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 related information was provided by the message!
  • No CSPEC computer assertion could be determined for this classification!

  • See Evidence submitted by expert panel for details.

Variant: NM_000018.4(ACADVL):c.538G>A (p.Ala180Thr)

CA295584

166641 (ClinVar)

Gene: ACADVL
Condition: very long chain acyl-CoA dehydrogenase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: bef919f1-3031-42e2-911a-bf0cd70e9570

HGVS expressions

NM_000018.4:c.538G>A
NM_000018.4(ACADVL):c.538G>A (p.Ala180Thr)
NC_000017.11:g.7221598G>A
CM000679.2:g.7221598G>A
NC_000017.10:g.7124917G>A
CM000679.1:g.7124917G>A
NC_000017.9:g.7065641G>A
NG_007975.1:g.6765G>A
NG_008391.2:g.3453C>T
ENST00000356839.10:c.538G>A
ENST00000322910.9:c.*493G>A
ENST00000350303.9:c.472G>A
ENST00000356839.9:c.538G>A
ENST00000543245.6:c.607G>A
ENST00000577191.5:n.615G>A
ENST00000577433.5:n.746G>A
ENST00000577857.5:n.354G>A
ENST00000579286.5:n.719G>A
ENST00000579886.2:c.376G>A
ENST00000580365.1:n.269G>A
ENST00000581378.5:c.256G>A
ENST00000581562.5:n.525-354G>A
ENST00000582166.1:n.519G>A
ENST00000583312.5:c.538G>A
ENST00000583760.1:n.320G>A
NM_000018.3:c.538G>A
NM_001033859.2:c.472G>A
NM_001270447.1:c.607G>A
NM_001270448.1:c.310G>A
NM_001033859.3:c.472G>A
NM_001270447.2:c.607G>A
NM_001270448.2:c.310G>A

Likely Pathogenic

Met criteria codes 4
PM2_Supporting PP4_Moderate PP3 PM3
Not Met criteria codes 1
PM1

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
ACADVL VCEP
The c.538G>A (NM_000018.4) variant in ACADVL is a missense variant predicted to cause substitution of alanine by threonine at amino acid 180 (p.Ala180Thr). This variant has been reported in patients affected with very-long chain acyl-CoA dehydrogenase (VLCAD) deficiency, and elevated C14:1 and reduced VLCAD activity measured in patient lymphocytes (PP4_Moderate, PMID: 26385305, 31844625, 32778825, 30194637). At least one individual was compound heterozygote with a second ACADVL variant, at least one of these variants is confirmed in trans and approved by the ACADVL VCEP as likely pathogenic (PM3, 1 point, PMID: 31844625, 30194637). The highest population minor allele frequency in gnomAD is 0.00003 in the Latino 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 0.92, 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: PM2_Supporting, PM3, PP3, PP4_Moderate (ACADVL VCEP specifications version 1; approved November 9, 2021). This variant was originally curated December 14, 2022 and the recurated classification was approved by the expert panel on April 23, 2023.
Met criteria codes
PM2_Supporting
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00003 in the Latino population, which is lower than the ClinGen ACADVL Variant Curation Expert Panel threshold (<0.001) for PM2_Supporting, meeting this criterion (PM2_Supporting).
PP4_Moderate
At least one patient with this variant displayed enzyme levels (activity 3% of normal controls) which is highly specific for VLCAD (PP4_moderate) (PMID 30194637). Enriched in VLCADD; 5 alleles (Miller et al.) 4 alleles: heterozygote 1 allele: with p.V283A
PP3
The computational predictor REVEL gives a score of 0.916, which is above the threshold of 0.75, evidence that correlates with impact to ACADVL function (PP3).
PM3
Seen with p.R456H in Hesse et al. in one patient with 3% residual enzyme activity in lymphocytes, confirmed in trans per personal communication with author. This variant is curated as likely pathogenic by the ACADVL VCEP.
Not Met criteria codes
PM1
This variant resides within a region of ACADVL that is not defined as a critical functional domain by the ClinGen ACADVL Variant Curation Expert Panel. Specifically the variant is located near the enzyme active site (PMID 26385305), but not within the active site.

Approved on: 2024-04-23
Published on: 2024-04-23
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