METAP1D

methionyl aminopeptidase type 1D, mitochondrial, the group of Aminopeptidases

Basic information

Region (hg38): 2:171999943-172082430

Links

ENSG00000172878 ∙ NCBI:254042 ∙ OMIM:610267 ∙ HGNC:32583 ∙ Uniprot:Q6UB28 ∙ 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 METAP1D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METAP1D 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			20	1		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	20	1	0

Variants in METAP1D

This is a list of pathogenic ClinVar variants found in the METAP1D region.

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

Position	Type	Phenotype	Significance	ClinVar
2-171999992-A-G		not specified	Uncertain significance (Sep 22, 2022)
2-172061585-G-A		not specified	Uncertain significance (Jan 24, 2023)
2-172061597-A-C		not specified	Uncertain significance (Jan 23, 2024)
2-172061608-A-G		not specified	Uncertain significance (Nov 21, 2023)
2-172061630-T-C		not specified	Uncertain significance (May 09, 2024)
2-172061645-C-T		not specified	Uncertain significance (May 20, 2024)
2-172063729-T-A		not specified	Uncertain significance (Jul 09, 2021)
2-172063736-C-T		not specified	Uncertain significance (Aug 02, 2021)
2-172063805-A-G		not specified	Likely benign (Aug 21, 2023)
2-172063825-C-T		not specified	Uncertain significance (Jun 28, 2022)
2-172065668-A-G		not specified	Uncertain significance (Feb 17, 2023)
2-172065676-C-T		not specified	Uncertain significance (Dec 13, 2022)
2-172065704-C-T		not specified	Uncertain significance (Aug 15, 2023)
2-172065727-G-A		not specified	Uncertain significance (Apr 05, 2023)
2-172065737-A-G		not specified	Uncertain significance (Apr 28, 2022)
2-172066266-G-A		not specified	Uncertain significance (Dec 04, 2023)
2-172070935-C-A		not specified	Uncertain significance (May 26, 2024)
2-172071033-G-C		not specified	Uncertain significance (Mar 30, 2024)
2-172071042-C-T		not specified	Uncertain significance (Apr 20, 2023)
2-172077804-A-G		not specified	Uncertain significance (Feb 06, 2024)
2-172077836-T-A		not specified	Uncertain significance (May 18, 2022)
2-172080329-T-G		not specified	Uncertain significance (Jan 03, 2024)
2-172080330-C-T		not specified	Uncertain significance (May 23, 2024)
2-172080359-A-C		not specified	Uncertain significance (Aug 16, 2022)
2-172080387-A-C		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METAP1D	protein_coding	protein_coding	ENST00000315796	10	82669

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000258	0.760	125565	0	183	125748	0.000728

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.637	160	184	0.868	0.00000953	2198
Missense in Polyphen		59	70.135	0.84124		815
Synonymous	0.885	58	67.2	0.863	0.00000393	643
Loss of Function	1.23	11	16.4	0.671	7.51e-7	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00262	0.00260
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000881	0.000879
Middle Eastern	0.000109	0.000109
South Asian	0.000370	0.000359
Other	0.00147	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 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). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed (By similarity). May play a role in colon tumorigenesis. {ECO:0000255|HAMAP-Rule:MF_03174, ECO:0000269|PubMed:16568094}.

Intolerance Scores

• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.286
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• 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: Metap1d

Gene ontology

• Biological process: proteolysis;peptidyl-methionine modification;N-terminal protein amino acid modification;protein initiator methionine removal
• Cellular component: mitochondrion;intracellular membrane-bounded organelle
• Molecular function: aminopeptidase activity;metalloexopeptidase activity;metal ion binding;metalloaminopeptidase activity