8-42179941-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_000930.5(PLAT):c.1348G>A(p.Gly450Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000562 in 1,601,268 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000930.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLAT | NM_000930.5 | c.1348G>A | p.Gly450Ser | missense_variant | Exon 12 of 14 | ENST00000220809.9 | NP_000921.1 | |
PLAT | NM_033011.4 | c.1210G>A | p.Gly404Ser | missense_variant | Exon 11 of 13 | NP_127509.1 | ||
PLAT | NM_001319189.2 | c.1081G>A | p.Gly361Ser | missense_variant | Exon 10 of 12 | NP_001306118.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000421 AC: 1AN: 237558Hom.: 0 AF XY: 0.00000779 AC XY: 1AN XY: 128452
GnomAD4 exome AF: 0.00000552 AC: 8AN: 1449022Hom.: 0 Cov.: 32 AF XY: 0.00000834 AC XY: 6AN XY: 719250
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1348G>A (p.G450S) alteration is located in exon 12 (coding exon 11) of the PLAT gene. This alteration results from a G to A substitution at nucleotide position 1348, causing the glycine (G) at amino acid position 450 to be replaced by a serine (S). 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