chr6-75922119-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001563.4(IMPG1):c.2364A>T(p.Glu788Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001563.4 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 | UniProt |
---|---|---|---|---|---|---|---|
IMPG1 | NM_001563.4 | c.2364A>T | p.Glu788Asp | missense_variant | 17/17 | ENST00000369950.8 | |
IMPG1 | NM_001282368.2 | c.2130A>T | p.Glu710Asp | missense_variant | 16/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IMPG1 | ENST00000369950.8 | c.2364A>T | p.Glu788Asp | missense_variant | 17/17 | 1 | NM_001563.4 | P2 | |
IMPG1 | ENST00000611179.4 | c.2130A>T | p.Glu710Asp | missense_variant | 16/16 | 5 | A2 | ||
IMPG1 | ENST00000369952.3 | c.447A>T | p.Glu149Asp | missense_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1224420Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0AN XY: 617056
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2023 | This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 788 of the IMPG1 protein (p.Glu788Asp). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with IMPG1-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.