PLSCR3

phospholipid scramblase 3, the group of Phospholipid scramblases

Basic information

Region (hg38): 17:7389726-7394842

Links

ENSG00000187838 ∙ NCBI:57048 ∙ OMIM:607611 ∙ HGNC:16495 ∙ Uniprot:Q9NRY6 ∙ 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 PLSCR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLSCR3 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					1	1
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	1

Variants in PLSCR3

This is a list of pathogenic ClinVar variants found in the PLSCR3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-7390432-A-G		not specified	Uncertain significance (Sep 17, 2021)
17-7390731-C-T		not specified	Uncertain significance (Jun 23, 2021)
17-7392914-G-A			Benign (Jul 30, 2018)
17-7393188-G-C		not specified	Uncertain significance (Nov 12, 2021)
17-7393206-C-T		not specified	Uncertain significance (Sep 15, 2021)
17-7393789-G-A		not specified	Uncertain significance (Aug 13, 2021)
17-7393806-G-A		not specified	Uncertain significance (Sep 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLSCR3	protein_coding	protein_coding	ENST00000535512	7	14371

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00595	0.975	124783	0	16	124799	0.0000641

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.827	136	166	0.819	0.00000996	1834
Missense in Polyphen		44	69.434	0.6337		722
Synonymous	0.0573	69	69.6	0.991	0.00000393	646
Loss of Function	2.05	6	14.4	0.417	8.84e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.000313	0.000298
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000624	0.0000618
Middle Eastern	0.00	0.00
South Asian	0.000136	0.000131
Other	0.000168	0.000165

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. Seems to play a role in apoptosis, through translocation of cardiolipin from the inner to the outer mitochondrial membrane which promotes BID recruitment and enhances tBid-induced mitochondrial damages. {ECO:0000269|PubMed:17226776}.

Recessive Scores

• pRec: 0.108

Haploinsufficiency Scores

• pHI: 0.401
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.658

Mouse Genome Informatics

• Gene name: Plscr3
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: apoptotic process;plasma membrane phospholipid scrambling;glucose homeostasis;cholesterol homeostasis;cellular response to lipopolysaccharide
• Cellular component: mitochondrion;plasma membrane;integral component of membrane;mitochondrial membrane
• Molecular function: calcium ion binding;protein binding;SH3 domain binding;phospholipid scramblase activity;calcium-dependent protein binding