chr2-218827311-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3
The NM_017431.4(PRKAG3):c.938C>T(p.Pro313Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,614,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P313P) has been classified as Likely benign.
Frequency
Consequence
NM_017431.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKAG3 | NM_017431.4 | c.938C>T | p.Pro313Leu | missense_variant | 9/14 | ENST00000439262.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKAG3 | ENST00000439262.7 | c.938C>T | p.Pro313Leu | missense_variant | 9/14 | 1 | NM_017431.4 | P1 | |
PRKAG3 | ENST00000529249.5 | c.938C>T | p.Pro313Leu | missense_variant | 9/13 | 1 | P1 | ||
PRKAG3 | ENST00000490971.1 | n.1096C>T | non_coding_transcript_exon_variant | 8/9 | 2 | ||||
PRKAG3 | ENST00000470307.6 | c.892C>T | p.Arg298Trp | missense_variant, NMD_transcript_variant | 8/11 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251306Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135836
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461856Hom.: 0 Cov.: 34 AF XY: 0.00000688 AC XY: 5AN XY: 727228
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2023 | The c.938C>T (p.P313L) alteration is located in exon 9 (coding exon 9) of the PRKAG3 gene. This alteration results from a C to T substitution at nucleotide position 938, causing the proline (P) at amino acid position 313 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at