rs137852784
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_000209.4(PDX1):c.176A>T(p.Gln59Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000649 in 1,540,744 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 risk factor (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q59K) has been classified as Uncertain significance.
Frequency
Consequence
NM_000209.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDX1 | NM_000209.4 | c.176A>T | p.Gln59Leu | missense_variant | 1/2 | ENST00000381033.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDX1 | ENST00000381033.5 | c.176A>T | p.Gln59Leu | missense_variant | 1/2 | 1 | NM_000209.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152070Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000146 AC: 2AN: 136534Hom.: 0 AF XY: 0.0000270 AC XY: 2AN XY: 74134
GnomAD4 exome AF: 0.00000576 AC: 8AN: 1388674Hom.: 0 Cov.: 33 AF XY: 0.0000117 AC XY: 8AN XY: 684526
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152070Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74268
ClinVar
Submissions by phenotype
Diabetes mellitus type 2, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Nov 01, 1999 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at