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Variant: NM_000018.4(ACADVL):c.642_643del (p.Phe214fs)

CA774742300

1073342 (ClinVar)

Gene: ACADVL
Condition: very long chain acyl-CoA dehydrogenase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 2b712c1a-a7fc-4ff4-8314-e2abd6f5a774
Approved on: 2022-12-14
Published on: 2022-12-15

HGVS expressions

NM_000018.4:c.642_643del
NM_000018.4(ACADVL):c.642_643del (p.Phe214fs)
NC_000017.11:g.7221971_7221972del
CM000679.2:g.7221971_7221972del
NC_000017.10:g.7125290_7125291del
CM000679.1:g.7125290_7125291del
NC_000017.9:g.7066014_7066015del
NG_007975.1:g.7138_7139del
NG_008391.2:g.3080_3081del
ENST00000356839.10:c.642_643del
ENST00000322910.9:c.*597_*598del
ENST00000350303.9:c.576_577del
ENST00000356839.9:c.642_643del
ENST00000543245.6:c.711_712del
ENST00000577191.5:n.719_720del
ENST00000577857.5:n.458_459del
ENST00000579286.5:n.823_824del
ENST00000580365.1:n.373_374del
ENST00000581378.5:n.360_361del
ENST00000581562.5:n.544_545del
ENST00000582379.1:n.26_27del
ENST00000583312.5:c.657_658del
ENST00000583760.1:n.424_425del
NM_000018.3:c.642_643del
NM_001033859.2:c.576_577del
NM_001270447.1:c.711_712del
NM_001270448.1:c.414_415del
NM_001033859.3:c.576_577del
NM_001270447.2:c.711_712del
NM_001270448.2:c.414_415del

Pathogenic

Met criteria codes 3
PVS1 PP4 PM2_Supporting
Not Met criteria codes 1
PM3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
ACADVL VCEP
The c.642_643del (p.Phe214LeufsTer38) variant in ACADVL is a frameshift variant predicted to cause a premature stop codon in biologically-relevant-exon 9/20 leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1; PMIDs 9973285, 11590124). At least one patient with this variant displayed increased acylcarnitine levels, which is highly specific for very long chain acyl CoA dehydrogenase (VLCAD) deficiency (PP4, PMID: 31620161). Additionally, two individuals carried a distinct likely pathogenic variant not confirmed to be in trans, but one of these individuals was not confirmed by biochemical testing to be affected with VLCAD deficiency (PMID: 35400565). The highest population minor allele frequency in gnomAD v3.1.2 is 0.00001470 in European (non-Finnish) population, which is lower than the ClinGen ACADVL Variant Curation Expert Panel threshold (<0.001) for PM2_Supporting, meeting this criterion (PM2_Supporting). 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: PVS1, PM2_Moderate, PP4 (ACADVL VCEP specifications version 1; approved November 8, 2021).
Met criteria codes
PVS1
The c.642_643del (p.Phe214LeufsTer38) variant in ACADVL is a frameshift variant predicted to cause a premature stop codon in biologically-relevant-exon 9/20 leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1; PMIDs 9973285, 11590124).
PP4
At least one patient with this variant displayed increased acylcarnitine levels, which is highly specific for very long chain acyl CoA dehydrogenase (VLCAD) deficiency (PP4, PMID: 31620161).
PM2_Supporting
The highest population minor allele frequency in gnomAD v3.1.2 is 0.00001470 in European (non-Finnish) population, which is lower than the ClinGen ACADVL Variant Curation Expert Panel threshold (<0.001) for PM2_Supporting, meeting this criterion (PM2_Supporting).
Not Met criteria codes
PM3
1 time not confirmed in trans to c.1349G>A, patient met PP4. 1 time not confirmed in trans to c.1349G>A, but patient didn't meet PP4. Not counted.
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