4-83581807-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_032717.5(GPAT3):c.454C>T(p.Arg152Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,256 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_032717.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPAT3 | NM_032717.5 | c.454C>T | p.Arg152Cys | missense_variant | Exon 3 of 12 | ENST00000264409.5 | NP_116106.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPAT3 | ENST00000264409.5 | c.454C>T | p.Arg152Cys | missense_variant | Exon 3 of 12 | 1 | NM_032717.5 | ENSP00000264409.4 | ||
GPAT3 | ENST00000395226.6 | c.454C>T | p.Arg152Cys | missense_variant | Exon 4 of 13 | 1 | ENSP00000378651.2 | |||
GPAT3 | ENST00000611707.4 | c.454C>T | p.Arg152Cys | missense_variant | Exon 4 of 13 | 5 | ENSP00000482571.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251012Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135680
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461160Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726770
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152096Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.454C>T (p.R152C) alteration is located in exon 3 (coding exon 3) of the GPAT3 gene. This alteration results from a C to T substitution at nucleotide position 454, causing the arginine (R) at amino acid position 152 to be replaced by a cysteine (C). 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