PPM1M

protein-coding

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

Gene summary

Predicted to enable [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity and manganese ion binding activity. Predicted to be involved in protein dephosphorylation. Predicted to be located in nucleus. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_144641.4

Inheritance

—

ClinVar variants

U:71B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr3:52,245,759-52,250,599

External References & Databases

Ensembl (ENSG00000164088)

Transcript & Mutation Effects

hg38 • Region Span ~4.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PPM1M variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 66

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144641.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			66 clinvar	2 clinvar		68
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	71	2	0	73

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144641.4	RefSeq	NP_653242.3	10	MANE Select
ENST00000323588.9	Ensembl	ENSP00000319894.5	10	MANE Select
NM_001122870.3	RefSeq	NP_001116342.1	7	Standard
ENST00000296487.8	Ensembl	ENSP00000296487.4	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein dephosphorylation

Molecular Function

protein serine/threonine phosphatase activity
magnesium-dependent protein serine/threonine phosphatase activity
manganese ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409502
Coding exons: 7
Length: 4773
Individuals with no LoFs: 125561
Homozygous LoFs: 0
Heterozygous LoFs: 48
Defined: 125609
p: 0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.371	126	138	0.911	0.00000806	1584
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00036	0.00036	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.731
RVIS EVS: 0.2
RVIS percentile EVS: 67.19

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.402

Gene Damage Prediction

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