rs527968606
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_005028.5(PIP4K2A):c.859G>T(p.Glu287*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,780 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_005028.5 stop_gained
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIP4K2A | ENST00000376573.9 | c.859G>T | p.Glu287* | stop_gained | Exon 8 of 10 | 1 | NM_005028.5 | ENSP00000365757.4 | ||
PIP4K2A | ENST00000545335.5 | c.682G>T | p.Glu228* | stop_gained | Exon 8 of 10 | 2 | ENSP00000442098.1 | |||
PIP4K2A | ENST00000323883.11 | c.439G>T | p.Glu147* | stop_gained | Exon 6 of 8 | 2 | ENSP00000326294.7 | |||
PIP4K2A | ENST00000604912.1 | c.397G>T | p.Glu133* | stop_gained | Exon 5 of 5 | 2 | ENSP00000473858.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251178 AF XY: 0.00000737 show subpopulations
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461780Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727206 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at