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Variant: NM_000018.4(ACADVL):c.562G>A (p.Gly188Ser)

CA397723170

838654 (ClinVar)

Gene: ACADVL
Condition: very long chain acyl-CoA dehydrogenase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 899e1465-0b1f-4c76-a4e9-f9669ff0edfd

HGVS expressions

NM_000018.4:c.562G>A
NM_000018.4(ACADVL):c.562G>A (p.Gly188Ser)
NC_000017.11:g.7221622G>A
CM000679.2:g.7221622G>A
NC_000017.10:g.7124941G>A
CM000679.1:g.7124941G>A
NC_000017.9:g.7065665G>A
NG_007975.1:g.6789G>A
NG_008391.2:g.3429C>T
ENST00000356839.10:c.562G>A
ENST00000322910.9:c.*517G>A
ENST00000350303.9:c.496G>A
ENST00000356839.9:c.562G>A
ENST00000543245.6:c.631G>A
ENST00000577191.5:n.639G>A
ENST00000577433.5:n.770G>A
ENST00000577857.5:n.378G>A
ENST00000579286.5:n.743G>A
ENST00000579886.2:c.400G>A
ENST00000580365.1:n.293G>A
ENST00000581378.5:n.280G>A
ENST00000581562.5:n.525-330G>A
ENST00000582166.1:n.543G>A
ENST00000583312.5:c.562G>A
ENST00000583760.1:n.344G>A
NM_000018.3:c.562G>A
NM_001033859.2:c.496G>A
NM_001270447.1:c.631G>A
NM_001270448.1:c.334G>A
NM_001033859.3:c.496G>A
NM_001270447.2:c.631G>A
NM_001270448.2:c.334G>A

Uncertain Significance

Met criteria codes 4
PP3 PP4_Moderate PM2_Supporting PM3_Supporting
Not Met criteria codes 7
BP2 BP7 PS1 PVS1 PM4 PM1 PM5

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
ACADVL VCEP
The c.562G>A variant in ACADVL is a missense variant predicted to cause substitution of glycine by serine at amino acid 188 (p.Gly188Ser). Information provided to the ACADVL VCEP provided by an external clinical laboratory shows increased C14:1 level in a pattern consistent with very long chain acyl-CoA dehydrogenase (VLCAD) deficiency in one patient (PP4_moderate) who was homozygous for the variant (PM3_supporting). One publication describes this variant in an affected individual, but this individual does not meet our PP4 guidelines and was not counted (Nikolayeva, E.A. et al., Symptomatic epilepsy as a manifestation of very long chain acyl-CoA dehydrogenase deficiency. 2008. Rossiiskii Vestnik Perinatologii i Pediatrii 53(3): 87-91 (in Russian)). This variant is absent from gnomAD v2.1.1. The computational predictor REVEL gives a score of 0.882, which is above the threshold of 0.75, evidence that correlates with impact to ACADVL function. In summary, this variant meets the criteria to be classified as a variant of uncertain significance 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_supporting, PP3, PP4_moderate (ACADVL VCEP specifications version 1; approved November 9, 2021). This variant was originally curated April 12, 2022 and the recurated classification was approved by the expert panel on April 11, 2023.
Met criteria codes
PP3
PP3 is met; REVEL score pre-calculated = 0.882; Alamut 3 of 4 predict variant affects protein function and/or stability.
PP4_Moderate
External clinical laboratory shows increased C14:1 level in a pattern consistent with VLCAD deficiency in one patient
PM2_Supporting
PM2_Supporting is met; Absent in gnomAD, ExAC, EVS, 1000 Genomes
PM3_Supporting
The VLCAD VCEP was provided information from an external laboratory regarding this variant being found in the homozygous state in an affected individual.
Not Met criteria codes
BP2
BP2 is not met; Variant has not been observed in cis with a pathogenic variant in ACADVL
BP7
BP7 is not met; Variant is a missense
PS1
No previously documented pathogenic nucleotide variant leading to the same amino acid change.
PVS1
PVS1 not met; variant is not LOF
PM4
PM4 is not met; variant is a missense
PM1
Variant located in critical and functional domain. p.Gly188 located on outer edge of hydrophbic pocket containing ligand (PMID:20060901).

PM5
No previously documented and different pathogenic missense at this codon.
Approved on: 2023-04-11
Published on: 2023-04-11
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