PLSCR4

Chr 3

phospholipid scramblase 4

Also known as: TRA1

NCBI Gene: 57088 ENSG00000114698 UniProt: Q9NRQ2 OMIM: 607612

Enables CD4 receptor binding activity; enzyme binding activity; and phospholipid scramblase activity. Involved in calcium activated phosphatidylcholine scrambling and calcium activated phosphatidylserine scrambling. Located in nucleus and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

—

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.15

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.15LOEUF

pLI 0.000

Z-score 1.12

OE 0.70 (0.44–1.15)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.43Z-score

OE missense 0.91 (0.80–1.03)

170 obs / 186.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.70 (0.44–1.15)

0≤0.351.4

Missense OE?0.91 (0.80–1.03)

0≤0.61.4

Synonymous OE?1.06

0≤1.21.6

LoF obs/exp: 11 / 15.8Missense obs/exp: 170 / 186.6Syn Z: -0.37

Background carrier burden — how many people carry a rare variant somewhere in PLSCR4?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 130

437 rare PASS variants

Rare truncating (LoF)

1 in 510

74 rare PASS variants

Rare synonymous (reference)

1 in 490

136 rare PASS variants

Rare missense and truncating variants are carried at similar rates in PLSCR4; 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 200	1 in 2,100
South Asian	~43k	1 in 150	1 in 1,500
Remaining (unassigned)	~30k	1 in 120	1 in 3,100
European (Finnish)	~27k	1 in 380	1 in 3,000
Admixed American	~22k	1 in 90	1 in 430
African / African American	~21k	1 in 70	1 in 2,600
East Asian	~20k	1 in 180	1 in 1,500
Ashkenazi Jewish	~13k	1 in 900	none seen
Middle Eastern	~2,884	1 in 110	1 in 520

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): 5 of 8 coding exons well covered in gnomAD exomes; exon 2 poorly covered; exons 5, 9 marginal. Genomes: all 8.? see exons ↓