METAP2
methionyl aminopeptidase 2, the group of Aminopeptidases|M24 metallopeptidase family
Basic information
Region (hg38): 12:95473520-95515839
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 METAP2 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 | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 15 | 0 | 0 |
Variants in METAP2
This is a list of pathogenic ClinVar variants found in the METAP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-95474186-G-A | not specified | Uncertain significance (May 07, 2024) | ||
| 12-95474258-G-A | not specified | Uncertain significance (Sep 06, 2024) | ||
| 12-95474301-A-G | not specified | Uncertain significance (Jun 24, 2022) | ||
| 12-95474327-G-T | not specified | Uncertain significance (Jan 08, 2024) | ||
| 12-95476071-C-G | not specified | Uncertain significance (Nov 12, 2021) | ||
| 12-95476164-A-T | not specified | Uncertain significance (Feb 13, 2023) | ||
| 12-95483273-G-T | not specified | Uncertain significance (Dec 22, 2023) | ||
| 12-95485893-G-T | not specified | Uncertain significance (Nov 07, 2023) | ||
| 12-95485908-C-T | not specified | Uncertain significance (May 17, 2023) | ||
| 12-95485977-G-T | not specified | Uncertain significance (Oct 01, 2024) | ||
| 12-95494058-G-A | not specified | Uncertain significance (Nov 29, 2021) | ||
| 12-95494076-C-T | not specified | Uncertain significance (Dec 13, 2022) | ||
| 12-95495136-G-A | not specified | Uncertain significance (Aug 12, 2024) | ||
| 12-95496055-C-T | not specified | Uncertain significance (Jul 31, 2024) | ||
| 12-95496084-A-G | not specified | Uncertain significance (Nov 08, 2022) | ||
| 12-95513687-A-G | not specified | Uncertain significance (Dec 30, 2023) | ||
| 12-95513695-T-C | not specified | Uncertain significance (Aug 20, 2024) | ||
| 12-95513732-G-A | not specified | Uncertain significance (May 22, 2023) | ||
| 12-95513753-T-C | not specified | Uncertain significance (Feb 05, 2024) | ||
| 12-95513815-A-G | not specified | Uncertain significance (Feb 03, 2022) | ||
| 12-95513893-G-A | not specified | Uncertain significance (Dec 19, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| METAP2 | protein_coding | protein_coding | ENST00000323666 | 11 | 42320 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00399 | 0.996 | 125729 | 1 | 17 | 125747 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.94 | 127 | 260 | 0.488 | 0.0000130 | 3128 |
| Missense in Polyphen | 18 | 109.65 | 0.16417 | 1336 | ||
| Synonymous | -1.38 | 105 | 88.5 | 1.19 | 0.00000436 | 877 |
| Loss of Function | 3.15 | 9 | 26.5 | 0.340 | 0.00000144 | 338 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000206 | 0.000206 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000896 | 0.0000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000101 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cotranslationally removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). The catalytic activity of human METAP2 toward Met-Val peptides is consistently two orders of magnitude higher than that of METAP1, suggesting that it is responsible for processing proteins containing N- terminal Met-Val and Met-Thr sequences in vivo.;
- Pathway
- Signaling by GPCR;Signal Transduction;G alpha (i) signalling events;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.166
Intolerance Scores
- loftool
- 0.0909
- rvis_EVS
- -0.8
- rvis_percentile_EVS
- 12.24
Haploinsufficiency Scores
- pHI
- 0.679
- hipred
- Y
- hipred_score
- 0.816
- ghis
- 0.706
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.923
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Metap2
- 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; cellular phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- metap2b
- Affected structure
- ventral wall of dorsal aorta
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- protein processing;peptidyl-methionine modification;regulation of rhodopsin mediated signaling pathway;N-terminal protein amino acid modification;protein initiator methionine removal
- Cellular component
- cytoplasm;cytosol;plasma membrane
- Molecular function
- RNA binding;aminopeptidase activity;metalloexopeptidase activity;metal ion binding;metalloaminopeptidase activity