Variant: NM_206933.2(USH2A):c.8559-2A>G

CA262122

48604 (ClinVar)

Gene: USH2A

Condition: Usher syndrome

Inheritance Mode: Autosomal recessive inheritance

UUID: fe785bf9-af38-456e-83ed-6717335dbde4

Approved on: 2018-10-09

Published on: 2019-07-17

HGVS expressions

NM_206933.2:c.8559-2A>G
NM_206933.2(USH2A):c.8559-2A>G
NC_000001.11:g.215877882T>C
CM000663.2:g.215877882T>C
NC_000001.10:g.216051224T>C
CM000663.1:g.216051224T>C
NC_000001.9:g.214117847T>C
NG_009497.1:g.550515A>G
NM_206933.3:c.8559-2A>G
ENST00000307340.7:c.8559-2A>G

Pathogenic

• Met criteria codes: PP1_Strong PM2_Supporting PP4 PM4 PM3_Very Strong

• Not Met criteria codes: BS2 BS4 BS1 BP3 BP4 BP2 BP5 BP7 PS1 PS4 PS2 PS3 PP3 PM5 PM1 PM6 PVS1 BA1

Expert Panel

Hearing Loss VCEP

Criteria Specification Information

Evidence submitted by expert panel

Hearing Loss VCEP

The c.8559-2A>G has been detected in >4 patients with Usher syndrome who were compound heterozygous for the this variant in trans with a truncating variant (PM3_VS; PMID: 25356976, 19737284, 26338283, 19023448). Segregation data was also available for two reported families with Usher syndrome. In one family, the variant was identified in trans with a frameshift variant in two affected siblings, and four unaffected siblings were either heterozygous for a single variant or wild-type for both variants. In the second family, an unaffected sibling was heterozygous for a single variant (PP1_Strong, PMID: 19023448). RT-PCR analysis of cells from a patient carrying the variant revealed that the variant causes skipping of exon 43, resulting in a 41 amino acid deletion of the USH2A protein (PM4, PMID: 20596040) The allele frequency of the c.8559-2A>G variant in the USH2A gene is 0.046% (8/17232) of East Asian chromosomes by the Genome Aggregation Database ( http://gnomad.broadinstitute.org), which is a low enough frequency to award PM2_supporting based on the thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss and Usher syndrome (PM2_Supporting). Several patients reported to harbor this variant displayed clinical features of Usher syndrome (PP4; PMID: 25356976, 19737284, 26338283, 19023448). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive Usher syndrome based on the ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: PM4, PM3_VS, PP1_S, PP4, PM2_P.

Met criteria codes

• PP1_Strong: Dai et al. 2008 is the only paper with genotyping data for family members. They have a total of 6 unaffected sibs across 2 families and 3 affected individuals with the variant between the two families. (Figure 1) This would actually be 1 affected segregation and 5 unaffected segregations, LOD = 0.75 The variant has been reported in two probands with Usher syndrome. In one family, the variant was identified in trans with a frameshift variant in two affected siblings, and four unaffected siblings were either heterozygous for a single variant or wild-type for both variants. In the second family, an unaffected sibling was heterozygous for a single variant (PP1_Strong, PMID: 19023448).
• PM2_Supporting: The allele frequency of the c.8559-2A>G variant in the USH2A gene is 0.046% (8/17232) of East Asian chromosomes by the Genome Aggregation Database ( http://gnomad.broadinstitute.org), which is a low enough frequency to award PM2 based on the thresholds defined by the ClinGen Hearing Loss Expert Panel for [autosomal dominant / autosomal recessive] hearing loss (PM2).
• PP4: Several patients reported to harbor this variant have clinical features of Usher syndrome, a condition highly specific for Usher syndrome (PP4).
• PM4: RT-PCR analysis of cells from a patient carrying the variant revealed that the variant causes skipping of exon 43, resulting in a 41 amino acid deletion of the USH2A protein (Nakanishi 2010; PM4). DECIDED TO USE PM4 OVER PS3 ON OUR VARIANT CURATION CALL
• PM3_Very Strong: This variant has been detected in >4 patients with Usher syndrome who were compound heterozygous for the c.8559-2A>G in trans with a truncating variant (PM3_VS; PMID: 25356976, 19737284, 26338283, 19023448).

Not Met criteria codes

• BS2: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BS1: The allele frequency of the c.8559-2A>G variant in the USH2A gene is 0.046% (8/17232) of East Asian chromosomes by the Genome Aggregation Database ( http://gnomad.broadinstitute.org), which is a low enough frequency to award PM2 based on the thresholds defined by the ClinGen Hearing Loss Expert Panel for [autosomal dominant / autosomal recessive] hearing loss (PM2).
• BP3: RT-PCR analysis of cells from a patient carrying the variant revealed that the variant causes skipping of exon 43, resulting in a 41 amino acid deletion of the USH2A protein (Nakanishi 2010; PM4). DECIDED TO USE PM4 OVER PS3 ON OUR VARIANT CURATION CALL
• BP4: All of the splicing predictors in Alamut including MaxEntScan indicate the loss of the splice site that causes the skipping of exon 43. RS: I wouldn't apply PP3, because it is a splice-site variant.
• BP5: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• BP7: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PS1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PS4: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PS2: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PS3: RT-PCR from RNA extracted from hair roots of Japanese Usher syndrome patients (Nakanishi et al 2010) showed that the varaint inactivated the splice acceptor site causing the skipping of the exon 43. (This is currently not in the HL rule document). AG: downgraded to PS3_Supporting as it is not a functional assay supported by the HL group for application of PS3 RS: not applied WE DECIDED TO USE PM4 OVER PS3 ON OUR VARIANT CALL
• PP3: All of the splicing predictors in Alamut including MaxEntScan indicate the loss of the splice site that causes the skipping of exon 43. RS: I wouldn't apply PP3, because it is a splice-site variant.
• PM5: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PM1: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PM6: No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
• PVS1: This variant occurs at the -2 site of exon 43, and though this exon is not included in the short transcript of the USH2A gene, the long transcript is the biologically relevant transcript. This change does not remove a significant portion of the protein so PM4 was applied which is equivalent to PVS1_M
• BA1: The allele frequency of the c.8559-2A>G variant in the USH2A gene is 0.046% (8/17232) of East Asian chromosomes by the Genome Aggregation Database ( http://gnomad.broadinstitute.org), which is a low enough frequency to award PM2 based on the thresholds defined by the ClinGen Hearing Loss Expert Panel for [autosomal dominant / autosomal recessive] hearing loss (PM2).