chr16-4883416-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_002705.5(PPL):c.5239G>A(p.Glu1747Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000403 in 1,614,060 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002705.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPL | NM_002705.5 | c.5239G>A | p.Glu1747Lys | missense_variant | Exon 22 of 22 | ENST00000345988.7 | NP_002696.4 | |
PPL | XM_017023374.3 | c.5326G>A | p.Glu1776Lys | missense_variant | Exon 22 of 22 | XP_016878863.1 | ||
PPL | XM_017023375.3 | c.5287G>A | p.Glu1763Lys | missense_variant | Exon 22 of 22 | XP_016878864.1 | ||
PPL | XM_006720902.5 | c.5278G>A | p.Glu1760Lys | missense_variant | Exon 22 of 22 | XP_006720965.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPL | ENST00000345988.7 | c.5239G>A | p.Glu1747Lys | missense_variant | Exon 22 of 22 | 1 | NM_002705.5 | ENSP00000340510.2 | ||
PPL | ENST00000590782.6 | c.5233G>A | p.Glu1745Lys | missense_variant | Exon 22 of 22 | 5 | ENSP00000465640.1 | |||
PPL | ENST00000592772.1 | c.*156G>A | downstream_gene_variant | 5 | ENSP00000467699.1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251376Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135876
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461854Hom.: 1 Cov.: 34 AF XY: 0.0000206 AC XY: 15AN XY: 727232
GnomAD4 genome AF: 0.000145 AC: 22AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5239G>A (p.E1747K) alteration is located in exon 22 (coding exon 22) of the PPL gene. This alteration results from a G to A substitution at nucleotide position 5239, causing the glutamic acid (E) at amino acid position 1747 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