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Variant: NM_000018.4(ACADVL):c.553G>A (p.Gly185Ser)

CA312291

203595 (ClinVar)

Gene: ACADVL
Condition: very long chain acyl-CoA dehydrogenase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 8afbaea5-9102-49ce-8a97-24f04d4611c1

HGVS expressions

NM_000018.4:c.553G>A
NM_000018.4(ACADVL):c.553G>A (p.Gly185Ser)
NC_000017.11:g.7221613G>A
CM000679.2:g.7221613G>A
NC_000017.10:g.7124932G>A
CM000679.1:g.7124932G>A
NC_000017.9:g.7065656G>A
NG_007975.1:g.6780G>A
NG_008391.2:g.3438C>T
ENST00000356839.10:c.553G>A
ENST00000322910.9:c.*508G>A
ENST00000350303.9:c.487G>A
ENST00000356839.9:c.553G>A
ENST00000543245.6:c.622G>A
ENST00000577191.5:n.630G>A
ENST00000577433.5:n.761G>A
ENST00000577857.5:n.369G>A
ENST00000579286.5:n.734G>A
ENST00000579886.2:c.391G>A
ENST00000580365.1:n.284G>A
ENST00000581378.5:n.271G>A
ENST00000581562.5:n.525-339G>A
ENST00000582166.1:n.534G>A
ENST00000583312.5:c.553G>A
ENST00000583760.1:n.335G>A
NM_000018.3:c.553G>A
NM_001033859.2:c.487G>A
NM_001270447.1:c.622G>A
NM_001270448.1:c.325G>A
NM_001033859.3:c.487G>A
NM_001270447.2:c.622G>A
NM_001270448.2:c.325G>A

Likely Pathogenic

Met criteria codes 4
PP3 PP4_Moderate PM3 PM2_Supporting
Not Met criteria codes 2
PS3 PM1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
ACADVL VCEP
The c.553G>A variant in ACADVL is a missense variant predicted to cause substitution of glycine by serine at amino acid 185 (p.Gly185Ser). This variant has been detected in at least 4 individuals with very long chain acyl CoA dehydrogenase (VLCAD) deficiency. Of those individuals, two were compound heterozygous for the variant and distinct pathogenic variants (PM3, PMIDs: 31620161, 17999356). Two patients with this variant displayed beta Oxidation Flux <20% of normal and at least one individual showed increased acylcarnitines, which is highly specific for very long chain acyl CoA dehydrogenase (VLCAD) deficiency (PP4_moderate, PMIDs: 17999356, 31620161, 22841441). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00005 in East Asian 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 0.971, 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: PM3, PP4_moderate, PM2_Supporting, PP3 (ACADVL VCEP specifications version 1; approved November 8, 2021).
Met criteria codes
PP3
The computational predictor REVEL gives a score of 0.971, which is above the threshold of 0.75, evidence that correlates with impact to ACADVL function (PP3).
PP4_Moderate
Two patients with this variant displayed ꞵ-Oxidation Flux <20% of normal and at least one individual showed increased acylcarnitines, which is highly specific for for very long chain acyl CoA dehydrogenase (VLCAD) deficiency (PP4_moderate, PMID 17999356, 31620161).
PM3
Presumed in trans to c.753-2A>C (0.5) Presumed in trans to c.848T>C (0.5) Presumed in trans to c.878+1G>C (not yet curated)
PM2_Supporting
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00005 in East Asian 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
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
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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