PPP1R12A
Basic information
Region (hg38): 12:79773563-79935460
Previous symbols: [ "MYPT1" ]
Links
Phenotypes
GenCC
Source:
- genitourinary and/or brain malformation syndrome (Strong), mode of inheritance: AD
- genitourinary and/or brain malformation syndrome (Strong), mode of inheritance: AD
- genitourinary and/or brain malformation syndrome (Strong), mode of inheritance: AD
- genitourinary and/or brain malformation syndrome (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Genitourinary and/or/brain malformation syndrome | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Genitourinary; Gastrointestinal; Neurologic | 31883643 |
ClinVar
This is a list of variants' phenotypes submitted to
- Genitourinary and/or brain malformation syndrome (4 variants)
- PPP1R12A-related disorder (2 variants)
- not provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R12A 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 | 21 | |||||
missense | 60 | 11 | 77 | |||
nonsense | 6 | |||||
start loss | 0 | |||||
frameshift | 8 | |||||
inframe indel | 5 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 3 | 4 | 2 | 9 | ||
non coding | 10 | |||||
Total | 5 | 9 | 73 | 22 | 20 |
Variants in PPP1R12A
This is a list of pathogenic ClinVar variants found in the PPP1R12A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
12-79775930-T-A | PPP1R12A-related disorder | Uncertain significance (Oct 01, 2022) | ||
12-79775976-C-T | Likely pathogenic (May 23, 2024) | |||
12-79779349-C-T | Benign (May 01, 2022) | |||
12-79781840-C-A | Uncertain significance (Mar 29, 2021) | |||
12-79781858-T-C | Uncertain significance (Sep 03, 2023) | |||
12-79781867-A-G | Benign (Aug 30, 2023) | |||
12-79781874-T-C | Likely benign (Nov 22, 2022) | |||
12-79786420-T-C | Inborn genetic diseases | Conflicting classifications of pathogenicity (Jun 02, 2023) | ||
12-79786428-AT-A | Genitourinary and/or brain malformation syndrome | Likely pathogenic (-) | ||
12-79786438-G-C | Inborn genetic diseases | Uncertain significance (Aug 04, 2022) | ||
12-79788632-T-C | Uncertain significance (Nov 23, 2022) | |||
12-79788648-CT-C | Genitourinary and/or brain malformation syndrome | Likely pathogenic (Aug 01, 2021) | ||
12-79788655-A-C | Inborn genetic diseases | Uncertain significance (Dec 17, 2021) | ||
12-79788661-G-C | Genitourinary and/or brain malformation syndrome | Uncertain significance (May 27, 2020) | ||
12-79788667-T-A | Uncertain significance (Nov 25, 2020) | |||
12-79788681-C-G | Inborn genetic diseases | Conflicting classifications of pathogenicity (Mar 07, 2023) | ||
12-79788749-A-G | PPP1R12A-related disorder | Likely benign (Aug 12, 2024) | ||
12-79788751-C-T | Inborn genetic diseases | Uncertain significance (Dec 22, 2023) | ||
12-79788752-G-A | Genitourinary and/or brain malformation syndrome | Pathogenic (Feb 02, 2023) | ||
12-79788772-CT-C | Genitourinary and/or brain malformation syndrome | Likely pathogenic (Jun 15, 2020) | ||
12-79788773-TG-T | Genitourinary and/or brain malformation syndrome | Likely pathogenic (Sep 03, 2020) | ||
12-79790482-G-A | Inborn genetic diseases | Conflicting classifications of pathogenicity (Jan 15, 2024) | ||
12-79793874-T-C | Uncertain significance (Mar 18, 2022) | |||
12-79793882-GA-G | PPP1R12A-related disorder | Pathogenic (Dec 09, 2023) | ||
12-79793893-T-C | Likely benign (Dec 01, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PPP1R12A | protein_coding | protein_coding | ENST00000450142 | 25 | 161898 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 4.82e-8 | 124534 | 0 | 28 | 124562 | 0.000112 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.64 | 342 | 509 | 0.671 | 0.0000254 | 6674 |
Missense in Polyphen | 133 | 259.93 | 0.51167 | 3302 | ||
Synonymous | 0.186 | 173 | 176 | 0.982 | 0.00000841 | 1942 |
Loss of Function | 6.81 | 3 | 59.8 | 0.0501 | 0.00000338 | 772 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000198 | 0.000198 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000214 | 0.000213 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Key regulator of protein phosphatase 1C (PPP1C). Mediates binding to myosin. As part of the PPP1C complex, involved in dephosphorylation of PLK1. Capable of inhibiting HIF1AN- dependent suppression of HIF1A activity. {ECO:0000269|PubMed:18477460, ECO:0000269|PubMed:19245366, ECO:0000269|PubMed:20354225}.;
- Pathway
- Platelet activation - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Focal Adhesion;Regulation of Actin Cytoskeleton;Signal Transduction;RHO GTPases Activate ROCKs;RHO GTPases activate PAKs;RHO GTPases activate PKNs;RHO GTPases activate CIT;RHO GTPase Effectors;Signaling by Rho GTPases;Regulation of PLK1 Activity at G2/M Transition;G2/M Transition;Mitotic G2-G2/M phases;Cell Cycle;TNFalpha;Integrin-linked kinase signaling;Cell Cycle, Mitotic;PLK1 signaling events;RhoA signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.418
Intolerance Scores
- loftool
- rvis_EVS
- -0.86
- rvis_percentile_EVS
- 10.85
Haploinsufficiency Scores
- pHI
- 0.983
- hipred
- Y
- hipred_score
- 0.745
- ghis
- 0.648
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.329
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppp1r12a
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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); digestive/alimentary phenotype; renal/urinary system phenotype; immune system phenotype; growth/size/body region phenotype; muscle phenotype;
Zebrafish Information Network
- Gene name
- ppp1r12a
- Affected structure
- neuroepithelial cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased accumulation
Gene ontology
- Biological process
- mitotic cell cycle;protein dephosphorylation;centrosome cycle;signal transduction;regulation of cell adhesion;regulation of myosin-light-chain-phosphatase activity;positive regulation of myosin-light-chain-phosphatase activity;cellular response to drug;negative regulation of catalytic activity;positive regulation of transcription by RNA polymerase II;regulation of nucleocytoplasmic transport;regulation of establishment of endothelial barrier
- Cellular component
- kinetochore;nucleoplasm;cytoplasm;centrosome;cytosol;focal adhesion;actin cytoskeleton;Z disc;A band;contractile fiber;PTW/PP1 phosphatase complex
- Molecular function
- enzyme inhibitor activity;protein binding;phosphatase regulator activity;protein kinase binding;14-3-3 protein binding