16-4883916-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000345988.7(PPL):c.4739G>A(p.Arg1580Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000116 in 1,613,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000345988.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPL | NM_002705.5 | c.4739G>A | p.Arg1580Gln | missense_variant | 22/22 | ENST00000345988.7 | NP_002696.4 | |
PPL | XM_017023374.3 | c.4826G>A | p.Arg1609Gln | missense_variant | 22/22 | XP_016878863.1 | ||
PPL | XM_017023375.3 | c.4787G>A | p.Arg1596Gln | missense_variant | 22/22 | XP_016878864.1 | ||
PPL | XM_006720902.5 | c.4778G>A | p.Arg1593Gln | missense_variant | 22/22 | XP_006720965.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPL | ENST00000345988.7 | c.4739G>A | p.Arg1580Gln | missense_variant | 22/22 | 1 | NM_002705.5 | ENSP00000340510 | P3 | |
PPL | ENST00000590782.6 | c.4733G>A | p.Arg1578Gln | missense_variant | 22/22 | 5 | ENSP00000465640 | A1 | ||
PPL | ENST00000592772.1 | c.3002G>A | p.Arg1001Gln | missense_variant | 10/10 | 5 | ENSP00000467699 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251204Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135790
GnomAD4 exome AF: 0.000118 AC: 172AN: 1461642Hom.: 0 Cov.: 36 AF XY: 0.000124 AC XY: 90AN XY: 727132
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 29, 2024 | The c.4739G>A (p.R1580Q) 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 4739, causing the arginine (R) at amino acid position 1580 to be replaced by a glutamine (Q). 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