PPM1N

protein phosphatase, Mg2+/Mn2+ dependent 1N (putative), the group of Protein phosphatases, Mg2+/Mn2+ dependent

Basic information

Region (hg38): 19:45488776-45502513

Links

ENSG00000213889 ∙ NCBI:147699 ∙ ∙ HGNC:26845 ∙ Uniprot:Q8N819 ∙ 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 PPM1N gene.

• Inborn genetic diseases (16 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPM1N 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			15	1		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	15	1	0

Variants in PPM1N

This is a list of pathogenic ClinVar variants found in the PPM1N region.

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

Position	Type	Phenotype	Significance	ClinVar
19-45488817-A-G			Benign (May 16, 2021)
19-45488840-CA-C		not specified	Likely benign (Feb 06, 2017)
19-45488847-C-A		Spastic paraplegia	Likely pathogenic (Dec 30, 2020)
19-45488853-G-A		Spastic paraplegia	Uncertain significance (Sep 21, 2017)
19-45488862-C-T		not specified	Uncertain significance (Mar 28, 2017)
19-45488887-C-G		Spastic paraplegia	Likely benign (Nov 12, 2023)
19-45488888-C-T		Spastic paraplegia • Hereditary spastic paraplegia 12	Uncertain significance (Nov 19, 2023)
19-45488889-G-A		Hereditary spastic paraplegia 12	Uncertain significance (Jan 12, 2018)
19-45488896-C-T		Spastic paraplegia	Likely benign (Apr 07, 2022)
19-45488902-C-T		Spastic paraplegia	Uncertain significance (Nov 04, 2021)
19-45488903-G-A		Spastic paraplegia • Inborn genetic diseases	Conflicting classifications of pathogenicity (May 01, 2023)
19-45488905-C-T		Spastic paraplegia	Likely benign (May 10, 2022)
19-45488906-G-A			Uncertain significance (Jan 14, 2019)
19-45488913-C-T		not specified	Uncertain significance (Mar 13, 2024)
19-45488915-C-T		Spastic paraplegia	Uncertain significance (May 08, 2022)
19-45488916-G-A		not specified • Spastic paraplegia	Benign/Likely benign (Dec 18, 2023)
19-45488923-G-A		Spastic paraplegia	Likely benign (Jan 12, 2023)
19-45488940-G-A		Spastic paraplegia	Uncertain significance (Feb 06, 2022)
19-45488944-C-T		Spastic paraplegia	Likely benign (Jul 22, 2023)
19-45488945-G-A		Spastic paraplegia	Uncertain significance (Aug 23, 2023)
19-45488945-G-T		Spastic paraplegia	Uncertain significance (Jan 31, 2018)
19-45488954-C-T		not specified • Spastic paraplegia	Benign (Nov 27, 2023)
19-45488955-G-A		Spastic paraplegia	Likely benign (Nov 22, 2022)
19-45488969-T-C		Spastic paraplegia	Uncertain significance (Dec 02, 2021)
19-45488974-A-T		Spastic paraplegia	Uncertain significance (May 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPM1N	protein_coding	protein_coding	ENST00000451287	5	13734

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000533	0.443	124585	0	59	124644	0.000237

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	153	201	0.762	0.00000946	2623
Missense in Polyphen		48	63.717	0.75333		833
Synonymous	1.10	76	89.2	0.852	0.00000439	953
Loss of Function	0.545	9	10.9	0.822	4.73e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000609	0.000591
Ashkenazi Jewish	0.000104	0.0000994
East Asian	0.00191	0.00189
Finnish	0.00	0.00
European (Non-Finnish)	0.0000555	0.0000531
Middle Eastern	0.00191	0.00189
South Asian	0.0000339	0.0000327
Other	0.000175	0.000165

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.247
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppm1n

Gene ontology

• Biological process: protein dephosphorylation
• Cellular component: nucleus;cytosol
• Molecular function: magnesium ion binding;protein serine/threonine phosphatase activity;magnesium-dependent protein serine/threonine phosphatase activity;manganese ion binding