PPM1H

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

Basic information

Region (hg38): 12:62643994-62935150

Previous symbols: [ "ARHCL1" ]

Links

ENSG00000111110 ∙ NCBI:57460 ∙ OMIM:616016 ∙ HGNC:18583 ∙ Uniprot:Q9ULR3 ∙ 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 PPM1H gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPM1H 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			37		1	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	0	1

Variants in PPM1H

This is a list of pathogenic ClinVar variants found in the PPM1H region.

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

Position	Type	Phenotype	Significance	ClinVar
12-62648540-G-T		not specified	Uncertain significance (Jul 30, 2024)
12-62648563-T-C		not specified	Uncertain significance (Jun 17, 2024)
12-62648572-G-A		not specified	Uncertain significance (Oct 26, 2022)
12-62648604-C-T		not specified	Uncertain significance (Jan 31, 2022)
12-62648625-G-A		not specified	Uncertain significance (Aug 17, 2022)
12-62648626-C-A		not specified	Uncertain significance (Aug 17, 2022)
12-62648632-T-C		not specified	Uncertain significance (Feb 08, 2023)
12-62667304-T-C		not specified	Uncertain significance (Jul 05, 2023)
12-62689737-T-C		not specified	Uncertain significance (Dec 17, 2023)
12-62689803-G-A		not specified	Uncertain significance (Aug 16, 2021)
12-62693940-T-C		not specified	Uncertain significance (Dec 04, 2024)
12-62693985-A-G		not specified	Uncertain significance (Aug 19, 2024)
12-62720178-T-C		not specified	Uncertain significance (Dec 18, 2023)
12-62720253-T-C		not specified	Uncertain significance (Sep 17, 2021)
12-62737518-T-C		not specified	Uncertain significance (Aug 26, 2024)
12-62737521-C-T		not specified	Uncertain significance (Mar 13, 2023)
12-62737569-T-C		not specified	Uncertain significance (Apr 04, 2023)
12-62788274-A-G		not specified	Uncertain significance (Dec 18, 2023)
12-62788322-C-T		not specified	Uncertain significance (Nov 14, 2024)
12-62788329-T-A		not specified	Uncertain significance (Mar 14, 2023)
12-62801830-C-T		not specified	Uncertain significance (Mar 15, 2024)
12-62801877-T-A		not specified	Uncertain significance (Feb 28, 2024)
12-62801887-A-C		not specified	Uncertain significance (Mar 18, 2024)
12-62801922-C-A		not specified	Uncertain significance (Jul 13, 2021)
12-62801959-T-G			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPM1H	protein_coding	protein_coding	ENST00000228705	10	291056

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.792	0.208	124642	0	8	124650	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	223	296	0.753	0.0000169	3282
Missense in Polyphen		79	120.81	0.65389		1325
Synonymous	0.192	123	126	0.978	0.00000783	1063
Loss of Function	3.64	4	22.8	0.176	0.00000115	278

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000392	0.0000354
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dephosphorylates CDKN1B at 'Thr-187', thus removing a signal for proteasomal degradation. {ECO:0000269|PubMed:22586611}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.447
• hipred: Y
• hipred_score: 0.706
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.336

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppm1h

Gene ontology

• Biological process: protein dephosphorylation
• Cellular component: nucleus;nucleoplasm;cytoplasm;glutamatergic synapse
• Molecular function: phosphoprotein phosphatase activity;protein serine/threonine phosphatase activity;magnesium-dependent protein serine/threonine phosphatase activity