PPM1J

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

Basic information

Region (hg38): 1:112709994-112715332

Links

ENSG00000155367 ∙ NCBI:333926 ∙ OMIM:609957 ∙ HGNC:20785 ∙ Uniprot:Q5JR12 ∙ 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 PPM1J gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPM1J 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				1		1
missense			45		1	46
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	47	1	1

Variants in PPM1J

This is a list of pathogenic ClinVar variants found in the PPM1J region.

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

Position	Type	Phenotype	Significance	ClinVar
1-112710228-G-C		not specified	Uncertain significance (Feb 28, 2023)
1-112710254-C-T		not specified	Uncertain significance (Apr 11, 2023)
1-112710478-T-C		not specified	Uncertain significance (May 17, 2023)
1-112710484-G-C		not specified	Uncertain significance (Apr 26, 2023)
1-112710515-C-A		not specified	Uncertain significance (Feb 28, 2024)
1-112710560-C-T		not specified	Uncertain significance (Feb 13, 2025)
1-112710568-T-G		not specified	Uncertain significance (Mar 03, 2025)
1-112710589-T-G		not specified	Uncertain significance (Feb 28, 2023)
1-112710592-G-A		not specified	Uncertain significance (Feb 13, 2023)
1-112710754-C-T		not specified	Uncertain significance (Aug 04, 2024)
1-112710756-G-C			Likely benign (Mar 01, 2023)
1-112710758-A-C		not specified	Uncertain significance (Oct 03, 2023)
1-112710836-T-C		not specified	Uncertain significance (Mar 01, 2024)
1-112710838-G-C		not specified	Uncertain significance (Jan 07, 2025)
1-112711016-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-112711067-A-G		not specified	Uncertain significance (Oct 25, 2023)
1-112711267-A-G		not specified	Uncertain significance (Nov 22, 2022)
1-112711287-C-T		not specified	Uncertain significance (Mar 13, 2023)
1-112711329-C-T		not specified	Uncertain significance (Jun 06, 2023)
1-112711330-G-A		not specified	Uncertain significance (Aug 17, 2022)
1-112711336-A-T		not specified	Uncertain significance (Feb 22, 2025)
1-112711341-A-C		not specified	Uncertain significance (Feb 22, 2025)
1-112711990-C-T		not specified	Uncertain significance (May 03, 2023)
1-112711991-G-A		not specified	Uncertain significance (Dec 28, 2024)
1-112712014-C-T		not specified	Uncertain significance (Mar 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPM1J	protein_coding	protein_coding	ENST00000309276	10	5484

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.25e-9	0.684	125495	1	250	125746	0.000999

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.657	247	278	0.889	0.0000158	3181
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00359	0.00358
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.00381	0.00376
Finnish	0.00	0.00
European (Non-Finnish)	0.000561	0.000545
Middle Eastern	0.00381	0.00376
South Asian	0.00109	0.00105
Other	0.000683	0.000652

dbNSFP

Source: dbNSFP

• Pathway: Wnt Signaling Pathway and Pluripotency;Direct p53 effectors (Consensus)

Recessive Scores

• pRec: 0.0838

Intolerance Scores

• loftool: 0.919
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.55

Haploinsufficiency Scores

• pHI: 0.400
• hipred: Y
• hipred_score: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.506

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppm1j
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: protein dephosphorylation
• Molecular function: protein serine/threonine phosphatase activity;magnesium-dependent protein serine/threonine phosphatase activity