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EIF1AX
Final classification
VUS
EIF1AX c.43G>T · p.Gly15Cys
EIF1AX

EIF1AX c.43G>T (p.Gly15Cys) is a missense variant located at a statistically significant mutational hotspot (cancerhotspots.org) within the N-terminal eIF1A functional domain critical for translation initiation (PM1_Moderate).

Gene
EIF1AX
Transcript
NM_001412.4
HGVS · transcript:coding
NM_001412.4:c.43G>T
Consequence
N/A
GRCh38
chrX:20138596 C>A
GRCh37
chrX:20156714 C>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate, BP4 supporting benign; combination = 2 moderate + 1 supporting benign, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate, BP4 supporting benign; combination = 2 moderate + 1 supporting benign, which maps to VUS.
Classification rationale
PM1PM2 BP4 VUS
EIF1AX c.43G>T

EIF1AX c.43G>T (p.Gly15Cys) is a missense variant located at a statistically significant mutational hotspot (cancerhotspots.org) within the N-terminal eIF1A functional domain critical for translation initiation (PM1_Moderate).1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada across all populations, meeting PM2 at moderate strength.2 Multiple lines of in silico evidence suggest no impact on gene product: SpliceAI predicts no splicing alteration (max delta = 0.00), and BayesDel score is negative (-0.143281), consistent with a tolerated/benign prediction (BP4_Supporting).3 No variant-specific functional data were identified. OncoKB notes no reviewed functional evidence for this variant, and the sole linked publication (PMID:31275557) is a pan-cancer splicing mutation resource that does not mention this variant.4 ClinVar variation 4484138 has 0 submissions, no classification, and no review status, providing no clinical classification data for this variant (PS5/PP5/BP6 not met).5 Overall, 2 moderate pathogenic criteria (PM1, PM2) and 1 supporting benign criterion (BP4) are met. Under the generic ACMG/AMP 2015 classification rules (PMID:25741868), this combination is insufficient to reach Likely Pathogenic (requires ≥3 moderate or 2 moderate + ≥2 supporting) and is also insufficient for Likely Benign (requires ≥1 strong benign + ≥1 supporting benign or ≥2 supporting benign). The variant is classified as a Variant of Uncertain Significance (VUS).6

PM1 + PM2 + BP4 VUS
Gene diagram · NM_001412.4 · variants mapped to exon structure
EIF1AX NM_001412.4
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 21 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM1 moderate Pathogenic
The variant is located at residue Gly15 in the N-terminal eIF1A domain of EIF1AX, a well-established functional domain critical for translation initiation. This residue lies within a statistically significant mutational hotspot (cancerhotspots.org). EIF1AX hotspot mutations in the N-terminal region are recurrent in uveal melanoma and other cancers, and no benign variation in the general population supports this being a tolerated position.
Cancerhotspots.org identifies residue G15 as a statistically significant hotspotvariant absent from gnomADN-terminal eIF1A domain is a critical functional domain.
PM2 moderate Pathogenic
The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 across all populations. Allele frequency is 0%, well below the 0.1% threshold for PM2 in the non-VCEP generic ACMG framework.
Absent from gnomAD v2.1 (exomes)v4.1 (exomes)and gnomAD-Canada v1.0 (genomes)
BP4 supporting Benign
Multiple lines of computational evidence suggest no impact on the gene product. SpliceAI predicts no splicing alteration (max delta = 0.00). BayesDel score is -0.143281, which falls in the negative range predictive of a tolerated or benign effect. Although REVEL is unavailable, the concordance of available in silico tools supports a neutral prediction.
SpliceAI max delta = 0.00 (no splice impact)BayesDel = -0.143281 (negative scoretolerated/benign prediction).
Assessed · not applied
Pathogenic
PVS1 This is a missense variant (NM_001412.4:c.43G>T, p.Gly15Cys) in exon 2 of EIF1AX.
PS1 No evidence of a different nucleotide change at codon 15 resulting in the same amino acid substitution (p.Gly15Cys) that is known to be pathogenic.
PS2 No de novo observation data available for this variant.
PS3 No variant-specific functional data were identified.
PS4 No case-control or prevalence data are available.
PM5 No same-residue comparator pathogenic missense variants were identified.
PM6 No de novo observation data are available for this variant.
PP1 No cosegregation data are available.
PP2 No missense constraint data (HCI prior) are available for EIF1AX to assess whether the gene has a low rate of benign missense variation.
PP3 In silico predictions do not support a deleterious effect.
PP4 No patient phenotype or family history data are available in the case materials to assess whether the phenotype is highly specific for EIF1AX-related disease.
PP5 ClinVar variation 4484138 has 0 submissions, no classification, and no review status.
Benign
BA1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS2 No data are available on observation of this variant in healthy adults where full penetrance would be expected at an early age.
BS3 No functional studies demonstrating a neutral or benign effect of this variant were identified.
BS4 No segregation data are available.
BP1 EIF1AX is not a gene where primarily truncating variants cause disease.
BP2 No observation of this variant in trans with a known pathogenic variant is available.
BP5 No case data are available identifying an alternate molecular basis for disease in a patient carrying this variant.
BP6 No reputable source reports this variant as benign.
N/A · 4 PM3 · PM4 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar but submission details could not be extracted. (ClinVarID = 4484138)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). BayesDel score = -0.143281.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. EIF1AX, a translation initiation factor, is most frequently altered by mutation in uveal melanomas and papillary thyroid carcinomas.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV115448712, n = 2 times).
Hotspots
This variant lies in a statistically significant hotspot.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 1 PMID not cited in assessment
31275557 ↗ Pan-cancer repository of validated natural and cryptic mRNA splicing mutations. CLINVAR