PPM1N
Basic information
Region (hg38): 19:45488777-45503129
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 21 | 23 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 21 | 2 | 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) | ||
19-45488970-C-T | Uncertain significance (Nov 06, 2023) |
GnomAD
Source:
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:
Haploinsufficiency Scores
- pHI
- 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
- Phenotype
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