PLSCR2

protein-coding

phospholipid scramblase 2, the group of Phospholipid scramblases

Gene summary

This gene encodes a member of the phospholipid scramblase family. Phospholipid scramblases are membrane proteins that mediate calcium-dependent, non-specific movement of plasma membrane phospholipids and phosphatidylserine exposure. The encoded protein contains a low affinity calcium binding motif and may play a role in blood coagulation and apoptosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]

MANE transcript

NM_001395437.1

Inheritance

—

ClinVar variants

U:27B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr3:146,391,421-146,495,991

External References & Databases

Ensembl (ENSG00000163746)

Transcript & Mutation Effects

hg38 • Region Span ~104.6 kb

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GenCC 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 PLSCR2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 28

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001395437.1. 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			1 clinvar			1
missense			26 clinvar	2 clinvar		28
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	27	2	0	29

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001395437.1	RefSeq	NP_001382366.1	6	MANE Select
ENST00000696113.1	Ensembl	ENSP00000512407.1	6	MANE Select
NM_001199978.3	RefSeq	NP_001186907.1	7	Standard
NM_001199979.1	RefSeq	NP_001186908.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

plasma membrane phospholipid scrambling

Molecular Function

calcium ion binding
phospholipid scramblase activity

Cellular Component

nucleus
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000497985
Coding exons: 7
Length: 104571
Individuals with no LoFs: 125715
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125722
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.877	125	156	0.802	0.00000753	1956
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000057	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000073	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.125

Gene Damage Prediction

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