Starting
Initialising…
0%
DDR2
Final classification
VUS
DDR2 c.1753A>G · p.Met585Val
DDR2

This variant is a missense substitution (c.1753A>G, p.Met585Val) in DDR2, a receptor tyrosine kinase associated with autosomal recessive 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.1753A>G
Consequence
N/A
GRCh38
chr1:162773493 A>G
GRCh37
chr1:162743283 A>G
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 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, 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 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
DDR2 c.1753A>G

This variant is a missense substitution (c.1753A>G, p.Met585Val) in DDR2, a receptor tyrosine kinase associated with autosomal recessive spondylo-meta-epiphyseal dysplasia with short limbs and abnormal calcifications (SMED-SL).1 The variant is extremely rare in large population databases: present in 5 of 282,840 alleles in gnomAD v2.1 (AF=0.00177%) and 44 of 1,613,842 alleles in gnomAD v4.1 (AF=0.00273%), with no homozygotes observed. It is absent from gnomAD-Canada.2 Multiple in silico predictors (REVEL 0.261, BayesDel -0.199, SpliceAI max delta 0.01) consistently suggest a benign impact on protein function and splicing.3 This variant has been reported in ClinVar as Uncertain significance by a single clinical laboratory (Ambry Genetics). No expert panel has reviewed this variant.4 No variant-specific functional studies, segregation data, de novo observations, or case-control data were identified in the literature or databases.5 All publications associated with this variant through ClinVar are general policy statements on newborn screening and carrier screening; none mention DDR2 or the specific variant NM_006182.3:c.1753A>G.6

PM2 + BP4 VUS
Gene diagram · NM_006182.3 · variants mapped to exon structure
DDR2 NM_006182.3
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= 2.72641e-05; MAF= 0.00273%, 44/1613842 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.47489e-05; MAF= 0.00347%, 41/1179892 alleles, homozygotes = 0); grpmax FAF= 2.585e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.76778e-05; MAF= 0.00177%, 5/282840 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 4.00481e-05; MAF= 0.00400%, 1/24970 alleles, homozygotes = 0); grpmax FAF= 7.01e-06.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0027% · 44 / 1,613,842
      0 hom · FAF 0.0026%
      European (non-Finnish)
      41 / 1,179,892
      0.0035%
      Remaining individuals
      2 / 62,456
      0.0032%
      African/African American
      1 / 74,918
      0.0013%
      + 7 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.0018% · 5 / 282,840
      0 hom · FAF 0.0007%
      African/African American
      1 / 24,970
      0.004%
      European (non-Finnish)
      4 / 129,156
      0.0031%
      + 6 not observed (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 has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 3080827)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.261. BayesDel score = -0.199945.
      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
      Triaged references · 5 PMIDs not cited in assessment
      23619275 ↗ ACMG position statement on prenatal/preconception expanded carrier screening. CLINVAR
      23652378 ↗ A framework to start the debate on neonatal screening policies in the EU: an Expert Opinion Document. CLINVAR
      25626707 ↗ Whole-genome sequencing in newborn screening? A statement on the continued importance of targeted approaches in newborn screening programmes. CLINVAR
      22947299 ↗ Specific guidelines for assessing and improving the methodological quality of economic evaluations of newborn screening. CLINVAR
      31022120 ↗ ACOG Committee Opinion No. 778 Summary: Newborn Screening and the Role of the Obstetrician-Gynecologist. CLINVAR