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EIF1AX
Final classification
VUS
EIF1AX c.17G>T · p.Gly6Val
EIF1AX

NM_001412.4:c.17G>T (p.Gly6Val) is a missense variant in the N-terminal tail (NTT) of EIF1AX, a critical functional domain involved in ribosomal scanning, AUG selection, and ribosomal protein binding.

Gene
EIF1AX
Transcript
NM_001412.4
HGVS · transcript:coding
NM_001412.4:c.17G>T
Consequence
N/A
GRCh38
chrX:20138622 C>A
GRCh37
chrX:20156740 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 supporting, BP4 supporting benign; combination = 1 moderate + 1 supporting + 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 supporting, BP4 supporting benign; combination = 1 moderate + 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM1PM2 BP4 VUS
EIF1AX c.17G>T

NM_001412.4:c.17G>T (p.Gly6Val) is a missense variant in the N-terminal tail (NTT) of EIF1AX, a critical functional domain involved in ribosomal scanning, AUG selection, and ribosomal protein binding.1 This variant is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada, indicating it is a rare variant not observed in large control populations.2 Residue Gly6 lies within a statistically significant mutational hotspot (cancerhotspots.org) and within the NTT functional domain, where recurrent missense mutations are documented in uveal melanoma. Functional studies of the G6D substitution at the same residue demonstrate altered translational regulation and reduced Rps10 binding.3 Multiple in silico tools predict no significant deleterious impact: BayesDel score is -0.263 (benign-leaning) and SpliceAI predicts no splicing alteration (max delta score = 0.00).4 This variant has been reported in ClinVar as Uncertain significance by a single clinical laboratory (ClinVar ID: 1708311). It has been observed in somatic cancers (COSMIC; n=2) but no germline clinical or functional evidence specific to this variant is available.5 No functional studies have directly tested the G6V substitution. Available functional data for other NTT mutants (G6D, G8R/G9R, K10E, R13H, G15D) demonstrate a gain-of-function mechanism with altered translational control, but these studies do not constitute variant-specific evidence for G6V.6 No de novo, segregation, or case-control data are available for this variant.

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 · 20 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM1 moderate Pathogenic
Residue Gly6 is located within the N-terminal tail (NTT) of EIF1AX (amino acids 1–15), a well-characterized functional domain critical for translational regulation, ribosomal scanning, AUG selection, and Rps3/Rps10 binding (PMID:30420357, PMID:28594900). This position lies within a statistically significant mutational hotspot identified by cancerhotspots.org, and the NTT is recurrently mutated in uveal melanoma. Missense alterations in this domain have been shown to alter EIF1AX function.
NTT (aa 1–15) is a critical functional domain for ribosomal protein binding and translation initiation (PMID:30420357PMID:28594900). cancerhotspots.org identifies this residue as a statistically significant mutational hotspot. Recurrent NTT mutations are documented across UM cohorts.
PM2 supporting Pathogenic
This variant is absent from all population databases (gnomAD v2.1, v4.1, and gnomAD-Canada), meeting the PM2 threshold of <0.1% population frequency for a rare variant absent from controls.
Absent from gnomAD v2.1 (0 alleles)gnomAD v4.1 (0 alleles)and gnomAD-Canada v1.0 (0 alleles).
BP4 supporting Benign
Multiple lines of computational evidence suggest no significant impact on the gene product. BayesDel predicts a benign effect (score -0.263, below the deleterious threshold) and SpliceAI predicts no splicing alteration (max delta score = 0.00). REVEL is not available for this variant.
BayesDel score: -0.263 (benign range). SpliceAI max delta: 0.00 (no predicted splice impact).
Assessed · not applied
Pathogenic
PS1 No alternative nucleotide change at codon 6 that would result in the same amino acid substitution (Gly6Val) has been identified in ClinVar or the literature.
PS2 No de novo occurrence of NM_001412.4:c.17G>T has been reported in the literature or in ClinVar submissions.
PS3 No functional studies directly tested NM_001412.4:c.17G>T (p.Gly6Val).
PS4 No case-control or statistical enrichment data are available for this variant.
PM5 No pathogenic missense variant at the same codon (Gly6) has been identified in ClinVar or the literature with an established pathogenic classification.
PM6 No de novo observation of this variant (with or without confirmed paternity/maternity) has been reported in the literature or ClinVar.
PP1 No segregation data are available for this variant.
PP2 Insufficient data to assess PP2.
PP3 In silico tools do not support a deleterious effect.
PP4 No patient-specific phenotype or clinical data are available for this case.
PP5 ClinVar classification is Uncertain significance from a single submitter.
Benign
BA1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS2 No data are available regarding observation of this variant in healthy adults.
BS3 Functional studies of EIF1AX NTT mutants (including G6D at the same residue, PMID:30420357, PMID:28594900) demonstrate altered translational regulation, reduced Rps10 binding, and enhanced scanning of long 5'UTR mRNAs — all indicative of a functional effect rather than no damaging effect.
BS4 No segregation data demonstrating lack of cosegregation with disease are available.
BP1 BP1 applies to missense variants in genes where primarily truncating variants cause disease.
BP2 No observation of this variant in trans with a pathogenic variant in a gene for a fully penetrant dominant/recessive disorder.
BP5 No observation of this variant in a case with an alternative molecular basis for disease.
BP6 No reputable source has classified this variant as benign or likely benign.
N/A · 5 PVS1 · 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 as Uncertain significance (1 clinical laboratory). (ClinVarID = 1708311)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). BayesDel score = -0.263094.
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; COSV105919481, n = 2 times).
Hotspots
This variant lies in a statistically significant hotspot.
Literature · how each cited paper was used
2papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 1 further PMID triaged but not cited — see Sources & References.
Systematic genomic and translational efficiency studies of uveal melanoma.
Searched
c.17G>TG6VGly6Valp.Gly6Val
Found
Characterized EIF1AX N-terminal tail (NTT) mutations in uveal melanoma. Identified G6D as a recurrent missense change at Gly6 in the 92.1 cell line. Functional studies showed EIF1AX NTT mutants are gain-of-function, with altered polysome profiles and impaired regulation of ribosomal protein translation. NM_001412.4:c.17G>T (p.Gly6Val) was not specifically identified.
Variant
◇ Residue / gene-level — variant not named
Applied to
PM1 supports · met
Why
G6D (different substitution at same Gly6 residue) was functionally characterized, demonstrating altered translational regulation. Provides domain-level evidence supporting PM1 (NTT as critical functional domain). Exact variant not tested; does not independently meet PS3.
We also identified a homozygous G→A mutation at the start of exon 2 in a single established UM cell line (92.1)… demonstrated faithful transcription of the G6D missense mutation, without evidence for altered mRNA splicing or wild type allele expression.
Location Results: 'Mutant and wild type EIF1AX play essential roles in uveal melanoma cells'; Figure 2A; S4 Fig  ·  Context Uveal melanoma cell lines (92.1, Omm2.3, Omm1); lentiviral shRNA knockdown; polysome profiling; RNAseq  ·  full text
Cancer-Associated Eukaryotic Translation Initiation Factor 1A Mutants Impair Rps3 and Rps10 Binding and Enhance Scanning of Cell Cycle Genes.
Searched
c.17G>TG6VGly6Valp.Gly6ValNM_001412
Found
Tested seven cancer-associated EIF1AX NTT mutants (G6D, G9D, G9R, G8RG9R, K10E, R13H, G15D) in MEFs and HEK293T cells. G6D reduced binding to ribosomal protein Rps10 and enhanced scanning of long 5'UTR-containing cell cycle genes. NM_001412.4:c.17G>T (p.Gly6Val) was not specifically tested.
Variant
◇ Residue / gene-level — variant not named
Applied to
PM1 supports · met
Why
G6D at the same Gly6 residue was functionally characterized, confirming NTT as a critical functional domain (PM1). Exact variant G6V not tested; does not independently meet PS3. Evidence of gain-of-function mechanism argues against BS3.
Rps10 all mutants G6D, G9D/R13H and K10E bound less efficiently.
Location Results: 'Cancer associated eIF1A NTT mutants primarily enhance translation of long 5'UTR mRNAs' and 'NTT mutants are defective in A-site Rps10 and Rps3 binding'; Figures 7-8; Methods: Plasmids section  ·  Context MEFs, HEK293T cells; dual-luciferase reporter gene assays; polysome profiling; His-pull down binding assays with recombinant Rps3 and Rps10  ·  full text
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
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR