chr6-75922121-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_001563.4(IMPG1):c.2362G>T(p.Glu788*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001563.4 stop_gained
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 |
---|---|---|---|---|---|---|---|---|
IMPG1 | NM_001563.4 | c.2362G>T | p.Glu788* | stop_gained | Exon 17 of 17 | ENST00000369950.8 | NP_001554.2 | |
IMPG1 | NM_001282368.2 | c.2128G>T | p.Glu710* | stop_gained | Exon 16 of 16 | NP_001269297.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IMPG1 | ENST00000369950.8 | c.2362G>T | p.Glu788* | stop_gained | Exon 17 of 17 | 1 | NM_001563.4 | ENSP00000358966.3 | ||
IMPG1 | ENST00000611179.4 | c.2128G>T | p.Glu710* | stop_gained | Exon 16 of 16 | 5 | ENSP00000481913.1 | |||
IMPG1 | ENST00000369952.3 | c.445G>T | p.Glu149* | stop_gained | Exon 4 of 4 | 3 | ENSP00000358968.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1230202Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0AN XY: 619738
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Vitelliform macular dystrophy 4 Uncertain:1
The variant c.2362G>T (p.(Glu788*)) in exon 17 of the IMPG1 gene is not found in the gnomAD database and it changes the protein sequence at position 788 and interrupts the reading frame prematurely by generating a STOP codon. As the variant most likely removes <10% of the protein, ACMG criterion PVS1_mod is applied. This variant was identified in a patient with a clinical diagnosis of Stargardt disease, who also carried two pathogenic ABCA4 mutations and one disease associated variant in ABCA4 (c.2588G>C (p.(Gly863Ala)), c.5882G>A (p.(Gly1961Glu)) and c.5603A>T (p.(Asn1868Ile)), respectively). ACMG criteria used for classification: PVS1_mod, PM2. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.