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Variant: NM_000260.4(MYO7A):c.3546C>A (p.Asn1182Lys)

CA381946913

438177 (ClinVar)

Gene: MYO7A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: 0ff89378-59ae-459b-9112-e954004ee08d
Approved on: 2023-06-27
Published on: 2023-10-05

HGVS expressions

NM_000260.4:c.3546C>A
NM_000260.4(MYO7A):c.3546C>A (p.Asn1182Lys)
NC_000011.10:g.77189386C>A
CM000673.2:g.77189386C>A
NC_000011.9:g.76900431C>A
CM000673.1:g.76900431C>A
NC_000011.8:g.76578079C>A
NG_009086.1:g.66122C>A
NG_009086.2:g.66141C>A
ENST00000409709.9:c.3546C>A
ENST00000670577.1:c.1387C>A
ENST00000409619.6:c.3513C>A
ENST00000409709.7:c.3546C>A
ENST00000458169.2:c.1089C>A
ENST00000458637.6:c.3546C>A
ENST00000467137.1:n.73C>A
ENST00000481328.7:n.1089C>A
NM_000260.3:c.3546C>A
NM_001127180.1:c.3546C>A
NM_001127180.2:c.3546C>A
NM_001369365.1:c.3513C>A
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Likely Pathogenic

Met criteria codes 4
PM3_Strong PM2_Supporting PP4 PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hearing Loss Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CDH23, COCH, GJB2, KCNQ4, MYO6, MYO7A, SLC26A4, TECTA and USH2A Version 2

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The p.Asn1182Lys variant in MYO7A is a missense variant predicted to cause substitution of asparagine to lysine at amino acid 1182. This variant is absent from large population studies (PM2_Supporting, gnomAD v2.1.1). The computational predictor REVEL gives a score of 0.833 which is above the threshold necessary to apply PP3; however, this information is not predictive of pathogenicity on its own (PP3). This variant has been detected in at least four probands with AR Usher syndrome. Two patients were homozygous for the variant, while the other two were compound heterozygous with a pathogenic or likely pathogenic variant; however only one was confirmed trans (c.721C>T (p.Arg241Cys), 2.0 PM3_Strong points, PMID:27460420, 28041643, 31479088, Invitae Internal Data (SCV001211338.4)). At least one patient with a variant identified in this gene displayed sensorineural hearing loss and retinitis pigmentosa, features consistent with Usher syndrome (PP4). The variant has been reported to segregate with AR Usher syndrome in 1 affected family member from 1 family (PP1; PMID: 31479088). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal recessive Usher syndrome based on ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP; PM2_Supporting, PP3, PM3_Strong, PP1, PP4. (The ClinGen Hearing Loss VCEP Specifications Version 2; 06/27/2023).
Met criteria codes
PM3_Strong
2.0 PM3_Strong points total. 0.5 for proband from Bonnet et al., homozygous. 0.5 for proband from Carss et al., assumed to be in trans with the c.721C>T (Arg241Cys) variant in MYO7A, which is classified as likely pathogenic by Counsyl and NIHR Bioresource Rare Diseases, University of Cambridge. 0.5 from Khateb et al., 2020 proband (CIC00072 Index) with the homozygous variant occurrence. 0.5 for Invitae internal proband with a second pathogenic variant in the gene and an unknown phase.
PM2_Supporting
Absent from gnomAD with high coverage.
PP4
Identified in 1 French patient with Usher syndrome type 1 (Bonnet et al.) and 1 European male with Usher syndrome (Carss et al.)
PP3
REVEL score 0.833. Splicing not predicted to be impacted by Alamut. No animals in UCSC database have an alternate amino acid at this site.
Curation History
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