15-43534979-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001394395.1(PPIP5K1):c.4168G>A(p.Glu1390Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000638 in 1,613,710 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001394395.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPIP5K1 | NM_001394395.1 | c.4168G>A | p.Glu1390Lys | missense_variant | 32/32 | ENST00000420765.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPIP5K1 | ENST00000420765.6 | c.4168G>A | p.Glu1390Lys | missense_variant | 32/32 | 5 | NM_001394395.1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 151702Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251454Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135910
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.0000550 AC XY: 40AN XY: 727248
GnomAD4 genome AF: 0.000145 AC: 22AN: 151818Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74180
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | The c.3997G>A (p.E1333K) alteration is located in exon 31 (coding exon 29) of the PPIP5K1 gene. This alteration results from a G to A substitution at nucleotide position 3997, causing the glutamic acid (E) at amino acid position 1333 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