CMTR2

cap methyltransferase 2, the group of 7BS 2'O-ribose DNA/RNA methyltransferases

Basic information

Region (hg38): 16:71281389-71289715

Previous symbols: [ "FTSJD1" ]

Links

ENSG00000180917 ∙ NCBI:55783 ∙ OMIM:616190 ∙ HGNC:25635 ∙ Uniprot:Q8IYT2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• lung cancer (Limited), mode of inheritance: AD
• melanoma (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CMTR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMTR2 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			51	4		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	51	4	0

Variants in CMTR2

This is a list of pathogenic ClinVar variants found in the CMTR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-71283620-C-A		not specified	Uncertain significance (Dec 13, 2023)
16-71283621-T-C		not specified	Uncertain significance (Dec 31, 2024)
16-71283622-G-C		not specified	Uncertain significance (Aug 26, 2024)
16-71283650-T-A		not specified	Uncertain significance (Aug 20, 2024)
16-71283658-T-A		not specified	Uncertain significance (Mar 07, 2025)
16-71283669-A-G		not specified	Uncertain significance (Mar 03, 2025)
16-71283736-C-A		not specified	Uncertain significance (Feb 08, 2025)
16-71283742-T-C		not specified	Uncertain significance (Aug 05, 2024)
16-71283773-G-C		not specified	Uncertain significance (Apr 16, 2024)
16-71283846-T-C		not specified	Uncertain significance (Dec 13, 2023)
16-71283865-G-C		not specified	Uncertain significance (Jun 28, 2022)
16-71283871-C-T		not specified	Uncertain significance (Sep 08, 2024)
16-71283964-T-C		not specified	Uncertain significance (Jul 20, 2021)
16-71284005-G-A		not specified	Uncertain significance (Dec 09, 2023)
16-71284017-C-T		not specified	Likely benign (Nov 17, 2023)
16-71284051-G-A		not specified	Uncertain significance (Dec 03, 2024)
16-71284068-C-T		not specified	Uncertain significance (Feb 08, 2025)
16-71284122-C-T		not specified	Likely benign (Jul 20, 2022)
16-71284126-C-A		not specified	Uncertain significance (Aug 11, 2024)
16-71284142-C-T		not specified	Uncertain significance (Nov 26, 2024)
16-71284155-C-A		not specified	Uncertain significance (Apr 25, 2022)
16-71284155-C-G		not specified	Uncertain significance (Jun 24, 2022)
16-71284156-G-A		not specified	Uncertain significance (Mar 01, 2023)
16-71284165-A-T		not specified	Uncertain significance (Dec 31, 2024)
16-71284189-T-G		not specified	Uncertain significance (Oct 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CMTR2	protein_coding	protein_coding	ENST00000338099	1	8327

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.35e-10	0.385	125650	0	92	125742	0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.127	402	395	1.02	0.0000190	5148
Missense in Polyphen		96	116.4	0.82473		1600
Synonymous	-0.488	153	146	1.05	0.00000726	1430
Loss of Function	0.983	17	22.0	0.774	0.00000108	300

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000480	0.000478
Ashkenazi Jewish	0.000893	0.000893
East Asian	0.000272	0.000272
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000480	0.000475
Middle Eastern	0.000272	0.000272
South Asian	0.000328	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that mediates mRNA cap2 2'-O-ribose methylation to the 5'-cap structure of mRNAs. Methylates the ribose of the second nucleotide of a m(7)GpppG-capped mRNA and small nuclear RNA (snRNA) (cap0) to produce m(7)GpppRmpNm (cap2). Recognizes a guanosine cap on RNA independently of its N(7) methylation status. Display cap2 methylation on both cap0 and cap1. Displays a preference for cap1 RNAs. {ECO:0000269|PubMed:21310715}.
• Pathway: Pathways Affected in Adenoid Cystic Carcinoma;mRNA capping (Consensus)

Intolerance Scores

• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.65

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.350
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: H

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cmtr2

Gene ontology

• Biological process: 7-methylguanosine mRNA capping;cap1 mRNA methylation;cap2 mRNA methylation
• Cellular component: nucleus;cytoplasm
• Molecular function: mRNA (nucleoside-2'-O-)-methyltransferase activity