PPM1B

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

Basic information

Region (hg38): 2:44167968-44244384

Links

ENSG00000138032 ∙ NCBI:5495 ∙ OMIM:603770 ∙ HGNC:9276 ∙ Uniprot:O75688 ∙ 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 PPM1B gene.

• Inborn genetic diseases (14 variants)
• not provided (8 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPM1B 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				4		4
missense			12	4		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	12	8	2

Variants in PPM1B

This is a list of pathogenic ClinVar variants found in the PPM1B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-44201251-G-A			Likely benign (May 17, 2018)
2-44201419-C-T		not specified	Uncertain significance (Dec 27, 2023)
2-44201595-A-T			Likely benign (May 25, 2018)
2-44201612-T-C		not specified	Uncertain significance (Jun 16, 2023)
2-44201632-T-C		not specified	Uncertain significance (Jan 08, 2024)
2-44201643-C-T			Likely benign (Dec 09, 2017)
2-44201657-G-A		not specified	Uncertain significance (Jun 30, 2022)
2-44201669-A-G		not specified	Uncertain significance (Jul 21, 2021)
2-44201677-G-A		not specified	Uncertain significance (Jul 12, 2022)
2-44201680-C-G		not specified	Uncertain significance (May 09, 2022)
2-44201693-C-T		not specified	Uncertain significance (Dec 09, 2023)
2-44201731-G-A		not specified	Uncertain significance (Sep 13, 2023)
2-44201767-C-G		not specified	Uncertain significance (Sep 29, 2023)
2-44201800-G-A		not specified	Uncertain significance (Jun 29, 2023)
2-44202008-A-G		not specified	Uncertain significance (Nov 07, 2022)
2-44202017-A-G		not specified	Uncertain significance (Mar 29, 2022)
2-44202030-C-G		not specified	Uncertain significance (Jan 18, 2022)
2-44209312-G-C		not specified	Uncertain significance (Jan 03, 2022)
2-44209318-C-T		not specified	Uncertain significance (Jul 12, 2022)
2-44217978-A-G		not specified	Uncertain significance (Nov 27, 2023)
2-44217986-C-T			Likely benign (Feb 25, 2018)
2-44217998-G-A		not specified	Uncertain significance (Oct 16, 2023)
2-44218020-C-T		not specified	Uncertain significance (Aug 16, 2021)
2-44218530-G-A		not specified	Likely benign (Sep 16, 2021)
2-44218542-GTTTTA-G			Benign (Jun 25, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPM1B	protein_coding	protein_coding	ENST00000282412	5	76416

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00908	0.989	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.600	236	263	0.896	0.0000136	3149
Missense in Polyphen		45	95.308	0.47215		1118
Synonymous	0.701	83	91.5	0.907	0.00000465	915
Loss of Function	2.68	7	19.9	0.352	0.00000116	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000156	0.000156
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000128	0.000114
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enzyme with a broad specificity. Dephosphorylates CDK2 and CDK6 in vitro. Dephosphorylates PRKAA1 and PRKAA2. Inhibits TBK1-mediated antiviral signaling by dephosphorylating it at 'Ser- 172'. Plays an important role in the termination of TNF-alpha- mediated NF-kappa-B activation through dephosphorylating and inactivating IKBKB/IKKB. {ECO:0000269|PubMed:18930133, ECO:0000269|PubMed:22750291}.
• Pathway: MAPK signaling pathway - Homo sapiens (human);MAPK Signaling Pathway;Cytokine Signaling in Immune system;Immune System;ISG15 antiviral mechanism;Antiviral mechanism by IFN-stimulated genes;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.212

Intolerance Scores

• loftool: 0.424
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.51

Haploinsufficiency Scores

• pHI: 1.00
• hipred: Y
• hipred_score: 0.792
• ghis: 0.638

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.965

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppm1b
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cellular phenotype

Gene ontology

• Biological process: protein dephosphorylation;N-terminal protein myristoylation;negative regulation of interferon-beta production;peptidyl-threonine dephosphorylation;negative regulation of I-kappaB kinase/NF-kappaB signaling;negative regulation of defense response to virus;negative regulation of NIK/NF-kappaB signaling
• Cellular component: nucleus;nucleolus;cytosol;membrane
• Molecular function: magnesium ion binding;protein serine/threonine phosphatase activity;magnesium-dependent protein serine/threonine phosphatase activity;protein binding;manganese ion binding