METTL16
methyltransferase 16, N6-methyladenosine, the group of 7BS N6-adenosine DNA/RNA methyltransferases
Basic information
Region (hg38): 17:2405562-2511891
Previous symbols: [ "METT10D" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL16 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 | 18 | 21 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 18 | 3 | 0 |
Variants in METTL16
This is a list of pathogenic ClinVar variants found in the METTL16 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-2419984-C-A | not specified | Uncertain significance (Feb 28, 2023) | ||
| 17-2420124-C-G | not specified | Uncertain significance (Sep 25, 2023) | ||
| 17-2420125-C-T | not specified | Uncertain significance (Sep 06, 2022) | ||
| 17-2420131-C-A | not specified | Uncertain significance (Sep 16, 2021) | ||
| 17-2420142-C-T | not specified | Likely benign (Apr 08, 2022) | ||
| 17-2420150-C-G | not specified | Uncertain significance (Mar 21, 2023) | ||
| 17-2420163-G-A | not specified | Uncertain significance (Dec 13, 2022) | ||
| 17-2420170-C-T | not specified | Likely benign (Dec 01, 2022) | ||
| 17-2420255-A-C | not specified | Uncertain significance (Aug 17, 2022) | ||
| 17-2420271-G-T | not specified | Uncertain significance (Sep 01, 2021) | ||
| 17-2420307-T-C | not specified | Uncertain significance (May 08, 2023) | ||
| 17-2420319-G-A | not specified | Uncertain significance (Jan 18, 2023) | ||
| 17-2420349-C-T | not specified | Likely benign (Nov 27, 2023) | ||
| 17-2420350-G-C | not specified | Uncertain significance (Dec 01, 2022) | ||
| 17-2420368-G-C | not specified | Uncertain significance (Apr 22, 2024) | ||
| 17-2420385-C-T | not specified | Uncertain significance (Jan 24, 2024) | ||
| 17-2420575-A-G | not specified | Uncertain significance (Oct 05, 2023) | ||
| 17-2420799-G-A | not specified | Uncertain significance (Jan 23, 2024) | ||
| 17-2420835-C-T | not specified | Uncertain significance (Feb 03, 2022) | ||
| 17-2420879-A-G | not specified | Uncertain significance (May 28, 2024) | ||
| 17-2464217-T-C | not specified | Uncertain significance (Jan 07, 2022) | ||
| 17-2477734-C-G | not specified | Uncertain significance (Jul 25, 2023) | ||
| 17-2477734-C-T | not specified | Uncertain significance (Oct 03, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| METTL16 | protein_coding | protein_coding | ENST00000263092 | 9 | 106330 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.612 | 0.388 | 124781 | 0 | 13 | 124794 | 0.0000521 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.35 | 194 | 310 | 0.625 | 0.0000177 | 3670 |
| Missense in Polyphen | 17 | 97.743 | 0.17392 | 1282 | ||
| Synonymous | 0.559 | 114 | 122 | 0.936 | 0.00000798 | 1079 |
| Loss of Function | 3.98 | 6 | 29.2 | 0.205 | 0.00000176 | 333 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000290 | 0.0000290 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000556 | 0.0000556 |
| Finnish | 0.0000464 | 0.0000464 |
| European (Non-Finnish) | 0.0000634 | 0.0000618 |
| Middle Eastern | 0.0000556 | 0.0000556 |
| South Asian | 0.000104 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: RNA N6-methyltransferase that methylates adenosine residues of a subset of RNAs and plays a key role in S-adenosyl-L- methionine homeostasis by regulating expression of MAT2A transcripts (PubMed:28525753). Able to N6-methylate a subset of mRNAs and U6 small nuclear RNAs (U6 snRNAs) (PubMed:28525753). In contrast to the METTL3-METTL14 heterodimer, only able to methylate a limited number of RNAs: requires both a 5'UACAGAGAA-3' nonamer sequence and a specific RNA structure (PubMed:28525753). In presence of S-adenosyl-L-methionine, binds the 3'-UTR region of MAT2A mRNA and specifically N6-methylates the first hairpin of MAT2A mRNA, impairing MAT2A expression (PubMed:28525753). In S- adenosyl-L-methionine-limiting conditions, binds the 3'-UTR region of MAT2A mRNA but stalls due to the lack of a methyl donor, preventing N6-methylation and promoting expression of MAT2A (PubMed:28525753). In addition to mRNAs, also able to mediate N6- methylation of U6 small nuclear RNA (U6 snRNA): specifically N6- methylates adenine in position 43 of U6 snRNAs (PubMed:28525753, PubMed:29051200). Also able to bind various lncRNAs (PubMed:29051200). Specifically binds the 3'-end of the MALAT1 long non-coding RNA (PubMed:27872311). {ECO:0000269|PubMed:27872311, ECO:0000269|PubMed:28525753, ECO:0000269|PubMed:29051200}.;
Recessive Scores
- pRec
- 0.0984
Intolerance Scores
- loftool
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.54
Haploinsufficiency Scores
- pHI
- 0.177
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.580
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mettl16
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); pigmentation phenotype;
Gene ontology
- Biological process
- mRNA catabolic process;S-adenosylmethionine biosynthetic process;posttranscriptional regulation of gene expression;regulation of mRNA splicing, via spliceosome;mRNA destabilization;rRNA base methylation;mRNA methylation;snRNA (adenine-N6)-methylation
- Cellular component
- nucleus
- Molecular function
- mRNA (N6-adenosine)-methyltransferase activity;RNA binding;U6 snRNA 3'-end binding;RNA stem-loop binding;23S rRNA (adenine(1618)-N(6))-methyltransferase activity;U6 snRNA (adenine-(43)-N(6))-methyltransferase activity