PPP1R42
protein-codingprotein phosphatase 1 regulatory subunit 42, the group of Protein phosphatase 1 regulatory subunits
Gene summary
The protein encoded by this gene can interact with gamma-tubulin and PP1 phosphatase, a regulator of centrosome separation. The encoded protein is a positive regulator of PP1 phosphatase and thus plays a role in the control of centrosome integrity. [provided by RefSeq, Feb 2017]
- LRRC67
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~92.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PPP1R42 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001364910.1. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 16 | 1 | 17 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 18 | 1 | 0 | 19 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001351839.1 | 7 | MANE Select | |
| Ensembl | ENSP00000508980.1 | 7 | MANE Select | |
| RefSeq | NP_001013648.1 | 5 | Standard | |
| RefSeq | NP_001335492.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of phosphatase activity
Molecular Function
- actin binding
- tubulin binding
- dynein complex binding
Cellular Component
- manchette
- cytoplasm
- centrosome
- microtubule organizing center
- microtubule cytoskeleton
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000324682
- Coding exons
- 5
- Length
- 92506
- Individuals with no LoFs
- 125354
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 358
- Defined
- 125714
- p
- 0.00143
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.01 | 74 | 103 | 0.719 | 0.00000458 | 1470 |
| Missense (PolyPhen) | 15 | 25.849 | 0.58028 | 400 | ||
| Synonymous | -0.165 | 42 | 40.7 | 1.03 | 0.00000184 | 432 |
| Loss of Function | 0.484 | 8 | 9.62 | 0.832 | 5.45e-7 | 136 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00057 | 0.00055 | rare |
| Latino/Admixed American | 0.0011 | 0.0010 | notable |
| Ashkenazi Jewish | 0.0018 | 0.0018 | notable |
| East Asian | 0.000058 | 0.000054 | rare |
| Finnish | 0.0010 | 0.0010 | notable |
| European (Non-Finnish) | 0.0024 | 0.0023 | notable |
| South Asian | 0.00035 | 0.00029 | rare |
| Other | 0.00069 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulates phosphatase activity of protein phosphatase 1 (PP1) complexes in the testis. {ECO:0000250|UniProtKB:Q8R1Z4}.;
Intolerance Scores
- RVIS EVS
- 0.37
- RVIS percentile EVS
- 74.95
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |