chr8-37762699-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007198.4(PLPBP):c.40G>C(p.Gly14Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000245 in 1,591,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. G14G) has been classified as Likely benign.
Frequency
Consequence
NM_007198.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLPBP | NM_007198.4 | c.40G>C | p.Gly14Arg | missense_variant | 1/8 | ENST00000328195.8 | |
LOC124901934 | XR_007060889.1 | n.453C>G | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLPBP | ENST00000328195.8 | c.40G>C | p.Gly14Arg | missense_variant | 1/8 | 1 | NM_007198.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000192 AC: 4AN: 208338Hom.: 0 AF XY: 0.0000265 AC XY: 3AN XY: 113120
GnomAD4 exome AF: 0.0000250 AC: 36AN: 1438944Hom.: 0 Cov.: 33 AF XY: 0.0000224 AC XY: 16AN XY: 714344
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74376
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 13, 2022 | This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 14 of the PROSC protein (p.Gly14Arg). This variant is present in population databases (rs780857882, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with PROSC-related conditions. ClinVar contains an entry for this variant (Variation ID: 1032529). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Epilepsy, early-onset, vitamin B6-dependent Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Oct 12, 2018 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at