1-75761161-A-G
Variant summary
Our verdict is Pathogenic. The variant received 11 ACMG points: 13P and 2B. PM1PM5PP2PP5_Very_StrongBP4BS2_Supporting
The NM_000016.6(ACADM):c.985A>G(p.Lys329Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00582 in 1,614,074 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K329Q) has been classified as Pathogenic.
Frequency
Consequence
NM_000016.6 missense
Scores
Clinical Significance
Conservation
Publications
- medium chain acyl-CoA dehydrogenase deficiencyInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, PanelApp Australia, ClinGen, Orphanet
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ACMG classification
Our verdict: Pathogenic. The variant received 11 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ACADM | NM_000016.6 | c.985A>G | p.Lys329Glu | missense_variant | Exon 11 of 12 | ENST00000370841.9 | NP_000007.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ACADM | ENST00000370841.9 | c.985A>G | p.Lys329Glu | missense_variant | Exon 11 of 12 | 1 | NM_000016.6 | ENSP00000359878.5 |
Frequencies
GnomAD3 genomes 0.00345 AC: 526AN: 152254Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00333 AC: 836AN: 251374 AF XY: 0.00302 show subpopulations
GnomAD4 exome AF: 0.00607 AC: 8872AN: 1461700Hom.: 19 Cov.: 31 AF XY: 0.00592 AC XY: 4306AN XY: 727162 show subpopulations
Age Distribution
GnomAD4 genome 0.00345 AC: 526AN: 152374Hom.: 0 Cov.: 32 AF XY: 0.00323 AC XY: 241AN XY: 74512 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Medium-chain acyl-coenzyme A dehydrogenase deficiency Pathogenic:35Other:1
This variant is classified as Pathogenic. Evidence in support of pathogenic classification: Variant is present in gnomAD (v4) <0.01 for a recessive condition (9,360 heterozygotes, 19 homozygotes). It is a known founder mutation within the Northern European population (PMID: 20301597); This variant has very strong previous evidence of pathogenicity in unrelated individuals. Also known as p.(Lys304Glu) in the literature, this variant accounts for 56-91% of MCAD-deficiency causing alleles (PMID: 20301597, ClinVar). This variant has also been reported in the heterozygous state in individuals with false positive newborn screening results for MCAD-deficiency who were later determined to be unaffected by confirmatory testing (PMID: 23151387). Additional information: Variant is predicted to result in a missense amino acid change from lysine to glutamic acid; This variant is heterozygous; This gene is associated with autosomal recessive disease; Variant is located in the annotated Acyl-CoA dehydrogenase, C-terminal domain (DECIPHER); Missense variant with conflicting in silico predictions and uninformative conservation; Loss of function is a known mechanism of disease in this gene and is associated with deficiency of medium chain acyl-CoA dehydrogenase (MCAD) (MIM#201450); Variants in this gene are known to have variable expressivity. Clinical presentation varies from asymptomatic to fulminant course (OMIM); This variant has been shown to be paternally inherited by trio analysis.
The ACADM c.985A>G; p.Lys329Glu variant (rs77931234) is the most common pathogenic variant associated with MCAD deficiency (Andresen 2001, Sturm 2012, Yokota 1990). Functional characterization of fibroblasts from homozygous individuals show reduced residual enzymatic activity (Sturm 2012) with the variant protein below the detection level in western blot analysis (Yokota 1990). The variant is listed as pathogenic in ClinVar (Variation ID: 3586), and observed in the general population in 0.33% (941/282,786 alleles, including 1 homozygote) in the Genome Aggregation Database (v2.1.1). Based on the above information, the p.Lys329Glu variant is classified as pathogenic. References: Andresen B et al. Medium-chain acyl-CoA dehydrogenase (MCAD) mutations identified by MS/MS-based prospective screening of newborns differ from those observed in patients with clinical symptoms: identification and characterization of a new, prevalent mutation that results in mild MCAD deficiency. Am J Hum Genet. 2001; 68(6):1408-18. PMID: 11349232. Sturm M et al. Functional effects of different medium-chain acyl-CoA dehydrogenase genotypes and identification of asymptomatic variants. PLoS One. 2012 7(9):e45110. PMID: 23028790. Yokota I et al. Molecular basis of medium chain acyl-coenzyme A dehydrogenase deficiency. An A to G transition at position 985 that causes a lysine-304 to glutamate substitution in the mature protein is the single prevalent mutation. J Clin Invest. 1990; 86(3):1000-3. PMID: 2394825.
PS3,PM3(very strong),PM2,PP3
NM_000016.4:c.985A>G in the ABCA4 gene has an allele frequency of 0.006 in European(non-Finnish) subpopulation in the gnomAD database. Sturm M et al found that 21 subjects with suspected MCAD deficiency were characterized as homozygous for the prevalent mutation c.985A>G and 4 were compound heterozygotes containing one copy of the prevalent mutation c.985A>G together with known or novel missense mutations, small deletions, or insertions and had residual activities between 0-12% (PMID: 23028790). Experimental studies have shown that c.985A>G causes a loss of enzymatic activity measured in lymphocytes from patients who are homozygous for this variant (PMID: 23028790; 22630369). The patient's phenotype is highly specific for ABCA4 gene(PMID: 16737882). Pathogenic computational verdict because pathogenic predictions from DANN, DEOGEN2, EIGEN, FATHMM-MKL, M-CAP, MVP, MutationTaster, PrimateAI and REVEL. Taken together, we interprete this variant as Pathogenic/Likely pathogenic variant. ACMG/AMP criteria applied: PM3_Strong; PS3; PP3; PP4.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 11349232; 1361190) - PS3_supporting. The c.985A>G;p.(Lys329Glu) missense variant has been observed in affected individual(s) (PMID: 20301597; 25940036; 25333063; 26223887; 16617240; 11349232; 23574375)PS4. The variant is present at low allele frequencies population databases (rs77931234 - gnomAD 0.03455%; ABraOM 0.000854 frequency - http://abraom.ib.usp.br/) - PM2_supporting. The p.(Lys329Glu) was detected in trans with a pathogenic variant (PMID:25333063; 25940036; 26223887) - PM3_very strong. Pathogenic missense variant in this residue have been reported (Clinvar ID: 226057) - PM5. The variant co-segregated with disease in multiple affected family members (PMID: 26223887; 11346377) - PP1. In summary, the currently available evidence indicates that the variant is pathogenic.
The c.985A>G, p.Lys329Glu variant (position is based on the precursor protein) variant has been observed in the homozygous state in several individuals who were diagnosed with MCAD deficiency (Matsubara, Y et al., 1990; Yokota et al., 1991). The prevalence of this variant in affected individuals is significantly increased compared with the prevalence in controls. Biochemically, this variant is in a domain that is critical for enzymatic activity and in vitro functional studies have demonstrated that the p.Lys329Glu variant results in protein misfolding, increased hydrophobicity and altered enzyme kinetics (Jank et al., 2014; Maier et al., 2009). The frequency of the variant in the population databases (Exome Sequencing Project and ExAC) is lower than the world-wide disease allele frequency. Finally, reputable sources have classified this variant as Pathogenic. In summary, this variant meets our criteria for a Pathogenic classification. We have confirmed this finding in our laboratory using Sanger sequencing.
The ACADM c.985A>G (p.Lys329Glu) missense variant is widely reported as the most common pathogenic variant in the Caucasian population accounting for approximately 67% of disease alleles for MCAD deficiency (Matern et al. 2000). Across a selection of the available literature, the p.Lys329Glu variant has been identified in over 168 MCAD deficiency patients including 103 in a homozygous state, 54 in a compound heterozygous state, and 11 in a heterozygous state (Matsubara et al. 1990; Andresen et al. 2001; Maier et al. 2005; Sturm et al. 2012; Fernández-Guerra et al. 2014). The variant was absent from 29 controls and is reported at a frequency of 0.00744 in the European American population of the Exome Sequencing Project. Functional studies have demonstrated that the variant results in significantly reduced enzyme activity compared to wild type of less than 10% in homozygotes and 12% in compound heterozygotes, which is significantly below the 20-30% threshold associated with disease phenotypic presentation (Sturm et al. 2012). The variant is reported to cause protein misfolding (Fernández-Guerra et al. 2014). Based on the collective evidence, the p.Lys329Glu variant is classified as pathogenic for medium-chain acyl-CoA dehydrogenase deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
The variant NM_000016.5:c.985A>G p.(Lys329Glu) in ACADM is present in gnomAD (0.3328%) and it is considered a common pathogenic variant associated with MCAD. Computational prediction tools support a deleterious effect on the gene and functional studies in fibroblasts confirm this variant reduces significatively MCAD´s activity (PMID: 23028790). It has been widely reported in homozygous and compound heterozygous individuals with MCADD (20301597, 35281663, 16737882, 19224950, 8770876, Hidalgo Mayoral I et al., in press).
The variant is observed at an extremely low frequency in the gnomAD v4.1.0 dataset (total allele frequency: 0.582%). Predicted Consequence/Location: Missense variant In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.69 (>=0.6, sensitivity 0.68 and specificity 0.92); 3Cnet: 0.99 (> 0.75, sensitivity 0.96 and precision 0.92)]. The same nucleotide change resulting in the same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000003586 / PMID: 2393404 / 3billion dataset). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least one similarly affected unrelated individual (3billion dataset). A different missense change at the same codon (p.Lys329Gln) has been reported to be associated with ACADM-related disorder (ClinVar ID: VCV000226057). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.
NM_000016.4(ACADM):c.985A>G(K329E, aka K304E) is classified as pathogenic in the context of medium chain acyl-CoA dehydrogenase deficiency. Sources cited for classification include the following: PMID 16763904, 23028790, 19224950, 15832312, 20434380, 23509891, 16291504, 18241067. Classification of NM_000016.4(ACADM):c.985A>G(K329E, aka K304E) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.
This sequence change replaces lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 329 of the ACADM protein (p.Lys329Glu). This variant is present in population databases (rs77931234, gnomAD 0.6%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individual(s) with MCAD deficiency (PMID: 15832312, 16291504, 16617240, 16737882, 16763904, 23574375). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as p.Lys304Glu or K304E. ClinVar contains an entry for this variant (Variation ID: 3586). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt ACADM protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects ACADM function (PMID: 22630369, 23028790). For these reasons, this variant has been classified as Pathogenic.
The p.Lys329Glu variant in ACADM has been reported in many individuals with medium-chain acyl-coenzyme A dehydrogenase (MCAD) deficiency in the homozygous and compound heterozygous states (Matsubara 1990, PMID: 2393404; Andresen 2001, PMID: 11349232; Sturm 2012, PMID: 23028790). This variant accounts for the majority of cases of MCAD deficiency (PMID: 20301597). Heterozygous carriers of this variant are unaffected by MCAD deficiency, but may have mild elevations in certain acylcarnitine species (Smith 2010, PMID: 20434380). This variant has been identified in 0.6% (800/129138) of European (non-Finnish) chromosomes, including 1 homozygous individual, by gnomAD (http://gnomad.broadinstitute.org) and has been reported in ClinVar as pathogenic by multiple labs (Variation ID: 3586). This variant has been demonstrated to lead to reduced enzyme activity in carrier individuals and in vitro studies provide evidence that it impacts protein function (Andresen 2001, PMID: 11349232; Sturm 2012, PMID: 23028790). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive medium-chain acyl-coenzyme A dehydrogenase deficiency. ACMG/AMP Criteria applied: PM3_VeryStrong, PS3.
The ACADM c.985A>G (p.K329E) missense variant has been reported as one of the most commonly observed pathogenic variants in individuals with medium-chain acyl-coA dehydrogenase deficiency (PMID: 1684086;1902818; 11349232).
This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3,PP2,PP3.
The ACADM c.985A>G variant is classified as PATHOGENIC (PM3, PS3, PS4) The ACADM c.985A>G variant is a single nucleotide change in exon 11 of the ACADM gene, which is predicted to change the amino acid lysine at position 329 in the protein to glutamic acid. This is a recurrent variant and has been reported in multiple individuals with MCADD (PS4). This variant has been reported in the literature in trans with another known pathogenic variant (PM3). Functional studies show impaired rate of protein folding and subunit assembly as well as reduced activity compared with wild type (PMID:8104486, PMID:27976856) (PS3). This variant is in dbSNP (rs77931234) and has been reported in population databases (gnomAD 941/282786 alleles, 1 homozygote). This variant has been reported in ClinVar as pathogenic by multiple other diagnostic laboratories (ClinVar Variation ID: 18625). It is also classed as damaging for MCADD in HGMD (CM900001). Computational predictions are equivocal.
GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.
ACMG: PS3_Supporting, PM1_Supporting, PP3, PP4_Strong
PS3, PM3_Very Strong
This variant is also referred to as p.Lys304Glu or K304E in the literature. This established pathogenic variant has been previously reported in the homozygous and compound heterozygous state in patients with MCAD deficiency (PMID: 16737882, 15832312, 16291504, 16617240, 16763904, 23574375). Experimental studies performed on lymphocytes from patients with this variant in the homozygous state have shown loss of enzyme activity (PMID: 23028790, 22630369). The c.997A>G (p.Lys333Glu) variant is present in the gnomAD population database at a frequency of 0.3% (941/282786). Based on the available evidence, the c.997A>G (p.Lys333Glu) variant is classified as Pathogenic.
Variant summary: The ACADM c.985A>G (p.Lys329Glu) variant involves the alteration of a conserved nucleotide. 1/4 in silico tools predict a damaging outcome. This variant was found in 402/121176 control chromosomes (including 1 homozygote) at a frequency of 0.0033175, which does not exceed the estimated maximal expected allele frequency of a pathogenic ACADM variant (0.0036228). The variant is the most common mutation causing MCAD. The variant is widely reported in literature with consistent genotype and functional assays show that it leads to defective enzymatic activity. Several clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as Pathogenic.
The missense c.985A>Gp.Lys329Glu variant in ACADM gene has been reported previously in homozygous state in individuals affected with medium-chain acyl-CoA dehydrogenase MCAD deficiency Leal et al., 2014. Experimental studies have shown that this missense change affects ACADM function Sturm et al., 2012. This variant is reported with the allele frequency of 0.3% in the gnomAD Exomes and novel in 1000 Genomes. This variant has been reported to the ClinVar database as Likely Pathogenic / Pathogenic multiple submitters. The amino acid Lys at position 329 is changed to a Glu changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Lys329Glu in ACADM is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic.
This sequence variant is a single nucleotide substitution (A>G) at coding position 985 in the ACADM gene which results in a lysine to glutamic acid amino acid change at residue 329 in the ACADM protein. Due to alterte protein numbering, this variant is sometimes described at protein position 304 in published literature reports. This is a previously reported variant (ClinVar) which has been identified as the most frequent causative variant in individuals with Medium-chain acyl-coenzyme A dehydrogese deficiency (PMID: 2393404, 1363805, 20301597). The variant is present in 941/282786 alleles in the gnomAD population dataset, including 1 homozygote. Multiple functiol assays indicate that the variant protein undergoes improper protein folding and solubilization, leading to a decrease in activity and substrate specificity (PMID: 8104486, 7730333, 19224950, 24966162). Given the available evidence, we consider this variant to be pathogenic. ACMG Criteria: BP2, PP2, PP5
not provided Pathogenic:12
The ACADM p.K329E is widely reported as the most common pathogenic variant associated with medium-chain acyl-CoA dehydrogenase deficiency (MCADD) in the Caucasian population, accounting for approximately 56-91% of disease alleles in this population (Rhead_2006_PMID 16763904; Gramer_2015_PMID:25940036). The p.K329E variant has been identified in over 168 MCADD patients including 103 in the homozygous state, 54 in the compound heterozygous state, and 11 in the heterozygous state (Matsubara 1990_PMID 2393404; Andresen 2001_PMID11349232; Maier 2005_ PMID 15832312; Sturm 2012_PMID 23028790; Fernández-Guerra 2014_PMID 25333063). The variant was identified in dbSNP (ID: rs77931234) and in ClinVar (classified as pathogenic by 14 laboratories and as a VUS by Genomic Research Center, Shahid Beheshti University of Medical Sciences). The variant was identified in control databases in 941 of 282786 chromosomes (1 homozygous) at a frequency of 0.003328 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (non-Finnish) in 800 of 129138 chromosomes (freq: 0.006195), Other in 24 of 7220 chromosomes (freq: 0.003324), African in 33 of 24948 chromosomes (freq: 0.001323), European (Finnish) in 27 of 25124 chromosomes (freq: 0.001075), Ashkenazi Jewish in 11 of 10370 chromosomes (freq: 0.001061), Latino in 37 of 35440 chromosomes (freq: 0.001044) and South Asian in 9 of 30602 chromosomes (freq: 0.000294), but was not observed in the East Asian population. Although the p.K329E variant is identified in controls, the prevalence of this variant in affected individuals is significantly increased compared with the prevalence in controls. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. The p.K329 residue is conserved in mammals but not in more distantly related organisms however computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. However, this variant is in a domain that is critical for enzymatic activity and in vitro functional studies have demonstrated that the p.K329E variant results in protein misfolding, increased hydrophobicity and altered enzyme kinetics (Jank_2014_PMID:24718418; Maier_2009_PMID:19224950; Koster_2014_PMID:24966162). In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.
Published functional studies demonstrate a damaging effect with decreased thermal stability (PMID: 26947917); Also known as p.(K304E); This variant is associated with the following publications: (PMID: 25763512, 23509891, 25333063, 19224950, 18188679, 35460704, 36591720, 36068006, 37595579, 37257730, 37443404, 26223887, 29317722, 27976856, 18534147, 16763904, 34670123, 34556655, 35026467, 26947917, 20301597, 2393404, 24718418, 12142359, 8104486, 23028790, 7730333, 7652482, 24966162, 25087612, 19780764, 23574375, 22975760, 20333879, 24799540, 24082139, 21228398, 24998633, 20036593, 23842438, 26404458, 27477829, 11763681, 26798524, 26215884, 29555771, 17186412, 29350094, 7904584, 30609409, 30626930, 31028937, 31012112, 25689098, 31836396, 31447099, 31980526, 34426522, 33580884, 31589614, 32853555, 32901917, 33726816, 24623196)
ACADM: PM3:Very Strong, PP4:Moderate, PM2:Supporting, PS3:Supporting
The ACADM c.985A>G (p.Lys329Glu) variant (also known as K304E, K329E, K333E) has been reported in the homozygous and compound heterozygous state in numerous individuals with MCAD deficiency (PMIDs: 26947917 (2016), 26798524 (2015), 26223887 (2015), 8102510 (1993), 1902818 (1991), 2394825 (1990), 2393404 (1990), 2251268 (1990)). This variant is the most common variant among Caucasian populations and reportedly accounts for approximately 80%-90% of alleles of symptomatic patients (PMID: 26947917 (2016)). In addition, functional studies indicate this variant causes a significant reduction in ACADM enzyme activity and protein stability (PMIDs: 26947917 (2016), 24966162 (2014), 1902818 (1991)). Based on the available information, this variant is classified as pathogenic.
See cases Pathogenic:2
ACMG categories: PS1,PM1,PM3,PP4,PP5
ACMG classification criteria: PS3, PS4, PM3
Inborn genetic diseases Pathogenic:1
The c.985A>G (p.K329E) alteration is located in coding exon 11 of the ACADM gene. This alteration results from an A to G substitution at nucleotide position 985, causing the lysine (K) at amino acid position 329 to be replaced by a glutamic acid (E). Based on data from gnomAD, the G allele has an overall frequency of 0.33% (941/282786) total alleles studied. The highest observed frequency was 0.62% (800/129138) of European (non-Finnish) alleles. This is the most common ACADM mutation in Western Europe population and has been reported in a homozygous state or compound heterozygous with other pathogenic alterations in ACADM in multiple unrelated patients (Matsubara, 1990; Waddell, 2006; Arnold, 2010). This amino acid position is highly conserved in available vertebrate species. Functional analysis on lymphocytes from individuals who are homozygous for the p.K329E alteration showed low enzyme activity (0-8%), and heterozygous carriers of the p.K329E alteration had reduced enzyme activity (12-87%; Sturm, 2012). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.
Epileptic spasm Pathogenic:1
ACADM-related disorder Pathogenic:1
The ACADM c.985A>G variant is predicted to result in the amino acid substitution p.Lys329Glu. This variant, also referred to in the literature as p.Lys304Glu, has been documented to be associated with autosomal recessive medium chain acyl-CoA dehydrogenase deficiency (MCADD) when present in the homozygous or compound heterozygous states (Matsubara et al. 1990. PubMed ID: 2393404). This is the most common pathogenic ACADM variant among patients of Northern European ancestry (Nichols et al. 2008. PubMed ID: 18241067). In summary, we interpret this variant as pathogenic. Of note, the c.985A>G (p.Lys329Glu) variant, in the heterozygous state without a second ACADM variant, has been reported to lead to false positive newborn screen results suggestive of MCADD (Merritt and Chang. 2019. PubMed ID: 20301597).
Computational scores
Source:
Splicing
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