ARHGEF39

Chr 9

Rho guanine nucleotide exchange factor 39

Also known as: C9orf100, XGEF

The protein functions as a guanyl-nucleotide exchange factor that promotes cell proliferation and regulates cell migration at the plasma membrane. Mutations cause autosomal recessive developmental and epileptic encephalopathy with onset in infancy, characterized by severe developmental delay, epilepsy, and brain malformations. The gene shows tolerance to loss-of-function variation, which is consistent with the recessive inheritance pattern observed in affected individuals.

OMIMResearchSummary from RefSeq, UniProt
LOEUF 1.28
Clinical SummaryARHGEF39
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
1.28LOEUF
pLI 0.000
Z-score 0.61
OE 0.85 (0.581.28)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.57Z-score
OE missense 0.89 (0.781.00)
173 obs / 195.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.85 (0.581.28)
00.351.4
Missense OE0.89 (0.781.00)
00.61.4
Synonymous OE0.90
01.21.6
LoF obs/exp: 17 / 19.9Missense obs/exp: 173 / 195.4Syn Z: 0.70

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

ARHGEF39 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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