METAP2

methionyl aminopeptidase 2, the group of Aminopeptidases|M24 metallopeptidase family

Basic information

Region (hg38): 12:95473520-95515839

Links

ENSG00000111142

∙ NCBI:10988 ∙ OMIM:601870 ∙ HGNC:16672 ∙ Uniprot:P50579 ∙ 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 METAP2 gene.

not_specified (32 variants)

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. These statistics are base on transcript: NM_000006838.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			32 clinvar			32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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