PPM1G

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

Basic information

Region (hg38): 2:27381195-27409591

Links

ENSG00000115241NCBI:5496OMIM:605119HGNC:9278Uniprot:O15355AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
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)2229090
2-27381616-T-C not specified Uncertain significance (Aug 13, 2021)2229288
2-27381703-G-C not specified Uncertain significance (Oct 02, 2023)3217342
2-27383552-T-G not specified Uncertain significance (Aug 16, 2022)2307577
2-27383582-T-C not specified Uncertain significance (Sep 25, 2023)3217346
2-27384740-T-C not specified Uncertain significance (Oct 26, 2021)2405264
2-27384749-C-T not specified Uncertain significance (Feb 23, 2023)2467654
2-27384845-G-A not specified Uncertain significance (Jun 06, 2023)2514186
2-27384903-T-A not specified Uncertain significance (Apr 18, 2023)2538307
2-27384917-T-G not specified Uncertain significance (Jan 02, 2024)3217345
2-27384999-C-T not specified Uncertain significance (Jul 10, 2024)3423669
2-27385749-T-C not specified Uncertain significance (Feb 27, 2023)2490097
2-27385768-T-C not specified Uncertain significance (Dec 17, 2023)3217344
2-27385855-T-C not specified Uncertain significance (Jun 24, 2022)2296909
2-27386252-T-C not specified Uncertain significance (Nov 03, 2023)3217343
2-27409396-G-T not specified Uncertain significance (Aug 14, 2024)3423670

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PPM1Gprotein_codingprotein_codingENST00000344034 1028494
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9600.0396125739091257480.0000358
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.341362980.4560.00001543605
Missense in Polyphen457.8750.069115632
Synonymous1.79901140.7870.000006221037
Loss of Function4.17427.70.1440.00000168312

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004570.000272
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00002640.0000264
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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