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Variant: NM_000260.4(MYO7A):c.401T>A (p.Ile134Asn)

CA278663

43230 (ClinVar)

Gene: MYO7A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: 28c29ee7-31d4-4833-afbd-15bf5b29aa05

HGVS expressions

NM_000260.4:c.401T>A
NM_000260.4(MYO7A):c.401T>A (p.Ile134Asn)
NM_000260.3:c.401T>A
NM_001127179.2:c.401T>A
NM_001127180.1:c.401T>A
NM_001127180.2:c.401T>A
NM_001369365.1:c.368T>A
ENST00000409619.6:c.368T>A
ENST00000409709.7:c.401T>A
ENST00000409893.5:c.401T>A
ENST00000458637.6:c.401T>A
ENST00000620575.4:c.401T>A
NC_000011.10:g.77156022T>A
CM000673.2:g.77156022T>A
NC_000011.9:g.76867068T>A
CM000673.1:g.76867068T>A
NC_000011.8:g.76544716T>A
NG_009086.1:g.32759T>A
NG_009086.2:g.32777T>A

Likely Pathogenic

Met criteria codes 5
PM3_Strong PP3 PP1 PP4 PM2

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The allele frequency of the c.401T>A (p.Ile134Asn) variant in the MYO7A gene is 0.0062% (7/112888) of European (non-Finnish) 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. This variant has been detected in 5 probands with Usher syndrome. For 2 of those probands, pathogenic variants (c.19-1G>A and Gly214Arg) were observed in trans, and in the other 3 probands, a pathogenic variant was observed with unknown phase (PM3_Strong, PMIDs: 25468891, 26969326, Partners LMM Internal Data ClinVar SCV000059786.6). The variant has been reported to segregate with hearing loss in one affected family member (PP1, Partners LMM Internal Data ClinVar SCV000059786.6). The REVEL computational prediction tool produced a score of 0.938, which is above the threshold necessary to apply PP3. At least one patient with this variant displayed features of sensorineural hearing loss and retinitis pigmentosa, which are consistent for Usher syndrome, a condition highly specific for MYO7A (PP4, Partners LMM Internal Data ClinVar SCV000059786.6). 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, PM2, PP1, PP3, PP4).
Met criteria codes
PM3_Strong
A total of 3 PM3 points lead to a strong classification. Both probands from the 2 publications were given a point each and the sisters (one proband scored) and 15 yo female from LMM were given 0.5 PM3 point each.

PP3
The REVEL score is 0.938 and there is no impact to splicing. The residue is conserved in all vertebrates in the UCSC browser.
PP1
2 sisters from LMM segregated with two MYO7A variants.
PP4
The 2 sisters both had SNHL and RP, which are highly specific for Usher syndrome.
PM2
The variant is present in 0.0062% (7/112888) of European (non-Finnish) alleles in gnomAD v2.1.1 and in 0.0073% (1/13654) of Latino (non-Finnish) alleles in gnomAD v3.
Approved on: 2020-11-02
Published on: 2020-11-02
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