PPME1

protein phosphatase methylesterase 1, the group of Abhydrolase domain containing|Protein phosphatase 2 modulatory subunits

Basic information

Region (hg38): 11:74171266-74254703

Links

ENSG00000214517 ∙ NCBI:51400 ∙ OMIM:611117 ∙ HGNC:30178 ∙ Uniprot:Q9Y570 ∙ 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 PPME1 gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPME1 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in PPME1

This is a list of pathogenic ClinVar variants found in the PPME1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-74171468-G-T		not specified	Uncertain significance (Dec 16, 2023)
11-74222316-C-A		not specified	Uncertain significance (Oct 05, 2022)
11-74230382-T-A		not specified	Uncertain significance (Aug 12, 2021)
11-74235947-A-G		not specified	Uncertain significance (Jan 17, 2024)
11-74239225-T-C		not specified	Uncertain significance (Feb 23, 2023)
11-74239239-A-C		not specified	Uncertain significance (Jun 28, 2023)
11-74246081-G-C		not specified	Uncertain significance (Dec 27, 2023)
11-74246161-A-G		not specified	Uncertain significance (Nov 09, 2021)
11-74251664-C-G		not specified	Uncertain significance (Apr 07, 2023)
11-74253493-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-74253499-C-T		not specified	Uncertain significance (Jan 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPME1	protein_coding	protein_coding	ENST00000328257	14	83605

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000964	124557	0	3	124560	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.75	139	210	0.661	0.0000106	2525
Missense in Polyphen		21	74.094	0.28342		885
Synonymous	1.92	47	67.0	0.701	0.00000305	720
Loss of Function	4.40	1	24.5	0.0408	0.00000133	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000995	0.0000994
East Asian	0.00	0.00
Finnish	0.0000467	0.0000464
European (Non-Finnish)	0.00000960	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Demethylates proteins that have been reversibly carboxymethylated. Demethylates PPP2CB (in vitro) and PPP2CA. Binding to PPP2CA displaces the manganese ion and inactivates the enzyme. {ECO:0000269|PubMed:10318862}.
• Pathway: Cyclin A/B1/B2 associated events during G2/M transition;G2/M Transition;Mitotic G2-G2/M phases;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Intolerance Scores

• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• pHI: 0.248
• hipred: Y
• hipred_score: 0.827
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppme1
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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)

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;protein demethylation;negative regulation of phosphoprotein phosphatase activity
• Cellular component: nucleoplasm
• Molecular function: protein phosphatase inhibitor activity;protein binding;protein phosphatase regulator activity;protein kinase binding;protein phosphatase binding;cadherin binding;protein phosphatase 2A binding;protein C-terminal methylesterase activity