PLSCR1
phospholipid scramblase 1, the group of Phospholipid scramblases
Basic information
Region (hg38): 3:146515180-146544856
Links
Phenotypes
GenCC
Source:
No genCC data.
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 PLSCR1 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 | 12 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 1 | 0 |
Variants in PLSCR1
This is a list of pathogenic ClinVar variants found in the PLSCR1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-146516076-C-T | not specified | Uncertain significance (Feb 28, 2023) | ||
| 3-146517027-C-T | not specified | Uncertain significance (Nov 09, 2022) | ||
| 3-146517059-A-C | not specified | Uncertain significance (Jul 19, 2022) | ||
| 3-146521563-C-A | not specified | Uncertain significance (Mar 13, 2023) | ||
| 3-146521649-G-T | not specified | Uncertain significance (Dec 27, 2022) | ||
| 3-146521904-C-A | not specified | Uncertain significance (Nov 21, 2022) | ||
| 3-146521994-C-T | not specified | Likely benign (Jun 30, 2022) | ||
| 3-146528675-G-A | not specified | Uncertain significance (Nov 13, 2023) | ||
| 3-146528748-C-A | not specified | Uncertain significance (Jul 26, 2024) | ||
| 3-146528751-C-T | not specified | Uncertain significance (Feb 21, 2024) | ||
| 3-146528772-C-T | not specified | Uncertain significance (Aug 02, 2022) | ||
| 3-146528775-C-T | not specified | Uncertain significance (Sep 27, 2024) | ||
| 3-146528780-G-C | not specified | Uncertain significance (Jul 20, 2022) | ||
| 3-146533484-G-A | not specified | Uncertain significance (Jun 24, 2022) | ||
| 3-146533512-G-T | not specified | Uncertain significance (Nov 17, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PLSCR1 | protein_coding | protein_coding | ENST00000342435 | 8 | 29685 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0119 | 0.981 | 125582 | 1 | 156 | 125739 | 0.000624 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.866 | 137 | 169 | 0.812 | 0.00000775 | 2095 |
| Missense in Polyphen | 24 | 28.926 | 0.82969 | 398 | ||
| Synonymous | 0.449 | 54 | 58.4 | 0.925 | 0.00000302 | 585 |
| Loss of Function | 2.35 | 6 | 16.2 | 0.370 | 7.70e-7 | 197 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.0129 | 0.0127 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000186 | 0.000185 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000835 | 0.000815 |
dbNSFP
Source:
- Function
- FUNCTION: May mediate accelerated ATP-independent bidirectional transbilayer migration of phospholipids upon binding calcium ions that results in a loss of phospholipid asymmetry in the plasma membrane. May play a central role in the initiation of fibrin clot formation, in the activation of mast cells and in the recognition of apoptotic and injured cells by the reticuloendothelial system.;
- Pathway
- EGF-EGFR Signaling Pathway;EGFR1
(Consensus)
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- loftool
- 0.840
- rvis_EVS
- 0.39
- rvis_percentile_EVS
- 76.05
Haploinsufficiency Scores
- pHI
- 0.204
- hipred
- Y
- hipred_score
- 0.512
- ghis
- 0.470
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.846
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Plscr1
- Phenotype
- hematopoietic system phenotype; immune system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- phosphatidylserine biosynthetic process;apoptotic process;acute-phase response;positive regulation of gene expression;plasma membrane phospholipid scrambling;platelet activation;regulation of mast cell activation;response to interferon-beta;negative regulation of viral genome replication;positive regulation of innate immune response;positive regulation of transcription by RNA polymerase II;defense response to virus;regulation of Fc receptor mediated stimulatory signaling pathway;positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity
- Cellular component
- nucleus;nucleolus;cytoplasm;Golgi apparatus;cytosol;plasma membrane;integral component of plasma membrane;membrane;membrane raft;perinuclear region of cytoplasm;collagen-containing extracellular matrix;extracellular exosome
- Molecular function
- DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;epidermal growth factor receptor binding;calcium ion binding;protein binding;SH3 domain binding;phospholipid scramblase activity;enzyme binding;CD4 receptor binding