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Variant: NM_000018.4(ACADVL):c.1376G>A (p.Arg459Gln)

CA312275

203585 (ClinVar)

Gene: ACADVL
Condition: very long chain acyl-CoA dehydrogenase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 10b5273f-7a1b-4007-882c-82d17b0ed875

HGVS expressions

NM_000018.4:c.1376G>A
NM_000018.4(ACADVL):c.1376G>A (p.Arg459Gln)
NC_000017.11:g.7224011G>A
CM000679.2:g.7224011G>A
NC_000017.10:g.7127330G>A
CM000679.1:g.7127330G>A
NC_000017.9:g.7068054G>A
NG_007975.1:g.9178G>A
NG_008391.2:g.1040C>T
NG_033038.1:g.15534C>T
ENST00000356839.10:c.1376G>A
ENST00000322910.9:c.*1331G>A
ENST00000350303.9:c.1310G>A
ENST00000356839.9:c.1376G>A
ENST00000542255.6:n.234G>A
ENST00000543245.6:c.1445G>A
ENST00000578711.1:n.507G>A
ENST00000579425.5:n.492G>A
ENST00000579546.1:n.213G>A
ENST00000579894.5:n.87G>A
ENST00000583074.5:n.95G>A
ENST00000583850.5:n.151G>A
ENST00000583858.5:n.405G>A
ENST00000585203.6:n.567G>A
NM_000018.3:c.1376G>A
NM_001033859.2:c.1310G>A
NM_001270447.1:c.1445G>A
NM_001270448.1:c.1148G>A
NM_001033859.3:c.1310G>A
NM_001270447.2:c.1445G>A
NM_001270448.2:c.1148G>A

Pathogenic

Met criteria codes 5
PP4_Moderate PP3 PM1 PM3_Strong PM2_Supporting
Not Met criteria codes 1
PM5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
ACADVL VCEP
The c.1376G>A variant is a missense variant predicted to cause substitution of arginine by glutamine at amino acid 459 (p.Arg459Gln). This variant has been reported in at least 11 individuals with very long chain acyl-CoA dehydrogenase (VLCAD) deficiency in the literature with either significantly reduced VLCAD activity or increased C14:1 acylcarnitine levels, with two individuals displaying both reduced VLCAD activity and increased C14:1 acylcarnitine levels, which is highly specific for VLCAD deficiency (PP4_moderate; PMID: 30194637; PMID: 21429517; PMID: 19327992). In these individuals, the variant was detected three times in the homozygous state plus 1 confirmed in-trans and 5 not confirmed in-trans with the pathogenic variant c.848T>C (PM3_strong; PMID: 30194637; PMID: 21429517). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00004646 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 (PM2_Supporting). The variant is located in a well-studied dimerization domain which is critical for the protein's dimer interaction (PM1; PMID: 14517516). The computational predictor REVEL gives a score of 0.864, 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; PM1; PP3 (ACADVL VCEP specifications version 1; approved November 8, 2021).
Met criteria codes
PP4_Moderate
Several patients display either significantly reduced VLCAD activity or increased C14:1 acylcarnitine levels, with two displaying both at once.
PP3
REVEL score of 0.864
PM1
Variant is present in the ACADVL dimerization domain which is critical for the protein's dimer interaction.
PM3_Strong
3 homozygous occurences plus 1 confirmed in-trans w/ ClinVarID:21025 (Pathogenic) and 5 not confirmed in-trans w/ ClinVarID:21025 (Pathogenic). 1.0 + 1.0 + 0.5 = 2.5 Points.
PM2_Supporting
Highest gnomAD frequency at 0.00004646 for European (Non-Finnish)
Not Met criteria codes
PM5
Two additional variants in ClinVar. Evaluate if needed.
Approved on: 2022-08-09
Published on: 2022-08-09
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