NM_000018.4(ACADVL):c.779C>T (p.Thr260Met) AND Very long chain acyl-CoA dehydrogenase deficiency

Germline classification:: Likely pathogenic (10 submissions)
Last evaluated:: May 16, 2024
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000020080.36

Allele description [Variation Report for NM_000018.4(ACADVL):c.779C>T (p.Thr260Met)]

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

Gene:

ACADVL:acyl-CoA dehydrogenase very long chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

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

Other names:

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

HGVS:

NC_000017.11:g.7222203C>T
NG_007975.1:g.7370C>T
NG_008391.2:g.2848G>A
NM_000018.4:c.779C>TMANE SELECT
NM_001033859.3:c.713C>T
NM_001270447.2:c.848C>T
NM_001270448.2:c.551C>T
NP_000009.1:p.Thr260Met
NP_001029031.1:p.Thr238Met
NP_001257376.1:p.Thr283Met
NP_001257377.1:p.Thr184Met
NC_000017.10:g.7125522C>T
NM_000018.2:c.779C>T
NM_000018.3:c.779C>T
P49748:p.Thr260Met

Protein change:

T184M

Links:

UniProtKB: P49748#VAR_000339; dbSNP: rs113994168

NCBI 1000 Genomes Browser:

rs113994168

Molecular consequence:

NM_000018.4:c.779C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001033859.3:c.713C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001270447.2:c.848C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001270448.2:c.551C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Very long chain acyl-CoA dehydrogenase deficiency (ACADVLD)
Synonyms:: VLCAD deficiency
Identifiers:: MONDO: MONDO:0008723; MedGen: C3887523; Orphanet: 26793; OMIM: 201475

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RecName: Full=Hedgehog-interacting protein; Short=HHIP; Short=HIP; Flags: Precur...
RecName: Full=Hedgehog-interacting protein; Short=HHIP; Short=HIP; Flags: Precursor
gi|118572655|sp|Q96QV1.3|HHIP_HUMAN

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000220919	Counsyl	criteria provided, single submitter (Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))	Likely pathogenic (Nov 25, 2014)	unknown	literature only	PubMed (8) [See all records that cite these PMIDs] 10077518, 20060901, 20480395, 17374501, 9973285, 19327992, 25087612, 21932095 Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015), Citation Link,
SCV000654968	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 27, 2023)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 20060901, 21932095, 9973285, 17374501, 19327992, 28492532
SCV000916407	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Jul 2, 2018)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 19327992, 16950999 Citation Link,
SCV001156588	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Pathogenic (Oct 23, 2023)	germline	clinical testing	Citation Link,
SCV001163798	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 20, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001364903	Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 1, 2019)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 8845838, 25741868
SCV001455129	Natera, Inc.	no assertion criteria provided	Pathogenic (Sep 16, 2020)	germline	clinical testing
SCV002780147	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Aug 16, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003808427	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 24, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005077914	ClinGen ACADVL Variant Curation Expert Panel, ClinGen	reviewed by expert panel (clingen acadvl acmg specifications v1)	Likely Pathogenic (May 16, 2024)	germline	curation	PubMed (2) [See all records that cite these PMIDs] 9973285, 17374501 Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing, curation
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing, literature only

Citations

PubMed

Molecular heterogeneity in very-long-chain acyl-CoA dehydrogenase deficiency causing pediatric cardiomyopathy and sudden death.

Mathur A, Sims HF, Gopalakrishnan D, Gibson B, Rinaldo P, Vockley J, Hug G, Strauss AW.

Circulation. 1999 Mar 16;99(10):1337-43.

PubMed [citation]

PMID:: 10077518

High-resolution melting analysis, a simple and effective method for reliable mutation scanning and frequency studies in the ACADVL gene.

Olsen RK, Dobrowolski SF, Kjeldsen M, Hougaard D, Simonsen H, Gregersen N, Andresen BS.

J Inherit Metab Dis. 2010 Jun;33(3):247-60. doi: 10.1007/s10545-010-9101-y. Epub 2010 May 18.

PubMed [citation]

PMID:: 20480395

See all PubMed Citations (12)

Details of each submission

From Counsyl, SCV000220919.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (8)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000654968.9

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 260 of the ACADVL protein (p.Thr260Met). This variant is present in population databases (rs113994168, gnomAD 0.003%). This missense change has been observed in individual(s) with very-long-chain acyl-CoA dehydrogenase deficiency (PMID: 9973285, 19327992, 20060901, 21932095). ClinVar contains an entry for this variant (Variation ID: 21024). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ACADVL protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects ACADVL function (PMID: 9973285, 17374501, 19327992). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000916407.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Variant summary: ACADVL c.779C>T (p.Thr260Met) results in a non-conservative amino acid change located in the Acyl-CoA oxidase/dehydrogenase, central domain of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2e-05 in 246264 control chromosomes (gnomAD). c.779C>T has been reported in the literature in multiple individuals affected with Very Long Chain Acyl-CoA Dehydrogenase Deficiency as both a homozygous and compound heterozygous allele (Liebig_2006, Laforet_2009). These data indicate that the variant is very likely to be associated with disease. One publication reports experimental evidence showing a significant decrease (<10% of normal) in VLCAD activity in patient fibroblasts (Laforet_2009). Two ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as "pathogenic." Based on the evidence outlined above, the variant was classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001156588.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The ACADVL c.779C>T; p.Thr260Met variant (rs113994168), also known as Thr220Met, has been reported in multiple individuals diagnosed with very long chain acyl-CoA dehydrogenase deficiency, often found in-trans with another pathogenic variant (Andresen 1996, Andresen 1999, Gobin-Limballe 2010, Laforet 2009, Mathur 1999). Additionally, functional characterization of the variant protein in patient fibroblasts demonstrate significantly decreased enzymatic activity (Andresen 1996, Andresen 1999, Hoffman 2012, Laforet 2009). This variant is reported in ClinVar (Variation ID: 21024) and observed in the general population at a low overall frequency of 0.002% (5/246264 alleles) in the Genome Aggregation Database. The threonine at residue 260 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.875). Based on available information, this variant is considered pathogenic. References: Andresen B et al. Cloning and characterization of human very-long-chain acyl-CoA dehydrogenase cDNA, chromosomal assignment of the gene and identification in four patients of nine different mutations within the VLCAD gene. Hum Mol Genet. 1996; 5(4):461-72. PMID: 8845838. Andresen B et al. Clear correlation of genotype with disease phenotype in very-long-chain acyl-CoA dehydrogenase deficiency. Am J Hum Genet. 1999; 64(2):479-94. PMID: 9973285. Gobin-Limballe S et al. Compared effects of missense mutations in Very-Long-Chain Acyl-CoA Dehydrogenase deficiency: Combined analysis by structural, functional and pharmacological approaches. Biochim Biophys Acta. 2010; 1802(5):478-84. PMID: 20060901. Hoffman L et al. VLCAD enzyme activity determinations in newborns identified by screening: a valuable tool for risk assessment. J Inherit Metab Dis. 2012; 35(2):269-77. PMID: 21932095. Laforet P et al. Diagnostic assessment and long-term follow-up of 13 patients with Very Long-Chain Acyl-Coenzyme A dehydrogenase (VLCAD) deficiency. Neuromuscul Disord. 2009; 19(5):324-9. PMID: 19327992. Mathur A et al. Molecular heterogeneity in very-long-chain acyl-CoA dehydrogenase deficiency causing pediatric cardiomyopathy and sudden death. Circulation. 1999; 99(10):1337-43. PMID: 10077518.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV001163798.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine, SCV001364903.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

The NM_000018.3:c.779C>T (NP_000009.1:p.Thr260Met) [GRCH38: NC_000017.11:g.7222203C>T] variant in ACADVL gene is interpretated to be Pathogenic based on ACMG guidelines (PMID: 25741868). This variant has been reported in PMID: 8845838. This variant meets the following evidence codes reported in the ACMG guidelines: PS1, PS3

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV001455129.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Fulgent Genetics, Fulgent Genetics, SCV002780147.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV003808427.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From ClinGen ACADVL Variant Curation Expert Panel, ClinGen, SCV005077914.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (2)

Description

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).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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