rs370257703
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_016203.4(PRKAG2):āc.1315A>Gā(p.Ile439Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000112 in 1,612,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_016203.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRKAG2 | NM_016203.4 | c.1315A>G | p.Ile439Val | missense_variant | Exon 12 of 16 | ENST00000287878.9 | NP_057287.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251466Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135900
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1459928Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 726402
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
The Ile439Val variant (PRKAG2) has not been reported in the literature nor previ ously identified by our laboratory. It is located in the CBS domain region of t he PRKAG2 protein, where all pathogenic PRKAG2 variants have been identified to date (Oliveira 2003). Computational analyses (biochemical amino acid properties, AlignGVGD, PolyPhen2, and SIFT) suggest that this variant may not impact the pr otein, though this information is not predictive enough to rule out pathogenicit y. Additional information is needed to fully assess the clinical significance of the Ile439Val variant. PRKAG2 variants cause a heart specific non-lysosomal g lycogenosis with typical clinical onset in adolescence or the 3rd decade. Howev er, neonatal onset of hypertrophy has also been described (Burwinkel 2005). -
not provided Uncertain:1
Has been reported as a variant of uncertain significance in association with HCM, DCM, or ARVC (PMID: 27532257); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 38254962, 27532257, 36243179) -
Hypertrophic cardiomyopathy 6 Uncertain:1
This variant has been identified as part of our research program. Refer to the 'condition' field for the phenotype of the proband(s) identified with this variant. For further information please feel free to contact us. -
Cardiovascular phenotype Uncertain:1
The c.1315A>G (p.I439V) alteration is located in exon 12 (coding exon 12) of the PRKAG2 gene. This alteration results from a A to G substitution at nucleotide position 1315, causing the isoleucine (I) at amino acid position 439 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Lethal congenital glycogen storage disease of heart Uncertain:1
This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 439 of the PRKAG2 protein (p.Ile439Val). This variant is present in population databases (rs370257703, gnomAD 0.003%). This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 27532257). ClinVar contains an entry for this variant (Variation ID: 45695). 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 PRKAG2 protein function with a negative predictive value of 95%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at