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
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  • No CSPEC computer assertion could be determined for this classification!

  • See Evidence submitted by expert panel for details.

Variant: NM_000018.4(ACADVL):c.779C>T (p.Thr260Met)

CA341526

21024 (ClinVar)

Gene: ACADVL
Condition: very long chain acyl-CoA dehydrogenase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 8f14329e-15cc-4ab5-9fba-0d1602837b17

HGVS expressions

NM_000018.4:c.779C>T
NM_000018.4(ACADVL):c.779C>T (p.Thr260Met)
NC_000017.11:g.7222203C>T
CM000679.2:g.7222203C>T
NC_000017.10:g.7125522C>T
CM000679.1:g.7125522C>T
NC_000017.9:g.7066246C>T
NG_007975.1:g.7370C>T
NG_008391.2:g.2848G>A
ENST00000356839.10:c.779C>T
ENST00000322910.9:c.*734C>T
ENST00000350303.9:c.713C>T
ENST00000356839.9:c.779C>T
ENST00000543245.6:c.848C>T
ENST00000577191.5:n.951C>T
ENST00000581378.5:c.497C>T
ENST00000582379.1:n.163C>T
NM_000018.3:c.779C>T
NM_001033859.2:c.713C>T
NM_001270447.1:c.848C>T
NM_001270448.1:c.551C>T
NM_001033859.3:c.713C>T
NM_001270447.2:c.848C>T
NM_001270448.2:c.551C>T

Likely Pathogenic

Met criteria codes 5
PP3 PM3 PP4_Moderate PM2_Supporting PS3_Supporting

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
ACADVL VCEP
The NM_000018.4(ACADVL): c.779C>T (p.Thr260Met) variant is a missense variant predicted to cause substitution of threonine by methionine at amino acid 260. This variant has been detected in individuals with very long chain acyl CoA dehydrogenase (VLCAD) deficiency and VLCAD enzyme activity of less than 20%, which is highly specific for VLCAD deficiency (PP4_Moderate, PMID: 8845838, 17374501, 32518924). This variant was found homozygous in two individuals with VLCAD deficiency (PM3, 1.0 point, PMIDs: 9327992, 32518924). Two enzyme activity assays in Cos-7 cells and E.coli showed residual enzyme activity between 3-5% of wildtype indicating that this variant impacts protein function (PMIDs: indicating that this variant impacts protein function (PMID: 9973285, 9973285; PS3_supporting). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00002 in the non-Finnish European 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 0.875, 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_moderate, PP3, PP4_Moderate, PS3_supporting (ACADVL VCEP specifications version 1; approved November 9, 2021).
Met criteria codes
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
2 homozygous occurrences
PP4_Moderate
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2_Supporting
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3_Supporting
Approved on: 2024-05-16
Published on: 2024-05-16
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