14-60283488-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_021003.5(PPM1A):āc.785A>Gā(p.Asp262Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,490 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 ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D262E) has been classified as Uncertain significance.
Frequency
Consequence
NM_021003.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPM1A | NM_021003.5 | c.785A>G | p.Asp262Gly | missense_variant | 2/6 | ENST00000395076.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPM1A | ENST00000395076.9 | c.785A>G | p.Asp262Gly | missense_variant | 2/6 | 1 | NM_021003.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000407 AC: 1AN: 245932Hom.: 0 AF XY: 0.00000750 AC XY: 1AN XY: 133354
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461490Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727000
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 26, 2022 | The c.1004A>G (p.D335G) alteration is located in exon 2 (coding exon 2) of the PPM1A gene. This alteration results from a A to G substitution at nucleotide position 1004, causing the aspartic acid (D) at amino acid position 335 to be replaced by a glycine (G). 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