rs374837022
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_181882.3(PRX):c.794G>T(p.Gly265Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000812 in 1,540,296 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 Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G265S) has been classified as Uncertain significance.
Frequency
Consequence
NM_181882.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRX | NM_181882.3 | c.794G>T | p.Gly265Val | missense_variant | 7/7 | ENST00000324001.8 | |
PRX | NM_001411127.1 | c.1079G>T | p.Gly360Val | missense_variant | 7/7 | ||
PRX | XM_017027047.2 | c.692G>T | p.Gly231Val | missense_variant | 4/4 | ||
PRX | NM_020956.2 | c.*999G>T | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRX | ENST00000324001.8 | c.794G>T | p.Gly265Val | missense_variant | 7/7 | 1 | NM_181882.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000258 AC: 36AN: 139730Hom.: 0 AF XY: 0.000249 AC XY: 19AN XY: 76456
GnomAD4 exome AF: 0.0000699 AC: 97AN: 1387962Hom.: 0 Cov.: 35 AF XY: 0.0000672 AC XY: 46AN XY: 684068
GnomAD4 genome ? AF: 0.000184 AC: 28AN: 152334Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74480
ClinVar
Submissions by phenotype
Charcot-Marie-Tooth disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Molecular Genetics Laboratory, London Health Sciences Centre | - | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 20, 2020 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Charcot-Marie-Tooth disease type 4 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at