The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_000260.3(MYO7A):c.3503G>A (p.Arg1168Gln)

CA184505

179479 (ClinVar)

Gene: MYO7A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: b16ffcc3-3e9d-4890-aca5-e535579a2453
Approved on: 2019-09-16
Published on: 2019-09-16

HGVS expressions

NM_000260.3:c.3503G>A
NM_000260.3(MYO7A):c.3503G>A (p.Arg1168Gln)
NC_000011.10:g.77184715G>A
CM000673.2:g.77184715G>A
NC_000011.9:g.76895760G>A
CM000673.1:g.76895760G>A
NC_000011.8:g.76573408G>A
NG_009086.1:g.61451G>A
NM_001127179.2:c.3503G>A
NM_001127180.1:c.3503G>A
NM_000260.4:c.3503G>A
ENST00000409619.6:c.3470G>A
ENST00000409709.7:c.3503G>A
ENST00000409893.5:c.3503G>A
ENST00000458169.2:n.1046G>A
ENST00000458637.6:c.3503G>A
ENST00000467137.1:n.30G>A
ENST00000481328.7:n.1046G>A
ENST00000620575.4:c.3500+12G>A
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Pathogenic

Met criteria codes 5
PM5 PM2 PP4 PP3 PM3_Strong

Evidence Links 3

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.3503G>A (p.Arg1168Gln) variant in MYO7A has been detected in at least 4 probands with Usher syndrome. For two of those probands, a pathogenic or suspected-pathogenic variants was observed in trans, and in one individual, the variant was observed with a pathogenic or suspected-pathogenic variant, but it was unclear if phasing was performed (PM3_Strong, PP4; PMID:25404053, 27460420, 28944237). The allele frequency of this variant is 0.004%% (1/26850) of South Asian chromosomes by gnomAD, which is a low enough frequency to apply PM2 based on the thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss (PM2). The c.3503G>A (p.Arg1168Gln) variant is located in the last base of the exon, which is part of the 5’ consensus sequence, and computational tools suggest an impact to splicing. Furthermore, tThe REVEL computational prediction analysis tool produced a score of 0.9, which is above the threshold necessary to apply PP3. A different likely pathogenic or suspected-pathogenic variant at the same nucleotide (c.3503G>C, Arg1168Pro) has been previously identified in an individual with Usher syndrome who was compound heterozygous for a second pathogenic truncating variant (PMID: 16470552). In addition, a minigene assay demonstrated that the 3503G>C variant led to skipping of exon 27 (PMID: 20052763) suggesting that variants that alter the c.3503G nucleotide may cause abnormal splicing (PM5_Supporting). In summary, this variant meets criteria to be classified as likely pathogenic for autosomal recessive Usher syndrome based on the ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: PM3_Strong, PP4, PM2, PP3, PM5_Supporting.
Met criteria codes
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
0.004%, 1/26850 of S. Asian chr in gnomad
PP4
Bonnet 2016, patient with USH1
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3_Strong
1 point from Aparisi 2014 (Gln1798X / Arg1168Gln, variants likely phased). 0.5 points from Bonnet 2016 (p.Arg1168Gln / exon 46 del (in frame), variants phased), 0.5 points from Neuhaus (Arg1168Gln / 6025delG, unclear if phased).

Curation History
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