PPP2R3C
Basic information
Region (hg38): 14:35085467-35122517
Previous symbols: [ "C14orf10" ]
Links
Phenotypes
GenCC
Source:
- gonadal dysgenesis, dysmorphic facies, retinal dystrophy, and myopathy (Limited), mode of inheritance: AR
- spermatogenic failure 36 (Limited), mode of inheritance: AD
- gonadal dysgenesis, dysmorphic facies, retinal dystrophy, and myopathy (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Spermatogenic failure 36; Myoectodermal gonadal dysgenesis syndrome | AD/AR | 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 | Audiologic/Otolaryngologic; Craniofacial; Dermatologic; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic | 30893644; 34750818; 35812758 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (45 variants)
- Gonadal_dysgenesis,_dysmorphic_facies,_retinal_dystrophy,_and_myopathy (7 variants)
- Spermatogenic_failure_36 (4 variants)
- PPP2R3C-related_disorder (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP2R3C gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017917.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 44 | 49 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 3 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 4 | 0 | 48 | 1 | 0 |
Highest pathogenic variant AF is 0.0000767094
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPP2R3C | protein_coding | protein_coding | ENST00000261475 | 13 | 37051 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 6.82e-9 | 0.881 | 125697 | 0 | 50 | 125747 | 0.000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.35 | 168 | 225 | 0.747 | 0.0000108 | 3008 |
| Missense in Polyphen | 51 | 72.51 | 0.70335 | 1015 | ||
| Synonymous | -0.830 | 90 | 80.5 | 1.12 | 0.00000407 | 777 |
| Loss of Function | 1.72 | 17 | 26.6 | 0.640 | 0.00000112 | 374 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000279 | 0.000279 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000273 | 0.000272 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000284 | 0.000281 |
| Middle Eastern | 0.000273 | 0.000272 |
| South Asian | 0.000215 | 0.000196 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: May regulate MCM3AP phosphorylation through phosphatase recruitment. May act as a negative regulator of ABCB1 expression and function through the dephosphorylation of ABCB1 by TFPI2/PPP2R3C complex. May play a role in the activation-induced cell death of B-cells. {ECO:0000250|UniProtKB:Q9JK24, ECO:0000269|PubMed:24333728}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Dopaminergic synapse - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway
(Consensus)
Recessive Scores
- pRec
- 0.132
Intolerance Scores
- loftool
- 0.530
- rvis_EVS
- -0.47
- rvis_percentile_EVS
- 23.25
Haploinsufficiency Scores
- pHI
- 0.177
- hipred
- N
- hipred_score
- 0.450
- ghis
- 0.609
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.941
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppp2r3c
- Phenotype
- immune system phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- microtubule cytoskeleton organization;B cell homeostasis;regulation of antimicrobial humoral response;cortical cytoskeleton organization;activation of protein kinase activity;regulation of dephosphorylation;T cell homeostasis;positive regulation of B cell differentiation;spleen development;regulation of mitochondrial depolarization
- Cellular component
- nucleus;Golgi apparatus;centrosome;spindle;cytosol
- Molecular function
- protein binding;metal ion binding