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DDR2
Final classification
VUS
DDR2 c.298G>A · p.Val100Met
DDR2

NM_006182.3:c.298G>A (p.Val100Met) is a missense variant in DDR2, a receptor tyrosine kinase gene in which missense variants cause spondylo-meta-epiphyseal dysplasia with short limbs and abnormal calcifications (SMED-SL).

Gene
DDR2
Transcript
NM_006182.3
HGVS · transcript:coding
NM_006182.3:c.298G>A
Consequence
N/A
GRCh38
chr1:162754736 G>A
GRCh37
chr1:162724526 G>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: PM2 moderate, PP3 supporting; combination = 1 moderate + 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: PM2 moderate, PP3 supporting; combination = 1 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
DDR2 c.298G>A

NM_006182.3:c.298G>A (p.Val100Met) is a missense variant in DDR2, a receptor tyrosine kinase gene in which missense variants cause spondylo-meta-epiphyseal dysplasia with short limbs and abnormal calcifications (SMED-SL).1 This variant is extremely rare in population databases: absent from gnomAD v2.1 and present at 2/1,614,106 alleles (AF=1.24e−06) in gnomAD v4.1, with a grpmax filtering allele frequency of 2.8e−07, meeting PM2 at moderate strength.2 In silico prediction tools support a deleterious effect: REVEL score 0.883 (strongly pathogenic), meeting PP3 at supporting strength.3 The variant is absent from ClinVar with no classifications from any submitter. No variant-specific functional data, de novo observations, or segregation information were available for assessment.4 Available evidence includes one moderate pathogenic criterion (PM2) and one supporting pathogenic criterion (PP3). No benign criteria are met. This evidence is insufficient to classify the variant as pathogenic or likely pathogenic under the ACMG/AMP 2015 framework. The variant is classified as a Variant of Uncertain Significance (VUS).5

PM2 + PP3 VUS
1 pvs1_gene_context
3 revel
5 generic_acmg_combination_rules
Gene diagram · NM_006182.3 · variants mapped to exon structure
DDR2 NM_006182.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 18 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
This variant is extremely rare in population databases. It is absent from gnomAD v2.1 and present at very low frequency in gnomAD v4.1 (total AF=1.24e−06; 2/1,614,106 alleles; 0 homozygotes; grpmax FAF=2.8e−07), well below the 0.1% threshold for PM2 application. The highest subpopulation frequency is in European (non-Finnish) at 1.69e−06 (2/1,179,998 alleles).
gnomAD v2.1: absent. gnomAD v4.1: 2/1614106 alleles (AF=1.24e−06
PP3 supporting Pathogenic
Multiple in silico prediction tools support a deleterious effect. REVEL score is 0.883 (strongly pathogenic; well above the 0.75 threshold). BayesDel score is 0.566 (intermediate, leaning deleterious). SpliceAI predicts no splicing impact (max delta=0.01), consistent with a missense-only effect. The high REVEL score provides supporting evidence for pathogenicity.
REVEL: 0.883 (strongly pathogenic>0.75). BayesDel: 0.566 (intermediate). SpliceAI: max delta=0.01 (no splice impact).
Assessed · not applied
Pathogenic
PS1 No pathogenic variant with the same amino acid change (p.Val100Met) arising from a different nucleotide substitution has been identified in ClinVar or the literature.
PS2 No proband phenotype, family history, or parental genotype data were provided.
PS3 No variant-specific functional studies or systematic range characterization that includes codon 100 were identified in the literature.
PS4 No case/control data or affected-vs-unaffected prevalence statistics were provided.
PM1 The variant p.Val100Met lies within the discoidin domain of DDR2, but it does not fall within a statistically significant mutational hotspot (cancerhotspots.org).
PM6 No de novo data or parental genotype information was available.
PP1 No family segregation data, pedigree, or co-segregation analysis was provided.
PP2 DDR2 missense variants are an established disease mechanism for SMED-SL (per PMID:24725993), but PP2 additionally requires evidence of a low rate of benign missense variation in the gene (high missense constraint).
PP4 No proband phenotype or clinical information was provided.
PP5 This variant is absent from ClinVar.
Benign
BA1 The variant frequency in gnomAD v4.1 (AF=1.24e−06, 0.00012%) is orders of magnitude below the BA1 threshold of 1% (>0.01).
BS1 The variant frequency in gnomAD v4.1 (AF=1.24e−06, 0.00012%) is well below the BS1 threshold of >0.3%.
BS2 No information was provided about whether this variant has been observed in healthy adults at an age when full penetrance of DDR2-related disease (SMED-SL) would be expected.
BS3 No well-established functional studies demonstrating a neutral or benign effect for this variant were identified.
BS4 No family segregation data were provided.
BP2 No phase data or co-occurrence information with a known pathogenic variant in DDR2 was available.
BP4 Multiple in silico predictors support a deleterious rather than benign effect.
BP6 This variant is absent from ClinVar.
N/A · 8 PVS1 · PM3 · PM4 · PM5 · BP1 · BP3 · BP5 · BP7
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= 1.23908e-06; MAF= 0.00012%, 2/1614106 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.69492e-06; MAF= 0.00017%, 2/1179998 alleles, homozygotes = 0); grpmax FAF= 2.8e-07.
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
0.00012% · 2 / 1,614,106
0 hom · FAF 2.8e-05%
European (non-Finnish)
2 / 1,179,998
0.00017%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
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 is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.883. BayesDel score = 0.566277.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. DDR2, a receptor tyrosine kinase, is mutated at low frequencies in various cancers.
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.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots