chr1-215998904-AT-A

Variant names:

• chr1-215998904-AT-A
• rs876657732
• NM_206933.4:c.6639delA

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_206933.4(USH2A):​c.6639delA​(p.Lys2213AsnfsTer16) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. K2213K) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: USH2A NM_206933.4 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 0.421

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 12 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 1-215998904-AT-A is Pathogenic according to our data. Variant chr1-215998904-AT-A is described in ClinVar as [Pathogenic]. Clinvar id is 228415.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
USH2A	NM_206933.4	c.6639delA	p.Lys2213AsnfsTer16	frameshift_variant	Exon 34 of 72	ENST00000307340.8	NP_996816.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
USH2A	ENST00000307340.8	c.6639delA	p.Lys2213AsnfsTer16	frameshift_variant	Exon 34 of 72	1	NM_206933.4	ENSP00000305941.3
USH2A	ENST00000674083.1	c.6639delA	p.Lys2213AsnfsTer16	frameshift_variant	Exon 34 of 73			ENSP00000501296.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Rare genetic deafness Pathogenic:1

Feb 26, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Lys2213fs variant in USH2A has not been previously reported in individuals with hearing loss or Usher syndrome in any other family or in large population studies. This variant is predicted to cause a frameshift, which alters the prote in?s amino acid sequence beginning at position 2213 and leads to a premature ter mination codon 16 amino acids downstream. This alteration is then predicted to l ead to a truncated or absent protein. Loss of function of the USH2A gene is an e stablished disease mechanism in Usher syndrome. In summary, this variant meets c riteria to be classified as pathogenic for autosomal recessive Usher syndrome ba sed on the predicted impact of the variant on the protein. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.12		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: rs876657732; hg19: chr1-216172246;