PLSCR2

Chr 3

phospholipid scramblase 2

NCBI Gene: 57047 ENSG00000163746 UniProt: Q9NRY7 OMIM: 607610

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]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.22

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.22LOEUF

pLI 0.000

Z-score 0.95

OE 0.74 (0.46–1.22)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.88Z-score

OE missense 0.80 (0.69–0.93)

125 obs / 155.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.74 (0.46–1.22)

0≤0.351.4

Missense OE?0.80 (0.69–0.93)

0≤0.61.4

Synonymous OE?0.86

0≤1.21.6

LoF obs/exp: 11 / 15.0Missense obs/exp: 125 / 155.8Syn Z: 0.82

Background carrier burden — how many people carry a rare variant somewhere in PLSCR2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 170

353 rare PASS variants

Rare truncating (LoF)

1 in 1,100

68 rare PASS variants

Rare synonymous (reference)

1 in 290

125 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PLSCR2. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 170	1 in 880
South Asian	~43k	1 in 130	1 in 790
Remaining (unassigned)	~30k	1 in 110	1 in 330
European (Finnish)	~27k	1 in 1,900	1 in 3,700
Admixed American	~22k	1 in 130	1 in 3,300
African / African American	~21k	1 in 130	1 in 570
East Asian	~20k	1 in 190	1 in 1,900
Ashkenazi Jewish	~13k	1 in 1,400	1 in 1,700
Middle Eastern	~2,884	1 in 210	≈ 1 in 1,400

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 4 of 6 coding exons well covered in gnomAD exomes; exons 3, 7 marginal. Genomes: all 6.? see exons ↓