METAP1

methionyl aminopeptidase 1, the group of Aminopeptidases|M24 metallopeptidase family|MicroRNA protein coding host genes

Basic information

Region (hg38): 4:98995659-99062809

Links

ENSG00000164024 ∙ NCBI:23173 ∙ OMIM:610151 ∙ HGNC:15789 ∙ Uniprot:P53582 ∙ 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 METAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METAP1 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	1

Variants in METAP1

This is a list of pathogenic ClinVar variants found in the METAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-98995775-G-A		not specified	Uncertain significance (Dec 16, 2022)
4-98995781-G-A		not specified	Uncertain significance (May 28, 2024)
4-98995824-C-G		not specified	Uncertain significance (Jul 22, 2024)
4-99028889-C-G		not specified	Uncertain significance (Jan 04, 2022)
4-99028898-A-G		not specified	Uncertain significance (Jul 14, 2024)
4-99039397-C-T		not specified	Uncertain significance (Jun 13, 2023)
4-99039452-G-A		not specified	Uncertain significance (Aug 05, 2024)
4-99041085-C-A		not specified	Uncertain significance (Dec 11, 2024)
4-99041115-G-A		not specified	Uncertain significance (Nov 08, 2022)
4-99043295-A-G		not specified	Uncertain significance (Nov 25, 2024)
4-99043360-C-G		not specified	Uncertain significance (Nov 17, 2023)
4-99045191-T-G		not specified	Uncertain significance (Mar 05, 2024)
4-99045200-A-G		not specified	Uncertain significance (Oct 06, 2021)
4-99045262-A-G		not specified	Uncertain significance (Apr 22, 2022)
4-99048792-A-G		not specified	Uncertain significance (Jul 25, 2023)
4-99048810-C-T		Intellectual disability	Likely pathogenic (Aug 06, 2020)
4-99048859-A-G		not specified	Uncertain significance (Dec 21, 2022)
4-99061190-C-G		not specified	Uncertain significance (Dec 21, 2023)
4-99061220-C-T		not specified	Uncertain significance (Jul 12, 2023)
4-99061259-G-A		not specified	Uncertain significance (Jul 12, 2023)
4-99061273-C-T		not specified	Uncertain significance (Jul 25, 2023)
4-99061277-G-A		not specified	Uncertain significance (Jun 26, 2024)
4-99061290-A-G			Benign (Apr 04, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METAP1	protein_coding	protein_coding	ENST00000296411	11	67194

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.105	0.895	124616	0	7	124623	0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.87	127	202	0.629	0.0000103	2504
Missense in Polyphen		27	70.302	0.38406		919
Synonymous	1.09	58	69.6	0.833	0.00000344	725
Loss of Function	3.20	6	22.3	0.269	0.00000123	275

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000106	0.0000989
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000570	0.0000556
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000270	0.0000265
Middle Eastern	0.0000570	0.0000556
South Asian	0.00	0.00
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). Required for normal progression through the cell cycle. {ECO:0000255|HAMAP- Rule:MF_03174, ECO:0000269|PubMed:16274222, ECO:0000269|PubMed:17114291}.
• 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: 0.152

Intolerance Scores

• loftool: 0.551
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.658
• hipred: Y
• hipred_score: 0.605
• ghis: 0.647

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.464

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Metap1

Gene ontology

• Biological process: regulation of translation;proteolysis;peptidyl-methionine modification;regulation of rhodopsin mediated signaling pathway;N-terminal protein amino acid modification;protein initiator methionine removal;platelet aggregation
• Cellular component: cytoplasm;cytosol
• Molecular function: aminopeptidase activity;metalloexopeptidase activity;metal ion binding;metalloaminopeptidase activity