RALGPS1

Chr 9

Ral GEF with PH domain and SH3 binding motif 1

Also known as: RALGEF2, RALGPS1A

The protein functions as a guanine nucleotide exchange factor for the small GTPase RALA and is involved in cytoskeletal organization. Loss-of-function mutations in RALGPS1 cause autosomal dominant neurodevelopmental disorder, as the gene is highly intolerant to loss-of-function variation (pLI=1.0, LOEUF=0.127). The pathogenic mechanism involves haploinsufficiency affecting Ral protein signal transduction pathways critical for normal neuronal development.

OMIMResearchSummary from RefSeq, UniProt, Mechanism
LOFmechanismLOEUF 0.13
Clinical SummaryRALGPS1
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Dual constrained — LoF & missense intolerant
LoF Constraint
0.13LOEUF
pLI 1.000
Z-score 5.51
OE 0.03 (0.010.13)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint
3.09Z-score
OE missense 0.51 (0.450.58)
163 obs / 318.2 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios
LoF OE0.03 (0.010.13)
00.351.4
Missense OE0.51 (0.450.58)
00.61.4
Synonymous OE0.89
01.21.6
LoF obs/exp: 1 / 37.3Missense obs/exp: 163 / 318.2Syn Z: 0.99
DN
0.4487th %ile
GOF
0.4875th %ile
LOF
0.68top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.13

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

RALGPS1 · 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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