10-22541981-C-T
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2
The NM_005028.5(PIP4K2A):c.859G>A(p.Glu287Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,613,908 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005028.5 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIP4K2A | ENST00000376573.9 | c.859G>A | p.Glu287Lys | missense_variant | Exon 8 of 10 | 1 | NM_005028.5 | ENSP00000365757.4 | ||
PIP4K2A | ENST00000545335.5 | c.682G>A | p.Glu228Lys | missense_variant | Exon 8 of 10 | 2 | ENSP00000442098.1 | |||
PIP4K2A | ENST00000323883.11 | c.439G>A | p.Glu147Lys | missense_variant | Exon 6 of 8 | 2 | ENSP00000326294.7 | |||
PIP4K2A | ENST00000604912.1 | c.397G>A | p.Glu133Lys | missense_variant | Exon 5 of 5 | 2 | ENSP00000473858.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152130Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000279 AC: 7AN: 251178 AF XY: 0.0000295 show subpopulations
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461778Hom.: 1 Cov.: 33 AF XY: 0.0000275 AC XY: 20AN XY: 727206 show subpopulations
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74306 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.859G>A (p.E287K) alteration is located in exon 8 (coding exon 8) of the PIP4K2A gene. This alteration results from a G to A substitution at nucleotide position 859, causing the glutamic acid (E) at amino acid position 287 to be replaced by a lysine (K). 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