PPM1F

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

Basic information

Region (hg38): 22:21919425-21952848

Links

ENSG00000100034 ∙ NCBI:9647 ∙ OMIM:619309 ∙ HGNC:19388 ∙ Uniprot:P49593 ∙ 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 PPM1F gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPM1F 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	7	7	15
missense			24	2	6	32
nonsense						0
start loss						0
frameshift						0
inframe indel			2		1	3
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding				5	3	8
Total	0	0	27	14	17

Variants in PPM1F

This is a list of pathogenic ClinVar variants found in the PPM1F region.

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

Position	Type	Phenotype	Significance	ClinVar
22-21923112-G-C			Benign (Jan 16, 2024)
22-21923168-G-A		not specified	Uncertain significance (Oct 26, 2024)
22-21923195-T-C		not specified	Uncertain significance (Oct 25, 2024)
22-21923198-A-C			Benign (Jan 29, 2024)
22-21923236-C-T			Likely benign (Apr 14, 2023)
22-21923264-C-T			Uncertain significance (Nov 27, 2023)
22-21923289-C-T		not specified	Uncertain significance (Apr 24, 2024)
22-21923294-C-T			Likely benign (Nov 13, 2023)
22-21923300-C-T		not specified	Uncertain significance (Jan 06, 2023)
22-21923302-G-A			Benign (Jan 22, 2024)
22-21923325-G-A		not specified	Uncertain significance (Feb 17, 2023)
22-21923411-G-A		not specified	Uncertain significance (Apr 09, 2024)
22-21923420-C-T		not specified	Uncertain significance (Apr 12, 2022)
22-21923429-G-C			Uncertain significance (May 19, 2022)
22-21923433-C-T			Uncertain significance (Aug 14, 2023)
22-21923440-C-G			Likely benign (Dec 21, 2023)
22-21923481-C-A			Likely benign (Oct 13, 2023)
22-21925556-C-T			Benign (Aug 04, 2023)
22-21925585-G-T			Benign (Jan 25, 2024)
22-21925592-G-A		not specified	Uncertain significance (May 25, 2022)
22-21925650-G-A			Uncertain significance (Dec 28, 2021)
22-21925651-C-A			Likely benign (Aug 07, 2022)
22-21931130-G-T			Likely benign (Jul 28, 2023)
22-21931132-G-A			Likely benign (Jun 10, 2022)
22-21931141-C-A			Likely benign (Aug 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPM1F	protein_coding	protein_coding	ENST00000263212	7	33417

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00388	0.989	125723	0	13	125736	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	224	286	0.782	0.0000184	2908
Missense in Polyphen		60	108.68	0.5521		1085
Synonymous	0.989	113	127	0.888	0.00000904	950
Loss of Function	2.34	7	17.6	0.398	8.39e-7	186

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000711	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dephosphorylates and concomitantly deactivates CaM- kinase II activated upon autophosphorylation, and CaM-kinases IV and I activated upon phosphorylation by CaM-kinase kinase. Promotes apoptosis.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.652
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.15

Haploinsufficiency Scores

• pHI: 0.947
• hipred: Y
• hipred_score: 0.550
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppm1f
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: ppm1f
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: apoptotic

Gene ontology

• Biological process: negative regulation of protein kinase activity;positive regulation of gene expression;positive regulation of epithelial cell migration;positive regulation of cell-substrate adhesion;histone dephosphorylation;positive regulation of cell migration;negative regulation of peptidyl-serine phosphorylation;cellular response to drug;peptidyl-threonine dephosphorylation;positive regulation of cysteine-type endopeptidase activity involved in apoptotic process;negative regulation of protein kinase activity by regulation of protein phosphorylation;negative regulation of transcription, DNA-templated;positive regulation of growth;positive regulation of chemotaxis;negative regulation of protein transport;positive regulation of stress fiber assembly;positive regulation of focal adhesion assembly;peptidyl-serine dephosphorylation;intrinsic apoptotic signaling pathway;regulation of cellular protein localization;negative regulation of cell-cell adhesion mediated by cadherin
• Cellular component: cytosol;protein-containing complex;perinuclear region of cytoplasm
• Molecular function: protein serine/threonine phosphatase activity;magnesium-dependent protein serine/threonine phosphatase activity;protein binding;protein tyrosine/serine/threonine phosphatase activity;calmodulin-dependent protein phosphatase activity;metal ion binding