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COL4A1
Final classification
VUS
COL4A1 c.343G>A · p.Gly115Ser
COL4A1

NM_001845.5:c.343G>A (p.Gly115Ser) is a missense variant in COL4A1 affecting a glycine residue in the collagen triple-helical Gly-X-Y repeat domain.

Gene
COL4A1
Transcript
NM_001845.5
HGVS · transcript:coding
NM_001845.5:c.343G>A
Consequence
N/A
GRCh38
chr13:110212461 C>T
GRCh37
chr13:110864808 C>T
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, PP3 supporting; combination = 1 moderate + 2 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: PM1 moderate, PM2 supporting, PP3 supporting; combination = 1 moderate + 2 supporting, which maps to VUS.
Classification rationale
PM1PM2PP3 VUS
COL4A1 c.343G>A

NM_001845.5:c.343G>A (p.Gly115Ser) is a missense variant in COL4A1 affecting a glycine residue in the collagen triple-helical Gly-X-Y repeat domain. The variant is extremely rare in population databases: gnomAD v2.1 allele frequency is 0.00177% (5/282,856 alleles) and gnomAD v4.1 allele frequency is 0.00192% (31/1,613,960 alleles), both well below the 0.1% PM2 threshold. It is absent from gnomAD-Canada.1 Gly115 lies within the collagen triple-helical domain, a critical functional domain where glycine substitutions are a well-established pathogenic mechanism across collagen genes and specifically in COL4A1-related disorders (PMID:25719457). This supports application of PM1 at moderate strength. In silico predictors support a deleterious effect: REVEL score 0.963 (highly pathogenic-leaning) and BayesDel score 0.571 (damaging), meeting PP3 at supporting strength.2 In ClinVar (ID 2158622), this variant has been reported as Uncertain significance by 5 clinical laboratories and as Likely pathogenic by 1 clinical laboratory (Labcorp Genetics). No expert panel review is available.3 Exploratory evidence recovery suggests potential functional evidence of impaired collagen IV secretion (PMID:15905400) and a possible de novo observation, but these could not be independently verified from available abstracts and require human review of full-text publications. Applying generic ACMG/AMP 2015 criteria: PM1 (moderate) + PM2 (supporting) + PP3 (supporting) = 1 moderate + 2 supporting, which does not reach the Likely Pathogenic threshold (requires ≥2 moderate OR ≥4 supporting OR 1 strong + ≥2 supporting). The classification is Variant of Uncertain Significance. Additional evidence (PS3 functional confirmation, PM6 de novo verification) could upgrade this to Likely Pathogenic.4

PM1 + PM2 + PP3 VUS
2 revelbayesdel
4 generic_acmg_combination_rules
Gene diagram · NM_001845.5 · variants mapped to exon structure
COL4A1 NM_001845.5
Fetching transcript structure from UCSC…
Applied criteria · 3 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= 1.92074e-05; MAF= 0.00192%, 31/1613960 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 2.67137e-05; MAF= 0.00267%, 2/74868 alleles, homozygotes = 0); grpmax FAF= 1.567e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.76768e-05; MAF= 0.00177%, 5/282856 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.09674e-05; MAF= 0.00310%, 4/129168 alleles, homozygotes = 0); grpmax FAF= 7.01e-06.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0019% · 31 / 1,613,960
      0 hom · FAF 0.0016%
      African/African American
      2 / 74,868
      0.0027%
      European (non-Finnish)
      27 / 1,180,042
      0.0023%
      Admixed American
      1 / 59,992
      0.0017%
      Remaining individuals
      1 / 62,482
      0.0016%
      + 6 not observed (European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.0018% · 5 / 282,856
      0 hom · FAF 0.0007%
      European (non-Finnish)
      4 / 129,168
      0.0031%
      Admixed American
      1 / 35,440
      0.0028%
      + 6 not observed (African/African 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 has been reported in ClinVar as Uncertain significance (5 clinical laboratories) and as Likely pathogenic (1 clinical laboratory). (ClinVarID = 2158622)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.963. BayesDel score = 0.571004.
      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 previously been reported in somatic cancers (COSMIC; COSV65433356, n = 1 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      1papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 10 further PMIDs triaged but not cited — see Sources & References.
      PMID 25719457
      Found
      Gly115 is a glycine residue within the collagen triple-helical Gly-X-Y repeat domain a well-established critical functional domain glycine substitutions in collagen triple-helical domains are a classic pathogenic mechanism PMID:25719457 describes 21 COL4A1 mutations concentrated in the triple-helical domain associated with porencephaly and cerebrovascular disease
      Applied to
      PM1 supports · met
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 10 PMIDs not cited in assessment
      17078022 ↗ Consortium for osteogenesis imperfecta mutations in the helical domain of type I collagen: regions rich in lethal mutations align with collagen binding sites for integrins and proteoglycans. CLINVAR
      19344236 ↗ Collagen structure and stability. CLINVAR
      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
      8218237 ↗ Characterization of collagen-like peptides containing interruptions in the repeating Gly-X-Y sequence. CLINVAR
      20301386 ↗ Alport Syndrome. CLINVAR
      20301768 ↗ COL4A1-Related Disorders. CLINVAR
      9016532 ↗ The human type I collagen mutation database. CLINVAR
      25355838 ↗ Guidelines for the primary prevention of stroke: a statement for healthcare professionals from the American Heart Association/American Stroke Association. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR
      7695699 ↗ Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution. CLINVAR