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B3GALT6
Final classification
VUS
B3GALT6 c.901_904dup · p.Arg302GlnfsTer142
B3GALT6

NM_080605.4:c.901_904dup is a frameshift variant in B3GALT6 predicted to alter the C-terminus (p.Arg302GlnfsTer142). B3GALT6 loss of function is a well-established disease mechanism for autosomal recessive spondylodysplastic Ehlers-Danlos syndrome. PVS1 is applied at strong strength, downgraded from very_strong due to the 3' location (codon 302/330) and confirmed NMD escape in this single-exon gene (PMC6185798).

Gene
B3GALT6
Transcript
NM_080605.4
HGVS · transcript:coding
NM_080605.4:c.901_904dup
Consequence
N/A
GRCh38
chr1:1233176 T>TGCAA
GRCh37
chr1:1168556 T>TGCAA
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: PVS1 strong, PM2 supporting; combination = 1 strong + 1 supporting, 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: PVS1 strong, PM2 supporting; combination = 1 strong + 1 supporting, which maps to VUS.
Classification rationale
PVS1PM2 VUS
B3GALT6 c.901_904dup

NM_080605.4:c.901_904dup is a frameshift variant in B3GALT6 predicted to alter the C-terminus (p.Arg302GlnfsTer142). B3GALT6 loss of function is a well-established disease mechanism for autosomal recessive spondylodysplastic Ehlers-Danlos syndrome. PVS1 is applied at strong strength, downgraded from very_strong due to the 3' location (codon 302/330) and confirmed NMD escape in this single-exon gene (PMC6185798).1 The variant is extremely rare in population databases, meeting PM2_Supporting: gnomAD v2.1 allele frequency 7.17e-06 (1/139,512 alleles) and gnomAD v4.1 allele frequency 9.06e-06 (14/1,544,998 alleles), both well below the 0.1% threshold. No homozygotes are observed.2 The variant is present in ClinVar (Variation ID 1323966) with four clinical testing submissions: two classify it as Likely Pathogenic and two as Uncertain Significance. No expert panel review is available, and the cited PubMed references (PMID:25741868, PMID:28492532) are methodology guidelines that do not specifically mention this variant.3 SpliceAI predicts no significant splicing impact (max delta score 0.03). In silico missense predictors (REVEL, BayesDel) are not applicable to this frameshift variant. PP3 is not met; BP4 is not met given insufficient benign computational evidence.4 Applying generic ACMG/AMP 2015 final classification rules (PMID:25741868): with one strong pathogenic criterion (PVS1_Strong) and one supporting pathogenic criterion (PM2_Supporting), the variant does not reach the threshold for Likely Pathogenic (requires 1 Strong + 1–2 Moderate OR 1 Strong + 2 Supporting). The variant is classified as a Variant of Uncertain Significance (VUS). Additional evidence, particularly verified publication reports of the variant in affected individuals (PS4/PM3) and segregation data (PP1), may upgrade the classification upon human curator review.5

PVS1 + PM2 VUS
1 pvs1_gene_contextpvs1_variant_assessmentpvs1_generic_framework ↗
5 generic_acmg_combination_rulesPMID:25741868 ↗
Gene diagram · NM_080605.4 · variants mapped to exon structure
B3GALT6 NM_080605.4
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 9.0615e-06; MAF= 0.00091%, 14/1544998 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 1.93964e-05; MAF= 0.00194%, 1/51556 alleles, homozygotes = 0); grpmax FAF= 6.31e-06.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 7.16784e-06; MAF= 0.00072%, 1/139512 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.89415e-05; MAF= 0.00189%, 1/52794 alleles, homozygotes = 0).
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00091% · 14 / 1,544,998
      0 hom · FAF 0.00063%
      Admixed American
      1 / 51,556
      0.0019%
      European (non-Finnish)
      13 / 1,149,594
      0.0011%
      + 8 not observed (Remaining individuals, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.00072% · 1 / 139,512
      0 hom
      European (non-Finnish)
      1 / 52,794
      0.0019%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant is present in ClinVar (Variation ID: 1323966); submission details unavailable.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03).
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      3papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 2 further PMIDs triaged but not cited — see Sources & References.
      PMID 23664118
      Found
      Frameshift variant c.901_904dup leading to p.Arg302GlnfsTer142 B3GALT6 LoF is an established disease mechanism for spEDS-B3GALT6 (supported by PMID:23664118 PMID:25331875 PMID:38065100) Single-exon gene NMD escape predicted variant in 3' region (codon 302/330) ClinGen SVI PVS1 downgrade framework (PMC6185798) applied
      Applied to
      PVS1 supports · met
      PMID 25331875
      Found
      Frameshift variant c.901_904dup leading to p.Arg302GlnfsTer142 B3GALT6 LoF is an established disease mechanism for spEDS-B3GALT6 (supported by PMID:23664118 PMID:25331875 PMID:38065100) Single-exon gene NMD escape predicted variant in 3' region (codon 302/330) ClinGen SVI PVS1 downgrade framework (PMC6185798) applied
      Applied to
      PVS1 supports · met
      PMID 38065100
      Found
      Frameshift variant c.901_904dup leading to p.Arg302GlnfsTer142 B3GALT6 LoF is an established disease mechanism for spEDS-B3GALT6 (supported by PMID:23664118 PMID:25331875 PMID:38065100) Single-exon gene NMD escape predicted variant in 3' region (codon 302/330) ClinGen SVI PVS1 downgrade framework (PMC6185798) applied
      Applied to
      PVS1 supports · met
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 2 PMIDs 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
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR