rs371137355
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_005391.5(PDK3):āc.51G>Cā(p.Glu17Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00045 in 1,208,786 control chromosomes in the GnomAD database, including 4 homozygotes. There are 319 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E17Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_005391.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDK3 | NM_005391.5 | c.51G>C | p.Glu17Asp | missense_variant | 1/11 | ENST00000379162.9 | |
PDK3 | NM_001142386.3 | c.51G>C | p.Glu17Asp | missense_variant | 1/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDK3 | ENST00000379162.9 | c.51G>C | p.Glu17Asp | missense_variant | 1/11 | 1 | NM_005391.5 | P1 | |
PDK3 | ENST00000568479.2 | c.51G>C | p.Glu17Asp | missense_variant | 1/12 | ||||
PDK3 | ENST00000493226.2 | n.263G>C | non_coding_transcript_exon_variant | 1/3 | 5 | ||||
PDK3 | ENST00000648777.1 | c.51G>C | p.Glu17Asp | missense_variant, NMD_transcript_variant | 1/12 |
Frequencies
GnomAD3 genomes ? AF: 0.000247 AC: 28AN: 113397Hom.: 1 Cov.: 25 AF XY: 0.000422 AC XY: 15AN XY: 35541
GnomAD3 exomes AF: 0.000845 AC: 149AN: 176389Hom.: 1 AF XY: 0.00136 AC XY: 87AN XY: 64079
GnomAD4 exome AF: 0.000471 AC: 516AN: 1095339Hom.: 3 Cov.: 28 AF XY: 0.000842 AC XY: 304AN XY: 361061
GnomAD4 genome ? AF: 0.000247 AC: 28AN: 113447Hom.: 1 Cov.: 25 AF XY: 0.000421 AC XY: 15AN XY: 35601
ClinVar
Submissions by phenotype
Charcot-Marie-Tooth disease X-linked dominant 6 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 13, 2023 | - - |
PDK3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 10, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at