The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000018.4(ACADVL):c.1405C>T (p.Arg469Trp)

CA341519

21017 (ClinVar)

Gene: ACADVL
Condition: very long chain acyl-CoA dehydrogenase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 761db2cd-44a8-4dbe-8084-fd08c20675c1
Approved on: 2024-12-10
Published on: 2024-12-10

HGVS expressions

NM_000018.4:c.1405C>T
NM_000018.4(ACADVL):c.1405C>T (p.Arg469Trp)
NC_000017.11:g.7224040C>T
CM000679.2:g.7224040C>T
NC_000017.10:g.7127359C>T
CM000679.1:g.7127359C>T
NC_000017.9:g.7068083C>T
NG_007975.1:g.9207C>T
NG_008391.2:g.1011G>A
NG_033038.1:g.15505G>A
ENST00000356839.10:c.1405C>T
ENST00000322910.9:c.*1360C>T
ENST00000350303.9:c.1339C>T
ENST00000356839.9:c.1405C>T
ENST00000542255.6:c.263C>T
ENST00000543245.6:c.1474C>T
ENST00000578711.1:n.536C>T
ENST00000579425.5:n.521C>T
ENST00000579546.1:c.242C>T
ENST00000579894.5:n.116C>T
ENST00000583074.5:n.124C>T
ENST00000583850.5:n.180C>T
ENST00000583858.5:c.434C>T
ENST00000585203.6:n.596C>T
NM_000018.3:c.1405C>T
NM_001033859.2:c.1339C>T
NM_001270447.1:c.1474C>T
NM_001270448.1:c.1177C>T
NM_001033859.3:c.1339C>T
NM_001270447.2:c.1474C>T
NM_001270448.2:c.1177C>T
More

Likely Pathogenic

Met criteria codes 6
PP4_Moderate PP3 PM3 PM1 PS3_Supporting PM2_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen ACADVL Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
ACADVL VCEP
The c.1405C>T variant in ACADVL is a missense variant predicted to cause substitution of Arginine by Tryptophan at amino acid 469 (p.Arg469Trp). This variant has been detected in at least 5 individuals with clinical signs of very long chain acyl CoA dehydrogenase (VLCAD) deficiency. Of these, 2 were heterozygous for the variant without an identified second variant in ACADVL (PMID: 9973285, Olpin SE et al. Int J Neonat Screen. 2017 3(1),2) and 3 individuals were homozygous for the variant (PM3 points = 1.0, PM3, PMID: 9973285). ACADVL activity in one patient's fibroblast cell line was observed at <=20% of normal (PMID: 17999356; PP4_Moderate). Expression of this variant using rACADVL in E. coli showed enzyme activity =< 20% of normal and absence of protein expression indicating that this variant impacts protein function; however, this assay did not use established benign variants as negative controls, and thus only meets criteria to be applied at supporting strength (PS3_Supporting; PMID: 17374501). This variant resides at a CpG di-nucleotide of ACADVL that is defined as a mutational hotspot by the ClinGen ACADVL Variant Curation Expert Panel (PM1; PMID: 9973285). The highest population minor allele frequency in gnomAD v2.1.1 is 0.0001087 in the EAS population, which is lower than the ClinGen ACADVL Variant Curation Expert Panel threshold (<0.001) for PM2_Supporting, meeting this criterion (PM2_Supporting). The computational predictor REVEL gives a score of 0.947, 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 very long chain acyl-CoA dehydrogenase (VLCAD) deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen ACADVL Variant Curation Expert Panel: PS3_Supporting, PM1, PM2_Supporting, PM3, PP3, PP4_Moderate (ACADVL VCEP specifications version 1; approved November 9, 2021).
Met criteria codes
PP4_Moderate
PP4_Moderate is met. This variant has been identified in at least 3 individuals in a homozygous state with clinical signs of very long chain acyl CoA dehydrogenase (VLCAD) (PMID: 9973285) where ACADVL activity in one patient's fibroblast cell line was observed at <=20% of normal (PMID: 17999356) (PP4_Moderate).
PP3
PP3 is met. The computational predictor REVEL gives a score of 0.947, which is above the threshold of 0.75, evidence that correlates with impact to ACADVL function (PP3).
PM3
PM3 is met. This variant has been detected in at least 5 individuals with very long chain acyl CoA dehydrogenase (VLCAD) deficiency. Of those individuals, 2 were heterozygous for the variant without an identified second distinct variant in ACADVL (PMIDs: 9973285, Olpin SE et al. Int J Neonat Screen. 2017 3(1),2); 3 individuals were homozygous for the variant (PM3 points = 1.0 max, PMID: 9973285) (PM3).
PM1
PM1 is met. This variant resides at a CpG di-nucleotide of ACADVL that is defined as a mutational hotspot by the ClinGen ACADVL Variant Curation Expert Panel (PMID: 9973285) (PM1).
PS3_Supporting
PS3_Supporting is met. rACADVL enzyme in E. coli showed enzyme activity =< 20% of normal and absence of protein expression indicating that this variant impacts protein function (PMID: 17374501); however, this assay did not use established benign variants as negative controls, and thus only meets criteria to be applied at supporting strength (PS3_Supporting).
PM2_Supporting
PM2_Supporting is met. The highest population minor allele frequency in gnomAD v2.1.1 is 0.0001087 in the EAS population, which is lower than the ClinGen ACADVL Variant Curation Expert Panel threshold (<0.001) for PM2_Supporting, meeting this criterion (PM2_Supporting).
Curation History
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