PLSCR1

Chr 3

phospholipid scramblase 1

Also known as: MMTRA1B

NCBI Gene: 5359 ENSG00000188313 UniProt: O15162 OMIM: 604170

This gene encodes a phospholipid scramblase family member. The encoded protein is involved in disruption of the asymmetrical distribution of phospholipids between the inner and outer leaflets of the plasma membrane, resulting in externalization of phosphatidylserine. This cell membrane disruption plays an important role in the blood coagulation cascade as well as macrophage clearing of apoptotic cells. The encoded protein has additionally been implicated in gene regulation and interferon-induced antiviral responses. [provided by RefSeq, May 2022]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.73

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.73LOEUF

pLI 0.012

Z-score 2.35

OE 0.37 (0.20–0.73)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.87Z-score

OE missense 0.81 (0.71–0.94)

137 obs / 168.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.37 (0.20–0.73)

0≤0.351.4

Missense OE?0.81 (0.71–0.94)

0≤0.61.4

Synonymous OE?0.93

0≤1.21.6

LoF obs/exp: 6 / 16.2Missense obs/exp: 137 / 168.6Syn Z: 0.45

Background carrier burden — how many people carry a rare variant somewhere in PLSCR1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 200

379 rare PASS variants

Rare truncating (LoF)

1 in 770

63 rare PASS variants

Rare synonymous (reference)

1 in 960

114 rare PASS variants

Rare missense and truncating variants are carried at similar rates in PLSCR1; this gene does not show strong loss-of-function constraint by this measure. 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 410	1 in 1,200
South Asian	~43k	1 in 150	1 in 1,600
Remaining (unassigned)	~30k	1 in 320	1 in 2,700
European (Finnish)	~27k	1 in 260	≈ 1 in 13,000
Admixed American	~22k	1 in 210	1 in 1,600
African / African American	~21k	1 in 160	1 in 1,300
East Asian	~20k	1 in 100	1 in 800
Ashkenazi Jewish	~13k	1 in 1,600	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 190	≈ 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): 3 of 8 coding exons well covered in gnomAD exomes; exons 2, 3, 5, 8, 9 marginal. Genomes: all 8.? see exons ↓