PPM1J

protein-coding

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

Gene summary

This gene encodes the serine/threonine protein phosphatase. The mouse homolog of this gene apparently belongs to the protein phosphatase 2C family of genes. The exact function of this gene is not yet known. [provided by RefSeq, Jul 2008]

MANE transcript

NM_005167.7

Inheritance

—

ClinVar variants

U:97B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chr1:112,709,994-112,715,332

External References & Databases

Ensembl (ENSG00000155367)

Transcript & Mutation Effects

hg38 • Region Span ~5.3 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 PPM1J variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 92

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005167.7. 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			2 clinvar	1 clinvar		3
missense			93 clinvar			93
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	97	1	0	98

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005167.7	RefSeq	NP_005158.5	10	MANE Select
ENST00000309276.11	Ensembl	ENSP00000308926.6	10	MANE Select
ENST00000464951.1	Ensembl	ENSP00000475711.1	9	Standard
ENST00000471106.5	Ensembl	ENSP00000474405.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Wnt Signaling Pathway and Pluripotency
Direct p53 effectors

Biological Process

protein dephosphorylation

Molecular Function

protein serine/threonine phosphatase activity
magnesium-dependent protein serine/threonine phosphatase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000309276
Coding exons: 10
Length: 5484
Individuals with no LoFs: 125495
Homozygous LoFs: 1
Heterozygous LoFs: 250
Defined: 125746
p: 0.000999

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.657	247	278	0.889	0.0000158	3181
Missense (PolyPhen)		87	98.209	0.88587		1115
Synonymous	1.71	90	113	0.795	0.00000594	1099
Loss of Function	1.37	17	24.3	0.700	0.00000148	243

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0022	0.0022	notable
Latino/Admixed American	0.0014	0.0014	notable
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.0038	0.0038	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00056	0.00055	rare
South Asian	0.0011	0.0010	notable
Other	0.00068	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0838

Intolerance Scores

LoFtool: 0.919
RVIS EVS: 0.66
RVIS percentile EVS: 84.55

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.506

Gene Damage Prediction

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