Heart Atrial Appendage	eqtl	7.4e-06	-1.22	11:62436264:C:T
Stomach	eqtl	7.8e-06	-1.24	11:62665312:C:T
Colon Transverse	eqtl	8.4e-06	-1.09	11:62665312:C:T
Thyroid	eqtl	1.6e-05	+0.22	11:62641762:TAG:T
Adipose Visceral Omentum	eqtl	2.4e-04	-0.97	11:62665312:C:T

FANTOM5 promoters

1 alternative TSS:

Promoter ID	TPM avg	Samples expressed
114722	23.2052	1753

Top tissues by expression

showing 100 of 256 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	99.42	gold quality
bone marrow cell	CL:0002092	97.92	gold quality
granulocyte	CL:0000094	90.05	gold quality
lower esophagus mucosa	UBERON:0035834	88.98	gold quality
pancreatic ductal cell	CL:0002079	85.58	silver quality
sural nerve	UBERON:0015488	82.18	gold quality
tibialis anterior	UBERON:0001385	81.45	silver quality
mucosa of transverse colon	UBERON:0004991	80.80	gold quality
right adrenal gland cortex	UBERON:0035827	80.65	gold quality
right uterine tube	UBERON:0001302	80.57	gold quality
left ovary	UBERON:0002119	79.38	gold quality
right adrenal gland	UBERON:0001233	78.65	gold quality
cerebellar cortex	UBERON:0002129	78.62	gold quality
cerebellar hemisphere	UBERON:0002245	78.60	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	78.58	gold quality
esophagus mucosa	UBERON:0002469	78.52	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.26	gold quality
right hemisphere of cerebellum	UBERON:0014890	78.25	gold quality
right ovary	UBERON:0002118	78.16	gold quality
left adrenal gland cortex	UBERON:0035825	77.79	gold quality
transverse colon	UBERON:0001157	77.65	gold quality
ectocervix	UBERON:0012249	77.52	gold quality
esophagus	UBERON:0001043	77.35	gold quality
left adrenal gland	UBERON:0001234	77.15	gold quality
spleen	UBERON:0002106	77.06	gold quality
body of stomach	UBERON:0001161	77.02	gold quality
metanephros cortex	UBERON:0010533	77.00	gold quality
ileal mucosa	UBERON:0000331	76.96	gold quality
left uterine tube	UBERON:0001303	76.76	gold quality
stromal cell of endometrium	CL:0002255	76.62	gold quality
uterine cervix	UBERON:0000002	76.57	gold quality
mucosa of stomach	UBERON:0001199	76.46	gold quality
right lobe of liver	UBERON:0001114	76.44	gold quality
cerebellum	UBERON:0002037	76.42	gold quality
tonsil	UBERON:0002372	76.41	gold quality
small intestine Peyer’s patch	UBERON:0003454	76.33	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	76.27	gold quality
leukocyte	CL:0000738	76.24	gold quality
adrenal gland	UBERON:0002369	76.12	gold quality
muscle layer of sigmoid colon	UBERON:0035805	76.09	gold quality
body of pancreas	UBERON:0001150	76.03	gold quality
monocyte	CL:0000576	75.91	gold quality
lower esophagus	UBERON:0013473	75.77	gold quality
adrenal cortex	UBERON:0001235	75.74	gold quality
lower esophagus muscularis layer	UBERON:0035833	75.74	gold quality
stomach	UBERON:0000945	75.65	gold quality
body of uterus	UBERON:0009853	75.55	gold quality
right lobe of thyroid gland	UBERON:0001119	75.35	gold quality
ascending aorta	UBERON:0001496	75.26	gold quality
thoracic aorta	UBERON:0001515	75.23	gold quality
skin of abdomen	UBERON:0001416	75.20	gold quality
omental fat pad	UBERON:0010414	75.08	gold quality
cortical plate	UBERON:0005343	75.00	gold quality
peritoneum	UBERON:0002358	74.99	gold quality
endocervix	UBERON:0000458	74.98	gold quality
adenohypophysis	UBERON:0002196	74.82	gold quality
descending thoracic aorta	UBERON:0002345	74.69	gold quality
left lobe of thyroid gland	UBERON:0001120	74.60	gold quality
gastrocnemius	UBERON:0001388	74.58	gold quality
upper lobe of left lung	UBERON:0008952	74.56	gold quality
apex of heart	UBERON:0002098	74.50	gold quality
aorta	UBERON:0000947	74.41	gold quality
left coronary artery	UBERON:0001626	74.40	gold quality
small intestine	UBERON:0002108	74.33	gold quality
tibial artery	UBERON:0007610	74.16	gold quality
popliteal artery	UBERON:0002250	74.15	gold quality
adipose tissue of abdominal region	UBERON:0007808	74.10	gold quality
muscle of leg	UBERON:0001383	74.02	gold quality
ganglionic eminence	UBERON:0004023	74.01	gold quality
hindlimb stylopod muscle	UBERON:0004252	74.00	gold quality
ovary	UBERON:0000992	73.93	gold quality
skin of leg	UBERON:0001511	73.91	gold quality
minor salivary gland	UBERON:0001830	73.91	gold quality
colon	UBERON:0001155	73.87	gold quality
prostate gland	UBERON:0002367	73.78	gold quality
thyroid gland	UBERON:0002046	73.70	gold quality
pancreas	UBERON:0001264	73.43	gold quality
adrenal tissue	UBERON:0018303	73.14	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	73.13	gold quality
intestine	UBERON:0000160	72.91	gold quality
right lung	UBERON:0002167	72.87	gold quality
large intestine	UBERON:0000059	72.75	gold quality
vermiform appendix	UBERON:0001154	72.62	gold quality
upper lobe of lung	UBERON:0008948	72.57	gold quality
cartilage tissue	UBERON:0002418	72.39	silver quality
coronary artery	UBERON:0001621	72.28	gold quality
tibial nerve	UBERON:0001323	72.09	gold quality
pituitary gland	UBERON:0000007	71.90	gold quality
right frontal lobe	UBERON:0002810	71.56	gold quality
prefrontal cortex	UBERON:0000451	71.52	gold quality
subcutaneous adipose tissue	UBERON:0002190	71.42	gold quality
Brodmann (1909) area 9	UBERON:0013540	71.23	gold quality
cortex of kidney	UBERON:0001225	71.10	gold quality
smooth muscle tissue	UBERON:0001135	71.09	gold quality
vagina	UBERON:0000996	71.07	gold quality
zone of skin	UBERON:0000014	71.02	gold quality
saliva-secreting gland	UBERON:0001044	70.95	gold quality
right coronary artery	UBERON:0001625	70.95	gold quality
anterior cingulate cortex	UBERON:0009835	70.94	gold quality
rectum	UBERON:0001052	70.88	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.61

HPA expression

RNA tissue specificity: Not detected

showing 60 of 73 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Cerebellum	tissue	8.9	low
Olfactory bulb	tissue	8.2
Cerebral cortex	tissue	7.4	medium
Insular cortex	tissue	7.4
Retrosplenial cortex	tissue	7.3
Amygdala	tissue	7.0
Cingulate cortex	tissue	7.0
Corpus callosum	tissue	6.9
Temporal cortex	tissue	6.7
Basal ganglia	tissue	6.5	low
Hippocampal formation	tissue	6.4
Entorhinal cortex	tissue	6.4
Prefrontal cortex	tissue	6.2
Ventral pallidum	tissue	6.2
Motor cortex	tissue	6.1
Occipital cortex	tissue	6.1
Putamen	tissue	5.9
Somatosensory cortex	tissue	5.9
Periaqueductal gray	tissue	5.7
Septum	tissue	5.5
Hypothalamus	tissue	5.1
Midbrain	tissue	4.7
Medulla oblongata	tissue	4.6
Substantia nigra	tissue	4.6
Spinal cord	tissue	4.5
Thalamus	tissue	4.3
Superior colliculi	tissue	4.1
Pons	tissue	4.0
Vagina	tissue	0.5	not detected
Skeletal muscle	tissue	0.5	not detected
Duodenum	tissue	0.5	medium
Fallopian tube	tissue	0.5	medium
Breast	tissue	0.4	medium
Seminal vesicle	tissue	0.4	low
Salivary gland	tissue	0.4	low
Rectum	tissue	0.4	medium
Pancreas	tissue	0.4	medium
Placenta	tissue	0.4	high
Ovary	tissue	0.3	not detected
Esophagus	tissue	0.3	not detected
Colon	tissue	0.3	medium
Endometrium 1	tissue	0.3	medium
Kidney	tissue	0.3	high
Prostate	tissue	0.3	medium
Adrenal gland	tissue	0.3	medium
Tonsil	tissue	0.3	medium
Cervix	tissue	0.2	not detected
Pituitary gland	tissue	0.2
Skin 1	tissue	0.2	not detected
Lymph node	tissue	0.2	low
Stomach 1	tissue	0.2	medium
Heart muscle	tissue	0.2	not detected
Urinary bladder	tissue	0.2	medium
Epididymis	tissue	0.2	medium
Tongue	tissue	0.2
Liver	tissue	0.2	not detected
Small intestine	tissue	0.2	medium
Retina	tissue	0.1
Adipose tissue	tissue	0.1	medium
Smooth muscle	tissue	0.1	not detected

Brain sub-regions (HPA Brain Atlas): detected in 55; highest nTPM — White matter (6.9), Ventral hippocampus (6.2), Subiculum (5.9), Dorsal hippocampus (5.8), Ventral spinal cord (4.5).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting CSKMT by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

29 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-518A-5P	99.70	69.01	2209
HSA-MIR-527	99.70	69.01	2209
HSA-MIR-7157-5P	99.66	69.33	1829
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-3975	99.62	65.97	697
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-2113	99.58	71.22	1521
HSA-MIR-6882-5P	99.35	71.13	1206
HSA-MIR-183-5P	99.31	72.27	1164
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-4504	99.10	69.14	1328
HSA-MIR-628-3P	99.04	68.37	814
HSA-MIR-4700-5P	98.63	67.43	1915
HSA-MIR-3188	98.58	65.60	878
HSA-MIR-7156-3P	98.25	67.66	859
HSA-MIR-4717-5P	98.19	67.97	894
HSA-MIR-8089	97.74	66.21	1698
HSA-MIR-4667-5P	97.61	66.67	1683
HSA-MIR-15A-3P	97.47	65.08	527
HSA-MIR-2467-5P	97.36	67.71	991
HSA-MIR-125A-3P	97.04	66.92	902
HSA-MIR-552-3P	96.68	64.12	1026
HSA-MIR-3139	96.68	66.77	652
HSA-MIR-28-5P	96.16	66.12	579
HSA-MIR-708-5P	96.16	66.12	576
HSA-MIR-5704	94.82	67.46	448

Functional genomics

gnomAD constraint: pLI 2.11e-07, LOEUF 1.86, missense Z -0.341 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000532971 — one region, missense o/e 1.10.

Literature-anchored findings (GeneRIF, showing 1)

• 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. (PMID:28391595)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	cskmt	ENSDARG00000054856
caenorhabditis_elegans	F52F12.9	WBGENE00009942
caenorhabditis_elegans		WBGENE00016868
caenorhabditis_elegans		WBGENE00021323

Paralogs (2): METTL13 (ENSG00000010165), EEF1AKMT4 (ENSG00000284753)

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Mus musculus	P0DPE0	100.0%	Diamond
Bos taurus	P0DPE1	100.0%	Diamond
Pongo abelii	Q5RCI5	97.5%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
GANAB	protein-coding	23193
SNORA57	snoRNA	692158
LBHD1	protein-coding	79081
UQCC3	protein-coding	790955
INTS5	protein-coding	80789
C11orf98	protein-coding	102288414
B3GAT3	protein-coding	26229
UBXN1	protein-coding	51035
LRRN4CL	protein-coding	221091
HNRNPUL2-BSCL2	ncRNA	100534595
BSCL2	protein-coding	26580
GNG3	protein-coding	2785

Protein

Protein identifiers

Citrate synthase-lysine N-methyltransferase CSKMT, mitochondrial — A8MUP2 (reviewed: A8MUP2)

Alternative names: Methyltransferase-like protein 12, mitochondrial

All UniProt accessions (1): A8MUP2

UniProt curated annotations — full annotation on UniProt →

Function. Protein-lysine methyltransferase that selectively trimethylates citrate synthase (CS) in mitochondria. Seems to conduct trimethylation in a highly distributive manner rather than in a processive manner, and thus introduces a single methyl group per binding event.

Subcellular location. Mitochondrion.

Activity regulation. Citrate synthase-lysine methyltransferase activity is inhibited by S-adenosylhomocysteine (AdoHcy) and oxaloacetate (OAA).

Similarity. Belongs to the methyltransferase superfamily.

RefSeq proteins (1): NP_001036694* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR025714	Methyltranfer_dom	Domain
IPR029063	SAM-dependent_MTases_sf	Homologous_superfamily
IPR051419	Lys/N-term_MeTrsfase_sf	Family

Pfam: PF13847

Catalyzed reactions (Rhea)

• L-lysyl-[citrate synthase] + S-adenosyl-L-methionine = N(6)-methyl-L-lysyl-[citrate synthase] + S-adenosyl-L-homocysteine + H(+) (RHEA:55544)
• N(6)-methyl-L-lysyl-[citrate synthase] + S-adenosyl-L-methionine = N(6),N(6)-dimethyl-L-lysyl-[citrate synthase] + S-adenosyl-L-homocysteine + H(+) (RHEA:55548)
• N(6),N(6)-dimethyl-L-lysyl-[citrate synthase] + S-adenosyl-L-methionine = N(6),N(6),N(6)-trimethyl-L-lysyl-[citrate synthase] + S-adenosyl-L-homocysteine + H(+) (RHEA:55552)

UniProt features (4 total): transit peptide 1, chain 1, sequence variant 1, mutagenesis site 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A8MUP2-F1	87.80	0.77

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Antibody reliability (HPA): IH approved

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (1)

Position	Phenotype
107	inhibits citrate synthase-lysine methyltransferase activity.

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 4; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

4 pathways:

ID	Pathway	Evidence
R-HSA-9854311	Maturation of TCA enzymes and regulation of TCA cycle	curated
R-HSA-1428517	Aerobic respiration and respiratory electron transport	—
R-HSA-71403	Citric acid cycle (TCA cycle)	—
R-HSA-1430728	Metabolism	—

MSigDB gene sets: 62 (showing top): GOBP_GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY, GOBP_PEPTIDYL_LYSINE_MODIFICATION, GOBP_PEPTIDYL_LYSINE_TRIMETHYLATION, GOBP_CELLULAR_RESPIRATION, GOBP_METHYLATION, GOBP_PEPTIDYL_LYSINE_METHYLATION, GOBP_PEPTIDYL_LYSINE_DIMETHYLATION, GOCC_MITOCHONDRIAL_MATRIX, GOMF_N_METHYLTRANSFERASE_ACTIVITY, GOMF_PROTEIN_METHYLTRANSFERASE_ACTIVITY, GOMF_S_ADENOSYLMETHIONINE_DEPENDENT_METHYLTRANSFERASE_ACTIVITY, GOMF_TRANSFERASE_ACTIVITY_TRANSFERRING_ONE_CARBON_GROUPS, GOMF_LYSINE_N_METHYLTRANSFERASE_ACTIVITY, GOBP_TRICARBOXYLIC_ACID_CYCLE, GOBP_PROTEIN_METHYLATION

GO Biological Process (6): tricarboxylic acid cycle (GO:0006099), protein methylation (GO:0006479), peptidyl-lysine trimethylation (GO:0018023), peptidyl-lysine monomethylation (GO:0018026), peptidyl-lysine dimethylation (GO:0018027), methylation (GO:0032259)

GO Molecular Function (5): lysine N-methyltransferase activity (GO:0016278), protein-lysine N-methyltransferase activity (GO:0016279), protein binding (GO:0005515), methyltransferase activity (GO:0008168), transferase activity (GO:0016740)

GO Cellular Component (2): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759)

Reactome top-level categories

3 top-level categories:

Category	Pathways
Citric acid cycle (TCA cycle)	1
Metabolism	1
Aerobic respiration and respiratory electron transport	1

GO top-level categories

17 GO namespaces:

Category	Terms
peptidyl-lysine methylation	3
aerobic respiration	1
primary metabolic process	1
protein alkylation	1
macromolecule methylation	1
metabolic process	1
N-methyltransferase activity	1
S-adenosylmethionine-dependent methyltransferase activity	1
protein methyltransferase activity	1
lysine N-methyltransferase activity	1
binding	1
transferase activity, transferring one-carbon groups	1
catalytic activity	1
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrion	1
intracellular organelle lumen	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 7 of 13 annotations. The rest are phylogenetic / computational / electronic (IEA).

7 experimentally-supported GO terms:

GO term	NS	Evidence
peptidyl-lysine dimethylation	BP	direct assay
peptidyl-lysine monomethylation	BP	direct assay
peptidyl-lysine trimethylation	BP	direct assay
protein methylation	BP	direct assay
mitochondrion	CC	high-throughput
lysine N-methyltransferase activity	MF	direct assay
protein-lysine N-methyltransferase activity	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 310 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CSKMT	ANTKMT	Q9BQD7	660
CSKMT	EEF1AKMT2	Q5JPI9	651
CSKMT	VCPKMT	Q9H867	642
CSKMT	ATPSCKMT	Q6P4H8	630
CSKMT	ETFBKMT	Q8IXQ9	621
CSKMT	METTL9	Q9H1A3	585
CSKMT	EEF1AKMT3	Q96AZ1	536
CSKMT	NDUFAF7	Q7L592	531
CSKMT	MTRF1L	Q9UGC7	525
CSKMT	EEF2KMT	Q96G04	507
CSKMT	SETD9	Q8NE22	506
CSKMT	METTL21A	Q8WXB1	497
CSKMT	N4BP3	O15049	490
CSKMT	TBC1D25	Q3MII6	473
CSKMT	METTL18	O95568	470

IntAct

Human interaction partners of CSKMT in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

6 partners by confidence:

Partner	Interaction type	MIscore	Records
BPIFA1	physical association	0.560	3
KRTAP11-1	physical association	0.560	3
KRTAP13-2	physical association	0.560	3
KRTAP19-6	physical association	0.560	3
STK16	physical association	0.560	3
TEKT5	physical association	0.560	3

SIGNOR signaling

showing 1 of 2 signaling interactions:

A	Effect	B	Mechanism
CSKMT	“down-regulates activity”	CS	methylation

Disease & clinical

Genetic variants

Variant evidence for CSKMT: 62 ClinVar records (0 pathogenic / likely pathogenic); 2 GWAS associations.

ClinVar

62 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	53
Likely benign	0
Benign	1

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 18 predictions of 159):

Position(s)	Effect	Δscore	Sites
11:62665927	donor_gain	0.9900
11:62665645–62665646	acceptor_loss	0.9200	5
11:62665646	acceptor_loss	0.9100
11:62665735	acceptor_gain	0.9000
11:62665333–62665334	donor_loss	0.8000	5
11:62665334	donor_loss	0.7700
11:62665337	donor_loss	0.7700
11:62665638	acceptor_loss	0.7600
11:62665736	acceptor_gain	0.7500
11:62665337	donor_loss	0.7300

AlphaMissense

362 missense substitutions predicted likely pathogenic (of 1,525 scored), across 98 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
D167	8	0.947	0.971
D107	8	0.942	0.971
D162	8	0.916	0.961
D81	8	0.813	0.913
D199	8	0.802	0.888
F55	8	0.780	0.907
D201	8	0.740	0.844
K163	7	0.913	0.994
W53	7	0.894	0.963
F140	7	0.883	0.964
W36	7	0.882	0.965
F54	7	0.874	0.955
F232	7	0.872	0.970
C84	7	0.842	0.966
F157	7	0.840	0.967
G85	6	0.912	0.973
G164	6	0.894	0.969
G83	6	0.886	0.948
F197	6	0.834	0.981
D52	6	0.821	0.908

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

1 prognostic cancer types:

Cancer	Prognostic	p-value
Glioblastoma Multiforme (validation)	favorable	1.16e-06

Disease associations

OMIM: gene MIM:617897 | disease phenotypes:

GWAS associations

2 associations:

Study	Trait	p-value
GCST005956_18	Waist-to-hip ratio adjusted for BMI	1e-8
GCST005962_16	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	1e-7

EFO canonical traits (from GWAS)

3 canonical traits:

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Acetaminophen	increases expression	2
2-methyl-4-isothiazolin-3-one	increases expression	1
beta-lapachone	decreases expression	1
sodium arsenite	increases stability	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	increases expression	1
Cisplatin	affects cotreatment, increases expression	1
DDT	increases expression	1
Doxorubicin	increases expression	1
Estradiol	affects cotreatment, decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Quercetin	increases expression	1
Silicon Dioxide	increases expression	1
Testosterone	decreases expression	1
Cyclosporine	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_SX88	HAP1 METTL12 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.