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Variant: NM_000018.4(ACADVL):c.104del (p.Pro35fs)

CA624861220

541718 (ClinVar)

Gene: ACADVL
Condition: very long chain acyl-CoA dehydrogenase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: d4bf1068-23a1-499a-842b-683684db2c60

HGVS expressions

NM_000018.4:c.104del
NM_000018.4(ACADVL):c.104del (p.Pro35fs)
NC_000017.11:g.7220163del
CM000679.2:g.7220163del
NC_000017.10:g.7123482del
CM000679.1:g.7123482del
NC_000017.9:g.7064206del
NG_007975.1:g.5330del
NG_008391.2:g.4890del
ENST00000356839.10:c.104del
ENST00000322910.9:c.*59del
ENST00000350303.9:c.104del
ENST00000356839.9:c.104del
ENST00000543245.6:c.173del
ENST00000577191.5:n.181del
ENST00000577857.5:n.194del
ENST00000578269.5:n.211del
ENST00000578421.1:n.238del
ENST00000579286.5:n.211del
ENST00000579886.2:c.104del
ENST00000580263.5:n.194del
ENST00000581562.5:n.151del
ENST00000582056.5:n.194del
ENST00000582356.5:n.229del
ENST00000583312.5:c.104del
ENST00000584103.5:c.104del
NM_000018.3:c.104del
NM_001033859.2:c.104del
NM_001270447.1:c.173del
NM_001270448.1:c.-125del
NM_001033859.3:c.104del
NM_001270447.2:c.173del
NM_001270448.2:c.-125del

Pathogenic

Met criteria codes 4
PVS1 PP4_Moderate PM3 PM2_Supporting
Not Met criteria codes 4
BP7 PS1 PM4 PM5

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.104del (p.(Pro35Leufs*26)) (NM_000018.4) variant in ACADVL is a frameshift variant predicted to cause a premature stop codon in biologically-relevant-exon 2/20 leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1; PMIDs: 9973285, 11590124). This variant has been detected in at least 4 individuals with VLCADD. Of those individuals, 1 was compound heterozygous for the variant and a pathogenic or likely pathogenic variant and was not confirmed in trans (PM3 0.5 pt, PMID: 25834949). 3 individuals were homozygous for the variant (PM3 1.0 point max., PMIDs: 25834949, 32276429) (PM3). The highest population minor allele frequency in gnomAD v2.1.1 is 0.007886%(2/25360 alleles) in AMR population, which is lower than the ClinGen ACADVL VCEP threshold (<0.1%) for PM2_Supporting, meeting this criterion (PM2_Supporting). To our knowledge, functional assays have not been reported for this variant. To our knowledge, this variant has not been reported in the literature for segregation in family members affected with VLCADD. In summary, this variant has been classified as pathogenic for autosomal recessive very long chain acyl-CoA dehydrogenase deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen ACADVL Curation Expert Panel: PVS1, PM3, PP4_Moderate, PM2_Supporting (ACADVL VCEP specifications v2.0; Approved on 10/11/2021).
Met criteria codes
PVS1
PVS1 met. The c.104del (p.(Pro35Leufs*26)) (NM_000018.4) variant in ACADVL is a frameshift variant predicted to cause a premature stop codon in biologically-relevant-exon 2/20 leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1; PMIDs: 9973285, 11590124).
PP4_Moderate
At least 4 patients with this variant displayed <=20% ACADVL enzyme activity and/or > 1uM C14:1, which is highly specific for VLCADD (PP4_Moderate, PMIDs: 25834949, 32276429).
PM3
PM3 is met. This variant has been detected in at least 4 individuals with VLCADD. Of those individuals, 1 was compound heterozygous for the variant and a pathogenic or likely pathogenic variant and was not confirmed in trans (PM3 0.5 pt, PMID: 25834949). 3 individuals were homozygous for the variant (PM3 1 point max., PMIDs: 25834949, 32276429) (PM3_Strong).
PM2_Supporting
PM2_Supporting (met). The highest population minor allele frequency in gnomAD v2.1.1 is 0.007886%(2/25360 alleles) in AMR population, which is lower than the ClinGen ACADVL VCEP threshold (<0.1%) for PM2_Supporting, meeting this criterion (PM2_Supporting).
Not Met criteria codes
BP7
Criterion not met because variant is a deletion predicted to result in a frameshift and premature termination codon.
PS1
Criterion not met because variant is a deletion predicted to result in a frameshift and premature termination codon.
PM4
Criterion not met because variant is a deletion predicted to result in a frameshift and premature termination codon.
PM5
Criterion not met because variant is a deletion predicted to result in a frameshift and premature termination codon.
Approved on: 2022-04-06
Published on: 2022-07-12
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