Variant classification summary

NM_001845.5:c.343G>A

COL4A1 · NP_001836.3:p.(Gly115Ser) · NM_001845.5

GRCh37: chr13:110864808 C>T · GRCh38: chr13:110212461 C>T

Gene: COL4A1 Transcript: NM_001845.5

Final call

VUS

PM1 moderate PM2 supporting PP3 supporting

Variant details

Gene

COL4A1

Transcript

NM_001845.5

Protein

NP_001836.3:p.(Gly115Ser)

gnomAD AF

1.9207415301494462e-05 (v4.1)

ClinVar

Uncertain significance

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

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.

2

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.

3

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.

4

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.

5

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.

6

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.

7

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.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	PVS1 is reserved for null variants (nonsense, frameshift, canonical ±1,2 splice site). NM_001845.5:c.343G>A is a missense variant (p.Gly115Ser) and does not qualify for any PVS1 strength tier under the ClinGen SVI PVS1 decision tree (PMC6185798).	pvs1_generic_framework
PS1	Not met	No alternative nucleotide change at codon 343 producing the same amino acid substitution (Gly115Ser) with a known pathogenic classification was identified in ClinVar or the literature. PS1 requires a different nucleotide change at the same codon resulting in the same missense change that has been established as pathogenic.
PS2	Not assessed	Exploratory evidence recovery suggests a de novo observation of this variant in a proband with porencephaly (Gould et al., 2005, PMID:15905400), but maternity/paternity was not confirmed and the variant-specific de novo observation could not be independently verified from the PubMed abstract. If confirmed with paternity testing, this would qualify as PS2. Without paternity confirmation, it falls to PM6_supporting.
PS3	Not assessed	Exploratory evidence recovery suggests functional studies in HEK293 cells showed intracellular accumulation and impaired collagen IV secretion for the p.Gly115Ser mutant (PMID:15905400), demonstrating a dominant-negative effect. However, the variant-specific functional data could not be independently verified from the PubMed abstract alone. If confirmed from full text, this well-established assay supports PS3_supporting.
PS4	Not met	The variant is present in ClinVar (ID 2158622) with multiple submissions from clinical laboratories, but no statistically significant enrichment (odds ratio) in affected individuals versus the general population has been computed. PS4 requires demonstration that the variant prevalence in cases significantly exceeds that in controls. The variant is also present in gnomAD at very low frequency (v2.1: 5/282,856; v4.1: 31/1,613,960), which would factor into an enrichment analysis.	clinvar gnomad_v2 gnomad_v4
PS5	Not met	ClinVar has one Likely pathogenic submission (Labcorp Genetics, SCV003470144) among six total submissions, with five clinical laboratories classifying as Uncertain significance. PS5 requires a reputable source to have recently reported the variant as pathogenic with the supporting evidence being unavailable for independent evaluation. A single LP submission against a majority VUS classification does not meet this threshold.	clinvar
PM1	Met	The variant substitutes Gly115 in the collagen triple-helical domain (Gly-X-Y repeat region). Glycine residues in the collagen triple-helical domain are structurally essential for proper helix formation; glycine substitutions in this domain are a well-established pathogenic mechanism across all collagen genes, including COL4A1. This residue lies within a critical functional domain where pathogenic missense variants cluster and benign variation is extremely rare. The COL4A1/COL4A2 clinical spectrum literature (PMID:25719457) confirms a high density of pathogenic mutations in this domain.
PM2	Met	The variant is extremely rare in population databases: gnomAD v2.1 allele frequency is 0.00177% (5/282,856 alleles, 0 homozygotes), gnomAD v4.1 allele frequency is 0.00192% (31/1,613,960 alleles, 0 homozygotes), and it is absent from gnomAD-Canada v1.0. All frequencies are well below the 0.1% PM2 threshold. The highest subpopulation frequency is 0.00310% in European (non-Finnish) in v2.1 and 0.00267% in African/African American in v4.1.	gnomad_v2 gnomad_v4
PM5	N/A	PM5 requires a different pathogenic missense variant at the same amino acid residue. No same-residue comparator variants at Gly115 were identified in ClinVar or the literature. The PM5 candidate harvest returned zero candidates at this residue.
PM6	Not assessed	Exploratory evidence recovery reports that a proband with porencephaly was heterozygous for c.343G>A with both parents wild-type (PMID:15905400, Gould et al. 2005). Paternity/maternity was not confirmed, placing this observation in the PM6 (assumed de novo) category. However, variant-specific confirmation could not be obtained from the PubMed abstract alone. If verified from full text, this qualifies as PM6_supporting.
PP1	Not met	No evidence of cosegregation of this variant with disease in multiple affected family members has been identified. The variant was reported as a de novo event in the index case (exploratory evidence, unverified), precluding cosegregation analysis from that family. No additional families with this variant and multiple affected members have been reported.
PP2	Not met	PP2 is applicable when a missense variant occurs in a gene with a low rate of benign missense variation and where pathogenic missense variants are a common mechanism. While COL4A1-related disorders are known to be caused by missense variants (particularly glycine substitutions), no specific COL4A1 missense constraint data (e.g., gnomAD missense Z-score, regional constraint metrics) was provided in the case evidence to support PP2 application.
PP3	Met	Multiple in silico predictors support a deleterious effect of this missense variant. REVEL score is 0.963 (highly pathogenic-leaning, well above the 0.5 threshold). BayesDel score is 0.571 (damaging, above the 0.5 threshold). SpliceAI predicts no significant splice impact (max delta = 0.01), which is expected for a deep exonic missense variant. The combination of REVEL and BayesDel scores provides supporting evidence for pathogenicity.	revel bayesdel spliceai
PP4	Not met	No patient phenotype or family history information was provided in the case summary. PP4 requires that the patient's phenotype or family history is highly specific for a disease with a single genetic etiology.
PP5	Not met	PP5 requires that a reputable source (e.g., clinical laboratory, expert panel) has recently reported the variant as pathogenic with the supporting evidence not available for independent evaluation. In ClinVar, 5 of 6 clinical laboratories classify this variant as Uncertain significance, with only 1 (Labcorp Genetics) classifying as Likely pathogenic. The majority classification is VUS, and no expert panel has reviewed this variant. This does not meet the PP5 threshold.	clinvar
BA1	Not met	The variant allele frequency in gnomAD is approximately 0.002% (v2.1: 0.00177%, v4.1: 0.00192%), far below the BA1 threshold of >1%. This criterion is clearly not met.	gnomad_v2 gnomad_v4
BS1	Not met	The variant allele frequency in gnomAD is approximately 0.002% (v2.1: 0.00177%, v4.1: 0.00192%), well below the BS1 threshold of >0.3%. This variant is too rare in population databases to meet BS1.	gnomad_v2 gnomad_v4
BS2	Not met	No evidence that this variant has been observed in healthy adult individuals for whom COL4A1-related disorders would be expected to manifest with full penetrance at an early age. The variant's extreme rarity in population databases and absence of homozygous observations are inconsistent with a benign variant observed in healthy adults.
BS3	Not met	BS3 requires well-established in vitro or in vivo functional studies demonstrating no damaging effect on protein function or splicing. The available evidence points in the opposite direction: exploratory evidence (PMID:15905400, unverified) suggests impaired collagen IV secretion, and in silico predictors (REVEL 0.963, BayesDel 0.571) support a deleterious effect. No studies suggest a benign functional impact.
BS4	Not met	No evidence of non-segregation with disease has been identified. No reports exist of this variant being present in unaffected family members while absent from affected members in the same family. The variant's extreme rarity and reported association with disease (ClinVar LP submission, exploratory de novo report) are inconsistent with BS4.
BP1	Not met	BP1 applies when a missense variant occurs in a gene where only truncating variants cause disease. COL4A1-related disorders (porencephaly, cerebral small vessel disease, HANAC syndrome) are well-established to be caused by missense variants, particularly glycine substitutions in the triple-helical domain. The disease mechanism is primarily dominant-negative, not haploinsufficiency. BP1 is clearly not applicable.
BP2	Not met	BP2 applies when a variant is observed in trans with a known pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant in any inheritance pattern. No such observations have been reported for this variant. COL4A1 disorders are autosomal dominant, and observation in trans with another pathogenic COL4A1 allele would not be expected.
BP4	Not met	BP4 requires multiple lines of computational evidence suggesting no impact on gene or gene product. REVEL score is 0.963 (highly pathogenic-leaning) and BayesDel is 0.571 (damaging), both predicting a deleterious effect, not a benign one. SpliceAI delta max of 0.01 predicts no splice impact, but this alone is insufficient to offset the strong pathogenic predictions from missense-specific tools.	revel bayesdel spliceai
BP5	Not met	BP5 requires that a reputable source has recently reported the variant as benign with the supporting evidence not available for independent evaluation. No clinical laboratory or expert panel has classified this variant as benign or likely benign. All ClinVar submissions classify as VUS or LP.	clinvar
BP6	Not met	BP6 requires that a reputable source has recently reported the variant as benign with the supporting evidence available for independent evaluation. No reputable source has classified this variant as benign. All ClinVar classifications are VUS or LP.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) variants for which splicing prediction algorithms predict no impact to the splice site consensus sequence nor creation of a new splice site. NM_001845.5:c.343G>A is a missense variant (p.Gly115Ser), not a synonymous variant. BP7 is not applicable.

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