ARMCX5

Chr X

armadillo repeat containing X-linked 5

Also known as: GASP5

NCBI Gene: 64860 ENSG00000125962 UniProt: Q6P1M9 OMIM: 301047

The protein localizes to mitochondria and is involved in cellular stress responses and mitochondrial function regulation. Mutations cause X-linked intellectual disability with variable features including developmental delay, seizures, and behavioral abnormalities. This gene shows X-linked inheritance and demonstrates low constraint against loss-of-function variants.

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.89

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.89LOEUF

pLI 0.033

Z-score 1.82

OE 0.39 (0.19–0.89)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

1.04Z-score

OE missense 0.79 (0.69–0.91)

156 obs / 196.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.39 (0.19–0.89)

0≤0.351.4

Missense OE?0.79 (0.69–0.91)

0≤0.61.4

Synonymous OE?1.00

0≤1.21.6

LoF obs/exp: 4 / 10.3Missense obs/exp: 156 / 196.9Syn Z: 0.00

Background carrier burden — how many people carry a rare variant somewhere in ARMCX5?

gnomAD v4 · ~732k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 180

380 rare PASS variants

Rare truncating (LoF)

1 in 18,000

16 rare PASS variants

Rare synonymous (reference)

1 in 270

159 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ARMCX5. 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)	~561k	1 in 240	1 in 37,000
South Asian	~36k	1 in 250	≈ 1 in 36,000
Remaining (unassigned)	~31k	1 in 240	≈ 1 in 10,000
European (Finnish)	~27k	1 in 340	none seen
Admixed American	~23k	1 in 200	none seen
African / African American	~21k	1 in 210	≈ 1 in 10,000
East Asian	~20k	1 in 170	≈ 1 in 20,000
Ashkenazi Jewish	~13k	1 in 1,800	none seen
Middle Eastern	~2,758	1 in 200	≈ 1 in 2,700

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 1 coding exons well covered in gnomAD exomes and genomes.? see exons ↓