rs1366496013

Positions:

• chr1-216325335-AAT-A

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_206933.4(USH2A):​c.1111_1112del​(p.Ile371PhefsTer3) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,750 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000017 (0 hom.)
• Consequence: USH2A NM_206933.4 frameshift
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:9
• Conservation: PhyloP100: 8.97

Genes affected

USH2A (HGNC:12601): (usherin) This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-216325335-AAT-A is Pathogenic according to our data. Variant chr1-216325335-AAT-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 495336.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-216325335-AAT-A is described in Lovd as [Pathogenic]. Variant chr1-216325335-AAT-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
USH2A	NM_206933.4	c.1111_1112del	p.Ile371PhefsTer3	frameshift_variant	6/72	ENST00000307340.8
USH2A	NM_007123.6	c.1111_1112del	p.Ile371PhefsTer3	frameshift_variant	6/21

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USH2A	ENST00000307340.8	c.1111_1112del	p.Ile371PhefsTer3	frameshift_variant	6/72	1	NM_206933.4	P1
USH2A	ENST00000366942.3	c.1111_1112del	p.Ile371PhefsTer3	frameshift_variant	6/21	1
USH2A	ENST00000674083.1	c.1111_1112del	p.Ile371PhefsTer3	frameshift_variant	6/73

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152208 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000171 AC: 25 AN: 1461542 Hom.: 0 AF XY: 0.0000151 AC XY: 11 AN XY: 727072

Gnomad4 AFR exome AF: 0.0000299

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: 0.0000216

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152208 Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1 AN XY: 74360

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000712 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Usher syndrome type 2A Pathogenic:3

Pathogenic, criteria provided, single submitter	research	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jun 25, 2017	Reportedly 1 case with this variant in the supplement but that is not available at the time of review (broken link). In trans to a known pathogenic variant. In gnomAD, not found in exomes, once in genomes (1/30960 chromosomes). (PM2, PM3, PVS1). -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Nov 04, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	May 23, 2022	The USH2A c.1111_1112del variant is classified as PATHOGENIC (PVS1, PM2, PS4_S) This variant is a deletion of two consecutive nucleotides in exon 6/72 of the USH2A gene, predicted to encode a frame shift of the mature mRNA with consequent premature termination of protein synthesis at codon 3 of the frame-shift, or 373 (USH2A:p.(Ile371PhefsTer3)) (PVS1). The variant has been identified in multiple unrelated individuals with Usher syndrome and non-syndromic Retinitis pigmentosa, and confirmed in trans with a second pathogenic variant in an individual with non-syndromic Retinitis pigmentosa (PMID:16963483, PMID:32176120, PMID:18641288). The variant is in dbSNP (rs1366496013) but it is rare in population databases (gnomAD: 1/152208, 0 homozygote) (PM2). This variant has been reported in ClinVar (VariationID: 495336) and HGMD (Accession: CD071406) as disease causing variant (PS4_S). -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jun 04, 2018	The c.1111_1112delAT variant in the USH2A gene has been reported previously in association with Usher syndrome (Sandberg et al., 2008). The c.1111_1112delAT variant causes a frameshift starting with codon Isoleucine 371, changes this amino acid to a Phenylalanine residue, and creates a premature Stop codon at position 3 of the new reading frame, denoted p.Ile371PhefsX3. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1111_1112delAT variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). We interpret c.1111_1112delAT as a pathogenic variant. -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Dec 16, 2023	This sequence change creates a premature translational stop signal (p.Ile371Phefs*3) in the USH2A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in USH2A are known to be pathogenic (PMID: 10729113, 10909849, 20507924, 25649381). This variant is present in population databases (no rsID available, gnomAD 0.007%). This premature translational stop signal has been observed in individual(s) with retinitis pigmentosa (PMID: 18641288). ClinVar contains an entry for this variant (Variation ID: 495336). For these reasons, this variant has been classified as Pathogenic. -

Retinitis pigmentosa 39 Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Sep 14, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Nov 04, 2023	- -

Usher syndrome type 2A;C3151138:Retinitis pigmentosa 39 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Counsyl

Aug 16, 2017

- -

Retinal dystrophy Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Blueprint Genetics

Aug 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1366496013; hg19: chr1-216498677;