PPM1M

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

Basic information

Region (hg38): 3:52245759-52250599

Links

ENSG00000164088 ∙ NCBI:132160 ∙ OMIM:608979 ∙ HGNC:26506 ∙ Uniprot:Q96MI6 ∙ 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 PPM1M gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPM1M 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in PPM1M

This is a list of pathogenic ClinVar variants found in the PPM1M region.

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

Position	Type	Phenotype	Significance	ClinVar
3-52245837-T-C		not specified	Uncertain significance (Jul 19, 2022)
3-52245921-C-G		not specified	Uncertain significance (Apr 09, 2024)
3-52245990-C-G		not specified	Uncertain significance (Sep 01, 2021)
3-52246011-C-G		not specified	Uncertain significance (Jan 23, 2024)
3-52246026-C-T		not specified	Uncertain significance (Jan 17, 2023)
3-52247017-G-T		not specified	Uncertain significance (Jan 10, 2023)
3-52247029-C-G		not specified	Uncertain significance (Nov 15, 2021)
3-52247064-C-T		not specified	Uncertain significance (May 10, 2022)
3-52247065-G-A		not specified	Uncertain significance (Aug 02, 2022)
3-52247202-G-A		not specified	Uncertain significance (Jan 17, 2024)
3-52247719-A-G		not specified	Uncertain significance (Nov 29, 2023)
3-52248184-C-T		not specified	Uncertain significance (Aug 30, 2022)
3-52248659-T-G		not specified	Uncertain significance (Jul 19, 2023)
3-52248660-C-T		not specified	Uncertain significance (Jun 16, 2024)
3-52249184-T-C		not specified	Uncertain significance (Mar 28, 2024)
3-52249246-T-C		not specified	Uncertain significance (Aug 17, 2022)
3-52249286-G-A		not specified	Uncertain significance (Apr 09, 2024)
3-52249318-C-T		not specified	Uncertain significance (Dec 19, 2023)
3-52249752-G-A		not specified	Uncertain significance (May 22, 2023)
3-52249790-G-T		not specified	Uncertain significance (Apr 07, 2022)
3-52249791-G-A		not specified	Uncertain significance (Jun 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPM1M	protein_coding	protein_coding	ENST00000409502	7	4773

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000906	0.945	125561	0	48	125609	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.371	126	138	0.911	0.00000806	1584
Missense in Polyphen		56	71.111	0.7875		785
Synonymous	-0.263	58	55.5	1.04	0.00000291	489
Loss of Function	1.70	7	13.8	0.506	6.80e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000417	0.000415
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000218
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000182	0.000176
Middle Eastern	0.000218	0.000218
South Asian	0.000362	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.731
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.19

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.254
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.402

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppm1m

Gene ontology

• Biological process: protein dephosphorylation
• Cellular component: nucleus
• Molecular function: protein serine/threonine phosphatase activity;magnesium-dependent protein serine/threonine phosphatase activity;manganese ion binding