ARFGAP1

Chr 20

ARF GTPase activating protein 1

Also known as: ARF1GAP, HRIHFB2281

NCBI Gene: 55738ENSG00000101199UniProt: Q8N6T3OMIM: 608377

ARFGAP1 encodes a GTPase-activating protein that promotes hydrolysis of ARF1-bound GTP, which is essential for dissociation of coat proteins from Golgi-derived membranes and vesicles to enable proper vesicle fusion and membrane trafficking. Mutations cause autosomal recessive developmental and epileptic encephalopathy with movement abnormalities. The gene shows significant constraint against loss-of-function variants (LOEUF 0.599), consistent with its essential cellular role.

OMIMResearchSummary from RefSeq, UniProt
MultiplemechanismLOEUF 0.60
Clinical Summary— ARFGAP1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
49 unique Pathogenic / Likely Pathogenic· 94 VUS of 174 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.60LOEUF
pLI 0.002
Z-score 3.19
OE 0.35 (0.22–0.60)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.42Z-score
OE missense 0.93 (0.83–1.03)
238 obs / 257.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.35 (0.22–0.60)
0≤0.351.4
Missense OE0.93 (0.83–1.03)
0≤0.61.4
Synonymous OE1.22
0≤1.21.6
LoF obs/exp: 10 / 28.3Missense obs/exp: 238 / 257.1Syn Z: -1.82
DN
0.7326th %ile
GOF
0.7029th %ile
LOF
0.3260th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

174 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic40
Likely Pathogenic9
VUS94
Likely Benign9
40
Pathogenic
9
Likely Pathogenic
94
VUS
9
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
40
0
40
Likely Pathogenic
0
0
9
0
9
VUS
0
69
25
0
94
Likely Benign
0
6
1
2
9
Benign
0
0
0
0
0
Total075752152

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

ARFGAP1 · 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

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 3 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients