MPPE1

metallophosphoesterase 1

Basic information

Region (hg38): 18:11882622-11908366

Links

ENSG00000154889 ∙ NCBI:65258 ∙ OMIM:611900 ∙ HGNC:15988 ∙ Uniprot:Q53F39 ∙ 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 MPPE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPPE1 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			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	27	2	0

Variants in MPPE1

This is a list of pathogenic ClinVar variants found in the MPPE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-11884454-C-G		not specified	Uncertain significance (Aug 12, 2021)
18-11884455-T-C		not specified	Uncertain significance (Jul 12, 2023)
18-11884459-G-A		not specified	Uncertain significance (Sep 30, 2021)
18-11884519-G-A		not specified	Uncertain significance (Mar 28, 2023)
18-11884551-C-T		not specified	Uncertain significance (Apr 12, 2023)
18-11884579-G-A		not specified	Uncertain significance (Aug 10, 2021)
18-11884581-G-A		not specified	Uncertain significance (Apr 20, 2023)
18-11884617-G-A		not specified	Uncertain significance (Jan 05, 2022)
18-11885771-G-C		not specified	Uncertain significance (Jan 03, 2024)
18-11886515-C-T		not specified	Likely benign (Feb 10, 2022)
18-11886569-G-A		not specified	Uncertain significance (Nov 01, 2022)
18-11886581-C-T		not specified	Uncertain significance (Feb 10, 2022)
18-11886584-G-C		not specified	Uncertain significance (Apr 16, 2024)
18-11886756-C-T		not specified	Uncertain significance (Dec 20, 2021)
18-11886763-G-A		not specified	Uncertain significance (Aug 16, 2022)
18-11886921-C-T		not specified	Uncertain significance (Jun 29, 2023)
18-11886936-C-G		not specified	Uncertain significance (Jun 06, 2023)
18-11888709-C-G		not specified	Uncertain significance (Sep 07, 2022)
18-11889404-G-C		not specified	Uncertain significance (Oct 12, 2021)
18-11889420-A-G		not specified	Uncertain significance (May 11, 2022)
18-11889424-C-T		not specified	Uncertain significance (Jun 11, 2021)
18-11889441-C-G		not specified	Uncertain significance (Mar 24, 2023)
18-11889483-G-A		not specified	Uncertain significance (Jun 30, 2022)
18-11893518-C-T		not specified	Uncertain significance (Feb 15, 2023)
18-11893556-G-A		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MPPE1	protein_coding	protein_coding	ENST00000588072	9	26602

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.22e-9	0.336	125548	0	200	125748	0.000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.352	210	225	0.934	0.0000133	2588
Missense in Polyphen		74	82.213	0.9001		998
Synonymous	-0.0502	90	89.4	1.01	0.00000572	769
Loss of Function	0.855	16	20.1	0.794	0.00000112	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00191	0.00191
Ashkenazi Jewish	0.00313	0.00298
East Asian	0.000387	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000222	0.000220
Middle Eastern	0.000387	0.000381
South Asian	0.00239	0.00239
Other	0.000848	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Metallophosphoesterase required for transport of GPI- anchor proteins from the endoplasmic reticulum to the Golgi. Acts in lipid remodeling steps of GPI-anchor maturation by mediating the removal of a side-chain ethanolamine-phosphate (EtNP) from the second Man (Man2) of the GPI intermediate, an essential step for efficient transport of GPI-anchor proteins. {ECO:0000269|PubMed:19837036}.

Recessive Scores

• pRec: 0.0830

Intolerance Scores

• loftool: 0.925
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.36

Haploinsufficiency Scores

• pHI: 0.0678
• hipred: N
• hipred_score: 0.170
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.236

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mppe1

Gene ontology

• Biological process: GPI anchor biosynthetic process;endoplasmic reticulum to Golgi vesicle-mediated transport
• Cellular component: nucleoplasm;endoplasmic reticulum;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;cis-Golgi network;integral component of membrane;endoplasmic reticulum-Golgi intermediate compartment membrane;endoplasmic reticulum exit site
• Molecular function: protein binding;phosphoric diester hydrolase activity;manganese ion binding;GPI anchor binding