PPM1E

protein phosphatase, Mg2+/Mn2+ dependent 1E, the group of Protein phosphatases, Mg2+/Mn2+ dependent

Basic information

Region (hg38): 17:58755853-58985179

Links

ENSG00000175175 ∙ NCBI:22843 ∙ OMIM:619308 ∙ HGNC:19322 ∙ Uniprot:Q8WY54 ∙ 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 PPM1E gene.

• Inborn genetic diseases (26 variants)
• not provided (2 variants)
• Mulibrey nanism syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPM1E 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			25	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		1		1		2
Total	0	1	25	3	0

Variants in PPM1E

This is a list of pathogenic ClinVar variants found in the PPM1E region.

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

Position	Type	Phenotype	Significance	ClinVar
17-58756055-G-C		not specified	Uncertain significance (Feb 01, 2023)
17-58756071-C-A		not specified	Uncertain significance (Apr 19, 2023)
17-58756130-T-C		not specified	Uncertain significance (Aug 09, 2021)
17-58756136-C-T		not specified	Uncertain significance (Aug 09, 2021)
17-58756169-G-T		not specified	Uncertain significance (Jul 30, 2023)
17-58756215-T-A		not specified	Uncertain significance (Aug 09, 2021)
17-58756261-G-C		not specified	Uncertain significance (Oct 25, 2023)
17-58756331-T-G		not specified	Uncertain significance (Feb 03, 2022)
17-58756338-T-G		not specified	Uncertain significance (Feb 03, 2022)
17-58756341-C-T		not specified	Uncertain significance (Jul 05, 2023)
17-58756356-A-G		not specified	Uncertain significance (Jun 01, 2023)
17-58756362-C-A		not specified	Uncertain significance (Dec 20, 2023)
17-58756397-C-A		not specified	Uncertain significance (Feb 22, 2023)
17-58756428-G-T		not specified	Uncertain significance (Mar 28, 2023)
17-58965759-G-A		not specified	Uncertain significance (May 30, 2023)
17-58965768-T-C		not specified	Uncertain significance (Feb 07, 2023)
17-58965789-C-G		not specified	Uncertain significance (Dec 14, 2023)
17-58969570-T-C		not specified	Uncertain significance (Aug 02, 2023)
17-58969636-G-A		not specified	Uncertain significance (Mar 07, 2023)
17-58980213-A-G		not specified	Uncertain significance (Aug 02, 2022)
17-58980255-A-G		not specified	Uncertain significance (Oct 27, 2023)
17-58980525-C-T		not specified	Uncertain significance (Nov 09, 2021)
17-58980537-T-G		not specified	Uncertain significance (May 06, 2022)
17-58980655-A-G		not specified	Uncertain significance (Dec 13, 2023)
17-58980729-C-G		not specified	Uncertain significance (Jun 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPM1E	protein_coding	protein_coding	ENST00000308249	7	225754

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.988	0.0124	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.66	250	400	0.625	0.0000203	4937
Missense in Polyphen		50	146.35	0.34164		1774
Synonymous	1.30	137	158	0.869	0.00000815	1473
Loss of Function	4.23	3	26.5	0.113	0.00000113	365

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000107	0.0000927
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000904	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein phosphatase that inactivates multifunctional CaM kinases such as CAMK4 and CAMK2 (By similarity). Dephosphorylates and inactivates PAK. May play a role in the inhibition of actin fiber stress breakdown and in morphological changes driven by TNK2/CDC42. Dephosphorylates PRKAA2 (By similarity). {ECO:0000250, ECO:0000269|PubMed:11864573}.

Recessive Scores

• pRec: 0.0904

Intolerance Scores

• loftool: 0.245
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.996
• hipred: Y
• hipred_score: 0.752
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.606

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppm1e

Zebrafish Information Network

• Gene name: ppm1e
• Affected structure: diencephalon
• Phenotype tag: abnormal
• Phenotype quality: apoptotic

Gene ontology

• Biological process: negative regulation of protein kinase activity;cellular response to drug;peptidyl-threonine dephosphorylation;positive regulation of stress fiber assembly
• Cellular component: nucleus;nucleolus;mitochondrion;protein-containing complex
• Molecular function: protein serine/threonine phosphatase activity;magnesium-dependent protein serine/threonine phosphatase activity;protein binding;metal ion binding