PLSCR1

phospholipid scramblase 1, the group of Phospholipid scramblases

Basic information

Region (hg38): 3:146515179-146544856

Links

ENSG00000188313 ∙ NCBI:5359 ∙ OMIM:604170 ∙ HGNC:9092 ∙ Uniprot:O15162 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLSCR1 gene.

• Inborn genetic diseases (10 variants)

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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	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)
3-146528751-C-T		not specified	Uncertain significance (Feb 21, 2024)
3-146528772-C-T		not specified	Uncertain significance (Aug 02, 2022)
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: gnomAD

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: dbNSFP

• 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