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Variant: NM_000018.4(ACADVL):c.1322G>A (p.Gly441Asp)

CA220193

21016 (ClinVar)

Gene: ACADVL
Condition: very long chain acyl-CoA dehydrogenase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 7632a574-ebef-41ce-8cb8-6a5028bf2de6

HGVS expressions

NM_000018.4:c.1322G>A
NM_000018.4(ACADVL):c.1322G>A (p.Gly441Asp)
NC_000017.11:g.7223865G>A
CM000679.2:g.7223865G>A
NC_000017.10:g.7127184G>A
CM000679.1:g.7127184G>A
NC_000017.9:g.7067908G>A
NG_007975.1:g.9032G>A
NG_008391.2:g.1186C>T
NG_033038.1:g.15680C>T
ENST00000356839.10:c.1322G>A
ENST00000322910.9:c.*1277G>A
ENST00000350303.9:c.1256G>A
ENST00000356839.9:c.1322G>A
ENST00000542255.6:n.180G>A
ENST00000543245.6:c.1391G>A
ENST00000578711.1:n.361G>A
ENST00000579425.5:n.346G>A
ENST00000579546.1:n.159G>A
ENST00000583074.5:n.41G>A
ENST00000583850.5:n.97G>A
ENST00000583858.5:n.351G>A
ENST00000585203.6:n.523+7G>A
NM_000018.3:c.1322G>A
NM_001033859.2:c.1256G>A
NM_001270447.1:c.1391G>A
NM_001270448.1:c.1094G>A
NM_001033859.3:c.1256G>A
NM_001270447.2:c.1391G>A
NM_001270448.2:c.1094G>A

Pathogenic

Met criteria codes 5
PP3 PM3_Strong PM1 PM2 PP4_Moderate
Not Met criteria codes 1
BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
ACADVL VCEP
The c.1322G>A (p.Gly441Asp) variant in ACADVL is a missense variant predicted to cause substitution of glycine by aspartic acid at amino acid 441. At least two individuals with this variant displayed VLCAD enzyme activity <20% of normal, which is highly specific for very long chain acyl CoA dehydrogenase (VLCAD) deficiency (PP4_Moderate; PMID: 25834949). The variant has been described in the homozygous state in at least 4 affected individuals, confirmed in trans to a pathogenic variant in at least one individual, and in at least one individual with a distinct pathogenic variant without determination of phase of the variants (PM3_Strong; PMIDs: 1648817, 17999356, 24305961, 30194637, 32061778). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00006 in the European (Non-Finnish) population, which is lower than the ClinGen ACADVL Variant Curation Expert Panel threshold (<0.001) for PM2_Supporting, meeting this criterion. This variant occurs adjacent to the FAD binding pocket and is located on a loop that contributes to dimer formation (PM1; PMID: 20060901). The computational predictor REVEL gives a score of 0.982, 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 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_Strong, PM2_Supporting, PP3 (ACADVL specifications version 1; approved November 8, 2021)
Met criteria codes
PP3
The computational predictor REVEL gives a score of 0.982, which is above the threshold of 0.75, evidence that correlates with impact to ACADVL function (PP3).
PM3_Strong
Variant has been described in the homozygous state in at least 4 individuals. Confirmed in trans to p.Arg366His (VCEP LP) Not confirmed in trans to c.753-2A>C (P by VCEP).
PM1
PMID 20060901 shows this is adjacent to the FAD binding pocket and is part of a Gly-Gly-x-Gly domain on the loop between monomers, contributing to dimer formation.
PM2
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00006 in the European (Non-Finnish) population, which is lower than the ClinGen ACADVL Variant Curation Expert Panel threshold (<0.001) for PM2_Supporting, meeting this criterion
PP4_Moderate
2 individuals in PMID 25834949 carried this variant and had VLCAD enzyme activity <20% of normal.
Not Met criteria codes
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2022-12-14
Published on: 2022-12-14
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