CMTR1

cap methyltransferase 1, the group of G-patch domain containing|7BS 2'O-ribose DNA/RNA methyltransferases

Basic information

Region (hg38): 6:37433219-37482827

Previous symbols: [ "KIAA0082", "FTSJD2" ]

Links

ENSG00000137200 ∙ NCBI:23070 ∙ OMIM:616189 ∙ HGNC:21077 ∙ Uniprot:Q8N1G2 ∙ 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 CMTR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMTR1 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in CMTR1

This is a list of pathogenic ClinVar variants found in the CMTR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-37435718-C-T		not specified	Uncertain significance (Jan 03, 2024)
6-37435732-C-T		not specified	Uncertain significance (Aug 19, 2021)
6-37444005-C-T		not specified	Uncertain significance (Feb 02, 2024)
6-37444029-G-A		not specified	Uncertain significance (Oct 13, 2023)
6-37444070-G-A		not specified	Uncertain significance (Mar 29, 2023)
6-37446315-G-A		not specified	Uncertain significance (Feb 14, 2023)
6-37446376-G-T		not specified	Uncertain significance (Dec 03, 2021)
6-37446403-G-A		not specified	Likely benign (Nov 13, 2023)
6-37450255-G-A		not specified	Uncertain significance (Mar 02, 2023)
6-37453087-C-G		not specified	Uncertain significance (Jun 29, 2023)
6-37453089-C-T		not specified	Uncertain significance (Feb 05, 2024)
6-37453288-C-G		not specified	Uncertain significance (Jan 26, 2022)
6-37459578-T-A		not specified	Uncertain significance (Apr 26, 2024)
6-37459625-C-T		not specified	Uncertain significance (Jun 12, 2023)
6-37461588-C-T		not specified	Uncertain significance (Dec 03, 2021)
6-37461640-G-A		not specified	Uncertain significance (Jan 23, 2023)
6-37461999-C-G		not specified	Uncertain significance (Aug 11, 2022)
6-37462921-C-T		not specified	Uncertain significance (Jun 07, 2023)
6-37462932-G-A		not specified	Uncertain significance (Jan 29, 2024)
6-37462990-T-C		not specified	Uncertain significance (May 24, 2024)
6-37462996-G-A		not specified	Uncertain significance (Apr 25, 2022)
6-37471050-C-A		not specified	Uncertain significance (Jun 14, 2023)
6-37473593-G-A		not specified	Uncertain significance (Nov 07, 2022)
6-37475348-A-G		not specified	Uncertain significance (Jul 20, 2021)
6-37476160-T-G		not specified	Uncertain significance (May 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CMTR1	protein_coding	protein_coding	ENST00000373451	23	49609

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00748	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.32	287	495	0.580	0.0000294	5554
Missense in Polyphen		49	131.28	0.37326		1611
Synonymous	-0.0389	180	179	1.00	0.0000102	1556
Loss of Function	5.50	8	49.9	0.160	0.00000287	539

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000142	0.000139
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that mediates mRNA cap1 2'-O-ribose methylation to the 5'-cap structure of mRNAs. Methylates the ribose of the first nucleotide of a m(7)GpppG-capped mRNA and small nuclear RNA (snRNA) to produce m(7)GpppRm (cap1). Displays a preference for cap0 transcripts. Cap1 modification is linked to higher levels of translation. May be involved in the interferon response pathway. {ECO:0000269|PubMed:18533109, ECO:0000269|PubMed:20713356, ECO:0000269|PubMed:21310715}.
• Pathway: mRNA capping (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• rvis_EVS: -1.09
• rvis_percentile_EVS: 7.11

Haploinsufficiency Scores

• pHI: 0.316
• hipred: Y
• hipred_score: 0.685
• ghis: 0.632

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: K

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cmtr1

Gene ontology

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