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Variant: NM_000018.4(ACADVL):c.790A>G (p.Lys264Glu)

CA397723695

941106 (ClinVar)

Gene: ACADVL
Condition: very long chain acyl-CoA dehydrogenase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 81022552-83d6-4505-8366-7915d471f92a

HGVS expressions

NM_000018.4:c.790A>G
NM_000018.4(ACADVL):c.790A>G (p.Lys264Glu)
NC_000017.11:g.7222214A>G
CM000679.2:g.7222214A>G
NC_000017.10:g.7125533A>G
CM000679.1:g.7125533A>G
NC_000017.9:g.7066257A>G
NG_007975.1:g.7381A>G
NG_008391.2:g.2837T>C
ENST00000356839.10:c.790A>G
ENST00000322910.9:c.*745A>G
ENST00000350303.9:c.724A>G
ENST00000356839.9:c.790A>G
ENST00000543245.6:c.859A>G
ENST00000577191.5:n.962A>G
ENST00000581378.5:n.508A>G
ENST00000582379.1:n.174A>G
NM_000018.3:c.790A>G
NM_001033859.2:c.724A>G
NM_001270447.1:c.859A>G
NM_001270448.1:c.562A>G
NM_001033859.3:c.724A>G
NM_001270447.2:c.859A>G
NM_001270448.2:c.562A>G

Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 5
PM3_Supporting PP3 PP4_Moderate PM2_Supporting PS3_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
ACADVL VCEP
The c.790A>G (NM_000018.4) variant in ACADVL is a missense variant predicted to cause substitution of lysine by glutamic acid at amino acid 264 (p.Lys264Glu). At least one patient with this variant displayed very long chain acyl-CoA dehydrogenase (VLCAD) activity <20% of normal, which is highly specific for VLCAD (PP4_Moderate, PMID: 17999356). This individual also carried a distinct pathogenic variant, though the variant was not confirmed to be in trans (PMID: 17999356; PM3_Supporting). The highest population minor allele frequency in gnomAD v2.1.1 is 0.0006 in the East Asian population, which is lower than the ClinGen ACADVL Variant Curation Expert Panel threshold (<0.001) for PM2_Supporting, meeting this criterion (PM2_Supporting). Transient transfection of this variant into fibroblasts showed reduced very long chain acyl-CoA dehydrogenase (VLCAD) activity indicating that this variant impacts protein function (PMID: 11914034; PS3_Supporting). The computational predictor REVEL gives a score of 0.871, which is above the threshold of 0.75, evidence that correlates with impact to ACADVL function (PP3). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal recessive VLCAD deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen ACADVL Variant Curation Expert Panel: PP4_Moderate, PM3_Supporting, PM2_supporting, PS3_Supporting (ACADVL VCEP specifications version 1; approved November 8, 2021).
Met criteria codes
PM3_Supporting
This variant has been detected in at least one individual with very long chain acyl CoA dehydrogenase (VLCAD) deficiency and a distinct pathogenic variant, though the variant was not confirmed to be in trans (PMID: 17999356; PM3_Supporting).
PP3
The computational predictor REVEL gives a score of 0.871, which is above the threshold of 0.75, evidence that correlates with impact to ACADVL function (PP3).
PP4_Moderate
At least one patient with this variant displayed very long chain acyl-CoA dehydrogenase (VLCAD) activity <20% of normal, which is highly specific for VLCAD (PP4_Moderate, PMID: 17999356).
PM2_Supporting
The highest population minor allele frequency in gnomAD v2.1.1 is 0.0006 in the East Asian population, which is lower than the ClinGen ACADVL Variant Curation Expert Panel threshold (<0.001) for PM2_Supporting, meeting this criterion (PM2_Supporting).
PS3_Supporting
Transient transfection of this variant into fibroblasts showed reduced very long chain acyl-CoA dehydrogenase (VLCAD) activity indicating that this variant impacts protein function (PMID: 11914034; PS3_Supporting).
Approved on: 2023-02-14
Published on: 2023-02-14
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