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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
      Population frequency
      Overall AF
      14 / 1,544,998
      0.00091%
      Highest · Admixed American
      0.0019%
      Homozygotes
      0
      grpmax FAF
      0.00063%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 2 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      Admixed American 1 / 51,556 0.0019% 0
      European (non-Finnish) 13 / 1,149,594 0.0011% 0
      European (Finnish) 0 / 49,418
      Amish 0 / 910
      East Asian 0 / 41,466
      Middle Eastern 0 / 5,508
      South Asian 0 / 84,394
      Ashkenazi Jewish 0 / 28,662
      African/African American 0 / 73,390
      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.
      Overall AF
      1 / 139,512
      0.00072%
      Highest · European (non-Finnish)
      0.0019%
      Homozygotes
      0
      Allele frequency by ancestry — gnomAD v2.1
      observed in 1 of 8 groups
      AncestryAllele countFrequencyHomozygotes
      European (non-Finnish) 1 / 52,794 0.0019% 0
      African/African American 0 / 7,348
      Admixed American 0 / 24,872
      Ashkenazi Jewish 0 / 8,192
      East Asian 0 / 11,148
      European (Finnish) 0 / 8,294
      Remaining individuals 0 / 4,164
      South Asian 0 / 22,700
      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).
      This variant is absent from gnomAD-Canada.
      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 · 2 PMIDs triaged · 1 high-priority
      2papers screened
      Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
      25741868 ↗ functional
      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.
      The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants.(1) In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic
      BS3PP5PS3PS4
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PP5PS4
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots