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.977T>A (p.Leu326Gln)

CA278720

164664 (ClinVar)

Gene: MYO7A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: 34743a4e-57ba-4093-8021-c5af895b54a0
Approved on: 2024-09-24
Published on: 2024-09-27

HGVS expressions

NM_000260.4:c.977T>A
NM_000260.4(MYO7A):c.977T>A (p.Leu326Gln)
NC_000011.10:g.77158404T>A
CM000673.2:g.77158404T>A
NC_000011.9:g.76869450T>A
CM000673.1:g.76869450T>A
NC_000011.8:g.76547098T>A
NG_009086.1:g.35141T>A
NG_009086.2:g.35159T>A
ENST00000409709.9:c.977T>A
ENST00000409619.6:c.944T>A
ENST00000409709.7:c.977T>A
ENST00000409893.5:c.977T>A
ENST00000458637.6:c.977T>A
ENST00000620575.4:c.977T>A
NM_000260.3:c.977T>A
NM_001127179.2:c.977T>A
NM_001127180.1:c.977T>A
NM_001127180.2:c.977T>A
NM_001369365.1:c.944T>A
More

Likely Pathogenic

Met criteria codes 4
PP4 PP3 PM2_Supporting PM3_Strong
Not Met criteria codes 1
BP4

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

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Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.977T>A variant in MYO7A is a missense variant predicted to cause substitution of leucine by glutamine at amino acid 326 (p.Leu326Gln). The highest population filtering allele frequency in gnomAD v4.1 is 0.00002995 (7/91056 alleles) in the South Asian 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 0.991, which is above the threshold of 0.7, evidence that correlates with impact to MYO7A function (PP3). This variant has been detected in 3 individuals with autosomal recessive Usher syndrome. Of those individuals, 2 were compound heterozygous for the variant and a pathogenic or likely pathogenic variant and both of those were confirmed in trans by family testing (1.5 PM3 points, SCV000199549.4, SCV000589578.6, Laboratory for Molecular Medicine, GeneDx). One individual was homozygous for the variant (0.5 PM3 points, PMID: 18181211) (PM3_Strong). At least one patient with this variant displayed sensorineural hearing loss with retinitis pigmentosa, which is highly specific for autosomal recessive Usher syndrome (PP4, SCV000199549.4, 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_Strong, PM2_Supporting, PP3, PP4. (ClinGen Hearing Loss VCEP specifications version 2; 9/24/2024)
Met criteria codes
PP4
At least one patient with this variant displayed sensorineural hearing loss with retinitis pigmentosa, which is highly specific for autosomal recessive Usher syndrome (PP4, SCV000199549.4, Laboratory for Molecular Medicine).
PP3
The computational predictor REVEL gives a score of 0.991, which is above the threshold of 0.7, evidence that correlates with impact to MYO7A function (PP3).
PM2_Supporting
The highest population filtering allele frequency in gnomAD v4.1 is 0.00002995 (7/91056 alleles) in the South Asian population, which is lower than the ClinGen Hearing Loss VCEP threshold (≤0.00007) for PM2_Supporting, meeting this criterion (PM2_Supporting).
PM3_Strong
This variant has been detected in 3 individuals with autosomal recessive Usher syndrome. Of those individuals, 2 were compound heterozygous for the variant and a pathogenic or likely pathogenic variant and both of those were confirmed in trans by family testing (1.5 PM3 points, SCV000199549.4, SCV000589578.6, Laboratory for Molecular Medicine, GeneDx). One individual was homozygous for the variant (0.5 PM3 points, PMID: 18181211) (PM3_Strong).
Not Met criteria codes
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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