rs1553123263

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3PP5

The NM_000016.6(ACADM):​c.461T>G​(p.Leu154Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: not found (cov: 30)

Consequence

ACADM
NM_000016.6 missense

Scores

8
4
7

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2U:1

Conservation

PhyloP100: 7.83
Variant links:
Genes affected
ACADM (HGNC:89): (acyl-CoA dehydrogenase medium chain) This gene encodes the medium-chain specific (C4 to C12 straight chain) acyl-Coenzyme A dehydrogenase. The homotetramer enzyme catalyzes the initial step of the mitochondrial fatty acid beta-oxidation pathway. Defects in this gene cause medium-chain acyl-CoA dehydrogenase deficiency, a disease characterized by hepatic dysfunction, fasting hypoglycemia, and encephalopathy, which can result in infantile death. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.792
PP5
Variant 1-75734864-T-G is Pathogenic according to our data. Variant chr1-75734864-T-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 557423.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=1, Uncertain_significance=1, Pathogenic=1}.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ACADMNM_000016.6 linkuse as main transcriptc.461T>G p.Leu154Trp missense_variant 6/12 ENST00000370841.9 NP_000007.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ACADMENST00000370841.9 linkuse as main transcriptc.461T>G p.Leu154Trp missense_variant 6/121 NM_000016.6 ENSP00000359878 P4P11310-1

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
30

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:2Uncertain:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Medium-chain acyl-coenzyme A dehydrogenase deficiency Pathogenic:2Uncertain:1
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 21, 2023For these reasons, this variant has been classified as Pathogenic. 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 not expected to disrupt ACADM protein function. ClinVar contains an entry for this variant (Variation ID: 557423). This missense change has been observed in individual(s) with medium-chain acyl-CoA dehydrogenase deficiency (PMID: 21239873, 33841490). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This sequence change replaces leucine, which is neutral and non-polar, with tryptophan, which is neutral and slightly polar, at codon 154 of the ACADM protein (p.Leu154Trp). This variant is not present in population databases (gnomAD no frequency). -
Uncertain significance, criteria provided, single submitterclinical testingCounsylMar 24, 2018- -
Likely pathogenic, criteria provided, single submitterclinical testingBaylor GeneticsOct 03, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.31
BayesDel_addAF
Pathogenic
0.37
D
BayesDel_noAF
Pathogenic
0.29
CADD
Pathogenic
29
DANN
Benign
0.96
DEOGEN2
Benign
0.39
T;D;T;.
Eigen
Uncertain
0.51
Eigen_PC
Uncertain
0.49
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.97
D;D;D;D
M_CAP
Pathogenic
0.32
D
MetaRNN
Pathogenic
0.79
D;D;D;D
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Benign
0.93
.;L;.;.
MutationTaster
Benign
0.92
D;D;D;D;D
PrimateAI
Benign
0.37
T
PROVEAN
Pathogenic
-5.1
D;D;D;D
REVEL
Pathogenic
0.71
Sift
Uncertain
0.022
D;D;D;D
Sift4G
Benign
0.12
T;T;T;T
Polyphen
1.0
D;D;D;D
Vest4
0.57
MutPred
0.37
.;.;Gain of catalytic residue at L187 (P = 0.005);.;
MVP
0.97
MPC
0.93
ClinPred
0.95
D
GERP RS
5.6
Varity_R
0.52
gMVP
0.87

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.17
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1553123263; hg19: chr1-76200549; API