CSKMT

citrate synthase lysine methyltransferase, the group of Small nucleolar RNA protein coding host genes|7BS protein lysine methyltransferases

Basic information

Region (hg38): 11:62665308-62668496

Previous symbols: [ "METTL12" ]

Links

ENSG00000214756 ∙ NCBI:751071 ∙ OMIM:617897 ∙ HGNC:33113 ∙ Uniprot:A8MUP2 ∙ 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 CSKMT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSKMT 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						0
missense			12			12
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	15	0	1

Variants in CSKMT

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

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

Position	Type	Phenotype	Significance	ClinVar
11-62666419-G-A		not specified	Uncertain significance (Jan 29, 2024)
11-62666509-C-T			Benign (Jan 12, 2018)
11-62666512-G-C		not specified	Uncertain significance (Jun 16, 2024)
11-62666557-C-G		not specified	Uncertain significance (May 20, 2024)
11-62666561-G-C		not specified	Uncertain significance (Aug 17, 2022)
11-62666576-G-C		not specified	Uncertain significance (Aug 04, 2021)
11-62666596-T-C		not specified	Uncertain significance (Dec 11, 2023)
11-62666675-T-G		not specified	Uncertain significance (Jun 24, 2022)
11-62666681-G-T		not specified	Uncertain significance (Dec 14, 2023)
11-62666726-A-G		not specified	Uncertain significance (Jan 24, 2024)
11-62666839-C-T		not specified	Uncertain significance (Nov 06, 2023)
11-62666840-G-C		not specified	Uncertain significance (Jan 17, 2024)
11-62666884-A-G		not specified	Uncertain significance (Jun 06, 2023)
11-62666978-C-G		not specified	Uncertain significance (Sep 13, 2023)
11-62666998-G-C		not specified	Uncertain significance (Jun 10, 2024)
11-62667002-C-T		not specified	Uncertain significance (May 25, 2022)
11-62667670-C-T		not specified	Uncertain significance (Jul 19, 2023)
11-62667671-C-G		not specified	Uncertain significance (Feb 22, 2023)
11-62667690-A-T		not specified	Uncertain significance (May 06, 2024)
11-62667715-G-C		not specified	Uncertain significance (Jan 24, 2023)
11-62667727-C-A		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSKMT	protein_coding	protein_coding	ENST00000532971	2	3188

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00198	0.752	124040	14	741	124795	0.00303

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.02	169	136	1.25	0.00000682	1516
Missense in Polyphen		54	45.735	1.1807		551
Synonymous	-0.817	69	60.9	1.13	0.00000322	547
Loss of Function	0.907	5	7.72	0.648	5.01e-7	65

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00239	0.00237
Ashkenazi Jewish	0.00	0.00
East Asian	0.000334	0.000334
Finnish	0.00418	0.00400
European (Non-Finnish)	0.000203	0.000194
Middle Eastern	0.000334	0.000334
South Asian	0.0191	0.0189
Other	0.00215	0.00215

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein-lysine methyltransferase that selectively trimethylates citrate synthase (CS) in mitochondria (PubMed:28391595, PubMed:28887308). Seems to conduct trimethylation in a highly distributive manner rather than in a processive manner, and thus introduces a single methly group per binding event (PubMed:28887308). {ECO:0000269|PubMed:28391595, ECO:0000269|PubMed:28887308}.

Intolerance Scores

• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.53

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.408

Essentials

• essential_gene_gene_trap: N

Gene ontology

• Biological process: protein methylation;peptidyl-lysine trimethylation;peptidyl-lysine monomethylation;peptidyl-lysine dimethylation
• Cellular component: mitochondrion
• Molecular function: lysine N-methyltransferase activity;protein-lysine N-methyltransferase activity