METTL1

methyltransferase 1, tRNA methylguanosine, the group of 7BS DNA/RNA methyltransferases

Basic information

Region (hg38): 12:57768470-57772119

Previous symbols: [ "C12orf1" ]

Links

ENSG00000037897 ∙ NCBI:4234 ∙ OMIM:604466 ∙ HGNC:7030 ∙ Uniprot:Q9UBP6 ∙ 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 METTL1 gene.

• Inborn genetic diseases (15 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL1 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			15			15
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in METTL1

This is a list of pathogenic ClinVar variants found in the METTL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-57769037-G-A		not specified	Uncertain significance (Dec 07, 2021)
12-57769040-C-T		not specified	Uncertain significance (Aug 12, 2021)
12-57769133-C-T		not specified	Uncertain significance (May 31, 2023)
12-57769330-C-T		not specified	Likely benign (Oct 20, 2023)
12-57769345-G-A		not specified	Likely benign (Feb 27, 2024)
12-57769380-C-T		not specified	Uncertain significance (Apr 07, 2022)
12-57769381-A-G		not specified	Likely benign (Dec 17, 2023)
12-57769396-C-T		not specified	Likely benign (Jan 31, 2024)
12-57769398-C-A		not specified	Uncertain significance (Nov 03, 2023)
12-57769572-C-T		not specified	Uncertain significance (Sep 29, 2023)
12-57769596-A-G		Abnormality of neuronal migration	Uncertain significance (Oct 31, 2014)
12-57769652-G-A		not specified	Likely benign (Jun 29, 2023)
12-57769812-T-C		not specified	Uncertain significance (Jan 26, 2022)
12-57769822-G-A		not specified	Uncertain significance (Apr 08, 2022)
12-57769860-C-T		not specified	Uncertain significance (Dec 06, 2022)
12-57769861-G-A		not specified	Uncertain significance (Dec 28, 2022)
12-57769876-G-A		not specified	Uncertain significance (Aug 30, 2021)
12-57769877-G-T		not specified	Uncertain significance (Dec 15, 2023)
12-57769905-C-T		not specified	Uncertain significance (Aug 27, 2021)
12-57769936-G-C		not specified	Uncertain significance (Jun 22, 2021)
12-57771121-T-C		not specified	Uncertain significance (Nov 17, 2022)
12-57771205-C-T		not specified	Uncertain significance (Sep 12, 2023)
12-57771977-C-T		not specified	Uncertain significance (Aug 17, 2022)
12-57772047-C-T		not specified	Uncertain significance (Aug 15, 2023)
12-57772050-C-G		not specified	Uncertain significance (Nov 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METTL1	protein_coding	protein_coding	ENST00000324871	6	4323

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00196	0.916	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.239	157	166	0.948	0.00000960	1782
Missense in Polyphen		50	57.192	0.87424		585
Synonymous	-0.207	67	64.9	1.03	0.00000374	559
Loss of Function	1.52	6	11.6	0.518	4.90e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000362	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA. {ECO:0000255|HAMAP-Rule:MF_03055, ECO:0000269|PubMed:12403464}.
• Pathway: tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.409
• rvis_EVS: -0.63
• rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

• pHI: 0.204
• hipred: Y
• hipred_score: 0.617
• ghis: 0.581

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.810

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mettl1

Gene ontology

• Biological process: tRNA modification;tRNA methylation;RNA (guanine-N7)-methylation;tRNA (guanine-N7)-methylation
• Cellular component: nucleus;nucleoplasm;nucleolus;cytosol
• Molecular function: tRNA binding;protein binding;tRNA (guanine-N7-)-methyltransferase activity