PLSCR2

phospholipid scramblase 2, the group of Phospholipid scramblases

Basic information

Region (hg38): 3:146391421-146495991

Links

ENSG00000163746 ∙ NCBI:57047 ∙ OMIM:607610 ∙ HGNC:16494 ∙ Uniprot:Q9NRY7 ∙ 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 PLSCR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLSCR2 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in PLSCR2

This is a list of pathogenic ClinVar variants found in the PLSCR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-146441813-C-T		not specified	Uncertain significance (May 30, 2024)
3-146449232-C-T		not specified	Uncertain significance (Dec 03, 2021)
3-146454123-A-T		not specified	Uncertain significance (Jul 12, 2023)
3-146455349-G-A		not specified	Uncertain significance (Dec 13, 2022)
3-146455352-C-T		not specified	Uncertain significance (Sep 12, 2023)
3-146455454-A-G		not specified	Uncertain significance (May 02, 2024)
3-146455459-A-C		not specified	Uncertain significance (Jul 08, 2022)
3-146459873-G-A		not specified	Uncertain significance (Mar 23, 2023)
3-146459985-G-A		not specified	Uncertain significance (Jan 08, 2024)
3-146460020-T-C		not specified	Uncertain significance (May 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLSCR2	protein_coding	protein_coding	ENST00000497985	7	104571

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000119	0.595	125715	0	7	125722	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.877	125	156	0.802	0.00000753	1956
Missense in Polyphen		36	46.856	0.7683		639
Synonymous	0.816	46	53.6	0.858	0.00000268	552
Loss of Function	0.948	11	15.0	0.735	7.83e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000131	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000574	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000179	0.0000176
Middle Eastern	0.0000574	0.0000544
South Asian	0.0000729	0.0000653
Other	0.00	0.00

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.

Recessive Scores

• pRec: 0.0962

Intolerance Scores

• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.14

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.125

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Plscr2
• Phenotype: hematopoietic system phenotype; limbs/digits/tail phenotype; immune system phenotype; skeleton phenotype

Gene ontology

• Biological process: plasma membrane phospholipid scrambling
• Cellular component: nucleus;plasma membrane;integral component of membrane
• Molecular function: calcium ion binding;phospholipid scramblase activity