RAB39A

Chr 11

RAB39A, member RAS oncogene family

Also known as: K28, RAB39

NCBI Gene: 54734 ENSG00000179331 UniProt: Q14964

Enables G protein activity. Involved in autophagosome-lysosome fusion; phagosome acidification; and phagosome-lysosome fusion. Located in autolysosome membrane and phagocytic vesicle. [provided by Alliance of Genome Resources, Jun 2026]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.21

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.21LOEUF

pLI 0.001

Z-score 1.12

OE 0.61 (0.34–1.21)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

1.14Z-score

OE missense 0.71 (0.59–0.85)

84 obs / 118.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.61 (0.34–1.21)

0≤0.351.4

Missense OE?0.71 (0.59–0.85)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 6 / 9.8Missense obs/exp: 84 / 118.9Syn Z: 0.12

Background carrier burden — how many people carry a rare variant somewhere in RAB39A?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 660

251 rare PASS variants

Rare truncating (LoF)

1 in 4,700

35 rare PASS variants

Rare synonymous (reference)

1 in 330

108 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for RAB39A. 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 720	1 in 4,700
South Asian	~43k	1 in 500	1 in 5,200
Remaining (unassigned)	~30k	1 in 550	1 in 5,000
European (Finnish)	~27k	≈ 1 in 13,000	1 in 1,900
Admixed American	~22k	1 in 350	1 in 3,700
African / African American	~21k	1 in 650	≈ 1 in 8,100
East Asian	~20k	1 in 480	1 in 3,300
Ashkenazi Jewish	~13k	≈ 1 in 6,500	≈ 1 in 13,000
Middle Eastern	~2,883	≈ 1 in 960	none seen

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): All 2 coding exons well covered in gnomAD exomes and genomes.? see exons ↓