PPM1G

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

Basic information

Region (hg38): 2:27381195-27409591

Links

ENSG00000115241 ∙ NCBI:5496 ∙ OMIM:605119 ∙ HGNC:9278 ∙ Uniprot:O15355 ∙ 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 PPM1G gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPM1G 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in PPM1G

This is a list of pathogenic ClinVar variants found in the PPM1G region.

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

Position	Type	Phenotype	Significance	ClinVar
2-27381615-T-G		not specified	Uncertain significance (Aug 13, 2021)
2-27381616-T-C		not specified	Uncertain significance (Aug 13, 2021)
2-27381703-G-C		not specified	Uncertain significance (Oct 02, 2023)
2-27383552-T-G		not specified	Uncertain significance (Aug 16, 2022)
2-27383582-T-C		not specified	Uncertain significance (Sep 25, 2023)
2-27384740-T-C		not specified	Uncertain significance (Oct 26, 2021)
2-27384749-C-T		not specified	Uncertain significance (Feb 23, 2023)
2-27384845-G-A		not specified	Uncertain significance (Jun 06, 2023)
2-27384903-T-A		not specified	Uncertain significance (Apr 18, 2023)
2-27384917-T-G		not specified	Uncertain significance (Jan 02, 2024)
2-27384999-C-T		not specified	Uncertain significance (Jul 10, 2024)
2-27385749-T-C		not specified	Uncertain significance (Feb 27, 2023)
2-27385768-T-C		not specified	Uncertain significance (Dec 17, 2023)
2-27385855-T-C		not specified	Uncertain significance (Jun 24, 2022)
2-27386252-T-C		not specified	Uncertain significance (Nov 03, 2023)
2-27409396-G-T		not specified	Uncertain significance (Aug 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPM1G	protein_coding	protein_coding	ENST00000344034	10	28494

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.960	0.0396	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.34	136	298	0.456	0.0000154	3605
Missense in Polyphen		4	57.875	0.069115		632
Synonymous	1.79	90	114	0.787	0.00000622	1037
Loss of Function	4.17	4	27.7	0.144	0.00000168	312

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000457	0.000272
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: mRNA Processing (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.100
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.999
• hipred: Y
• hipred_score: 0.728
• ghis: 0.641

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppm1g
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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)

Zebrafish Information Network

• Gene name: ppm1g
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: protein dephosphorylation;cell cycle arrest;peptidyl-threonine dephosphorylation
• Cellular component: nucleus;nucleoplasm;cytoplasm;membrane
• Molecular function: protein serine/threonine phosphatase activity;magnesium-dependent protein serine/threonine phosphatase activity;protein binding;metal ion binding