chr6-75922121-C-A

Variant names:

• chr6-75922121-C-A
• NM_001563.4:c.2362G>T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_Moderate PM2

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:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IMPG1 NM_001563.4 stop_gained
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.661

Genes affected

IMPG1 (HGNC:6055): (interphotoreceptor matrix proteoglycan 1) This gene encodes a protein that is a major component of the retinal interphotoreceptor matrix. The encoded protein is a proteoglycan that is thought to play a role in maintaining viability of photoreceptor cells and in adhesion of the neural retina to the retinal pigment epithelium. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0134 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage

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: 0 AN: 1230202 Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0 AN XY: 619738

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Vitelliform macular dystrophy 4 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Institute of Human Genetics, University of Goettingen

Jan 11, 2023

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: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.55	D
BayesDel_noAF	Pathogenic	0.55
CADD	Pathogenic	38
DANN	Uncertain	0.99
Eigen	Uncertain	0.43
Eigen_PC	Benign	0.19
FATHMM_MKL	Benign	0.76	D
Vest4		0.10
GERP RS		2.4

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.21		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.21		Position offset: 45

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-76631838;