METTL22
protein-codingmethyltransferase 22, Kin17 lysine, the group of 7BS protein lysine methyltransferases
Gene summary
This gene encodes a member of the non-histone lysine methyltransferases. It interacts with its substrate, Kin17, which is involved in DNA repair and replication and mRNA processing. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
- C16orf68
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~28.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to METTL22 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024109.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 103 | 8 | 111 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 105 | 9 | 0 | 114 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_077014.4 | 10 | MANE Select | |
| Ensembl | ENSP00000371345.3 | 10 | MANE Select | |
| Ensembl | ENSP00000163678.6 | 3 | Standard | |
| Ensembl | ENSP00000457152.1 | 11 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| mettl22 | Danio rerio | Structure: hematopoietic stem cell differentiation Quality: disrupted abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Post-translational protein modification
- Metabolism of proteins
- Protein methylation
Biological Process
- protein methylation
- peptidyl-lysine methylation
Molecular Function
- protein binding
- protein methyltransferase activity
- protein-lysine N-methyltransferase activity
- heat shock protein binding
Cellular Component
- nucleus
- nucleoplasm
- nucleolus
- protein-containing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000381920
- Coding exons
- 10
- Length
- 24542
- Individuals with no LoFs
- 124649
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 159
- Defined
- 124809
- p
- 0.000641
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.98 | 331 | 244 | 1.36 | 0.0000148 | 2612 |
| Missense (PolyPhen) | 113 | 84.086 | 1.3439 | 951 | ||
| Synonymous | -1.15 | 123 | 108 | 1.14 | 0.00000785 | 817 |
| Loss of Function | 0.261 | 21 | 22.3 | 0.940 | 0.00000140 | 214 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00026 | 0.00026 | rare |
| Latino/Admixed American | 0.00082 | 0.00081 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0013 | 0.0013 | notable |
| Finnish | 0.00080 | 0.00079 | rare |
| European (Non-Finnish) | 0.00060 | 0.00059 | rare |
| South Asian | 0.00068 | 0.00062 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Protein N-lysine methyltransferase. In vitro methylates KIN. {ECO:0000269|PubMed:23349634}.;
Intolerance Scores
- RVIS EVS
- 0.58
- RVIS percentile EVS
- 82.3
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |