The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000260.4(MYO7A):c.5804T>C (p.Leu1935Pro)

CA278691

43298 (ClinVar)

Gene: MYO7A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: 1f484128-351e-49bd-a7a1-877c462ffac6
Approved on: 2024-09-24
Published on: 2024-09-24

HGVS expressions

NM_000260.4:c.5804T>C
NM_000260.4(MYO7A):c.5804T>C (p.Leu1935Pro)
NC_000011.10:g.77207350T>C
CM000673.2:g.77207350T>C
NC_000011.9:g.76918395T>C
CM000673.1:g.76918395T>C
NC_000011.8:g.76596043T>C
NG_009086.1:g.84086T>C
NG_009086.2:g.84105T>C
ENST00000409709.9:c.5804T>C
ENST00000670577.1:c.3631T>C
ENST00000409619.6:c.5657T>C
ENST00000409709.7:c.5804T>C
ENST00000458169.2:c.3230T>C
ENST00000458637.6:c.5690T>C
ENST00000481328.7:n.3340T>C
ENST00000605744.1:n.718T>C
NM_000260.3:c.5804T>C
NM_001127180.1:c.5690T>C
NM_001127180.2:c.5690T>C
NM_001369365.1:c.5657T>C

Likely Pathogenic

Met criteria codes 4
PP4 PP3 PM2 PM3

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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.5804T>C variant in MYO7A is a missense variant predicted to cause substitution of leucine by proline at amino acid 1935 (p.Leu1935Pro). The highest population minor allele frequency in gnomAD v4.1 is 0.00002204 (26/1179460 alleles) in the European (non-Finnish) population, which is lower than the ClinGen Hearing Loss VCEP threshold (≤0.00007) for PM2_Supporting, meeting this criterion (PM2_Supporting). The computational predictor REVEL gives a score of 0.961, which is above the threshold of 0.7, evidence that correlates with impact to MYO7A function (PP3). This variant has been detected in 2 individuals with autosomal recessive Usher syndrome. Both were compound heterozygous for the variant and a pathogenic or likely pathogenic variant and both of those were confirmed in trans by family testing (2 PM3 points, SCV001239772.1, SCV000059855.6, Blueprint Genetics, Laboratory for Molecular Medicine) (PM3). At least one patient with this variant displayed sensorineural hearing loss with retinitis pigmentosa, which is highly specific for autosomal recessive Usher syndrome (PP4, SCV000059855.6, Laboratory for Molecular Medicine). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal recessive Usher syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: PM3, PM2_Supporting, PP3, PP4. (ClinGen Hearing Loss VCEP specifications version 2; 9/24/2024)
Met criteria codes
PP4
Proband from Blueprint Genetics has hearing loss and RP.
PP3
The REVEL score is 0.961, the residue is conserved across all vertebrates in the UCSC genome browser, and there is a possible 3' cryptic splice site creation predicted by MaxEntScan.
PM2
Present in 0.00236% (3/127394) of European (non-Finnish) chromosomes in gnomAD v2.1.1 and in 0.00155% (1/64574) of European (non-Finnish) chromosomes in gnomAD v3.
PM3
Present in one proband with severe to profound SNHL with delayed walking and balance issues in trans with the pathogenic c.1200+1G>A variant in MYO7A. No mention of RP but report mentions that the proband should be followed to see if the phenotype develops.
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