METTL6

methyltransferase 6, methylcytidine, the group of 7BS DNA/RNA methyltransferases

Basic information

Region (hg38): 3:15381275-15440566

Links

ENSG00000206562 ∙ NCBI:131965 ∙ OMIM:618903 ∙ HGNC:28343 ∙ Uniprot:Q8TCB7 ∙ 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 METTL6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL6 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				1		1
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in METTL6

This is a list of pathogenic ClinVar variants found in the METTL6 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-15411294-G-A		not specified	Uncertain significance (Dec 28, 2023)
3-15411315-A-G		not specified	Uncertain significance (Jan 10, 2022)
3-15411404-T-C		not specified	Uncertain significance (Dec 06, 2022)
3-15414086-C-G		not specified	Uncertain significance (Jan 19, 2022)
3-15414131-C-T		not specified	Uncertain significance (Aug 09, 2021)
3-15415795-G-A		not specified	Uncertain significance (Oct 03, 2022)
3-15415846-C-T		not specified	Uncertain significance (Dec 26, 2023)
3-15415860-G-T		not specified	Uncertain significance (Apr 22, 2024)
3-15415911-T-A		not specified	Uncertain significance (May 08, 2023)
3-15415914-C-T		not specified	Uncertain significance (Mar 07, 2023)
3-15425085-T-C		not specified	Uncertain significance (Dec 07, 2021)
3-15426376-C-G		not specified	Uncertain significance (Oct 03, 2022)
3-15426391-C-G		not specified	Uncertain significance (Jun 29, 2023)
3-15426419-A-G			Likely benign (Oct 01, 2023)
3-15426437-G-T		not specified	Uncertain significance (Aug 10, 2021)
3-15426460-C-T		not specified	Uncertain significance (Aug 26, 2022)
3-15427796-A-G		not specified	Uncertain significance (Sep 25, 2023)
3-15427820-A-G		not specified	Uncertain significance (Jun 28, 2023)
3-15429988-T-C		not specified	Uncertain significance (Feb 17, 2023)
3-15432190-A-T		not specified	Uncertain significance (Dec 14, 2023)
3-15432209-G-C		not specified	Uncertain significance (Dec 16, 2021)
3-15434369-C-G		not specified	Uncertain significance (Dec 08, 2023)
3-15434394-A-G		not specified	Uncertain significance (Mar 22, 2023)
3-15434411-G-A			Benign (Dec 31, 2019)
3-15434451-G-T		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METTL6	protein_coding	protein_coding	ENST00000443029	5	59292

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000210	0.734	124761	0	32	124793	0.000128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.705	120	144	0.835	0.00000676	1887
Missense in Polyphen		21	30.457	0.6895		410
Synonymous	0.574	49	54.4	0.901	0.00000278	516
Loss of Function	1.09	9	13.3	0.678	6.24e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000317	0.000316
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.0000469	0.0000464
European (Non-Finnish)	0.000151	0.000150
Middle Eastern	0.0000556	0.0000556
South Asian	0.000204	0.000196
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable methyltransferase. {ECO:0000250}.
• Pathway: Selenoamino Acid Metabolism (Consensus)

Recessive Scores

• pRec: 0.0996

Intolerance Scores

• loftool: 0.645
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.0476
• hipred: N
• hipred_score: 0.294
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.785

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mettl6
• Phenotype: cellular phenotype

Gene ontology

• Biological process: tRNA C5-cytosine methylation
• Molecular function: tRNA (cytosine-5-)-methyltransferase activity