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Variant: NM_000260.4(MYO7A):c.2904G>T (p.Glu968Asp)

CA278647

43196 (ClinVar)

Gene: MYO7A
Condition: Usher syndrome type 1B
Inheritance Mode: Autosomal recessive inheritance
UUID: 19a2a2ac-617d-4a6b-ba5a-d3c5b8766be6
Approved on: 2022-08-03
Published on: 2022-08-03

HGVS expressions

NM_000260.4:c.2904G>T
NM_000260.4(MYO7A):c.2904G>T (p.Glu968Asp)
NC_000011.10:g.77181589G>T
CM000673.2:g.77181589G>T
NC_000011.9:g.76892635G>T
CM000673.1:g.76892635G>T
NC_000011.8:g.76570283G>T
NG_009086.1:g.58326G>T
NG_009086.2:g.58344G>T
ENST00000409709.9:c.2904G>T
ENST00000409893.6:n.969G>T
ENST00000670577.1:n.745G>T
ENST00000409619.6:c.2871G>T
ENST00000409709.7:c.2904G>T
ENST00000409893.5:c.2904G>T
ENST00000458169.2:n.447G>T
ENST00000458637.6:c.2904G>T
ENST00000481328.7:n.447G>T
ENST00000620575.4:c.2904G>T
NM_000260.3:c.2904G>T
NM_001127179.2:c.2904G>T
NM_001127180.1:c.2904G>T
NM_001127180.2:c.2904G>T
NM_001369365.1:c.2871G>T
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Likely Pathogenic

Met criteria codes 4
PM2_Supporting PP1 PP4 PM3_Strong
Not Met criteria codes 3
BP4 PP3 PM5

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.2904G>T variant in MYO7A is a missense variant predicted to cause substitution of glutamic acid by aspartic acid at amino acid 968. The highest population minor allele frequency in gnomAD v2.1.1 is 0.0000064 (3/126898 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 0.563, which is neither above nor below the thresholds predicting a damaging or benign impact on MYO7A function. At least one patient with this variant displayed Usher syndrome (PP4, PMID: 33089500). This variant has been detected in at least five individuals with Usher syndrome. Of those individuals, two were compound heterozygous for the variant and a pathogenic or likely pathogenic variant and presumed to be in trans (c.631A>G (p.S211G) and c.3719G>A (p.D1240Q)) and three of those were confirmed in trans by family testing and all of whom had different variants on the other allele (c.224dup (p.D75fs), c.487G>C (p.G163R), c.1189G>A (p.A397T); 2.5 PM3 points, PMID: 25472526, 26969326, 33089500; ClinVar Variation ID: 43325, 43218, 553215) (PM3_Strong). The variant has been reported to segregate with Usher syndrome in three affected family members from one family (PP1; PMID:33089500). Another missense variant, c.2904G>C (p.E968D), in the same codon has been reported in a patient with Usher syndrome (PMID:27460420). However, this variant has not yet met the criteria to be classified as pathogenic or likely pathogenic by the ClinGen Hearing Loss VCEP (PM5 not met). 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: PM2_P, PP1, PP4, PM3_S (ClinGen Hearing Loss VCEP specifications version 2; 7/26/2022).
Met criteria codes
PM2_Supporting
The highest population minor allele frequency in gnomAD v2.1.1 is 0.0000064 (3/126898 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).
PP1
The variant has been reported to segregate with Usher syndrome in three affected family members from one family (PP1; PMID:33089500).
PP4
At least one patient with this variant displayed Usher syndrome (PP4, PMID: 33089500).
PM3_Strong
This variant has been detected in at least five individuals with Usher syndrome. Of those individuals, two were compound heterozygous for the variant and a pathogenic or likely pathogenic variant and presumed to be in trans (c.631A>G (p.S211G) and c.3719G>A (p.D1240Q)) and three of those were confirmed in trans by family testing and all of whom had different variants on the other allele (c.224dup (p.D75fs), c.487G>C (p.G163R), c.1189G>A (p.A397T); 2.5 PM3 points, PMID: 25472526, 26969326, 33089500; ClinVar Variation ID: 43325, 43218, 553215) (PM3_Strong).
Not Met criteria codes
BP4
The computational predictor REVEL gives a score of 0.563, which is neither above nor below the thresholds predicting a damaging or benign impact on MYO7A function.
PP3
The computational predictor REVEL gives a score of 0.563, which is neither above nor below the thresholds predicting a damaging or benign impact on MYO7A function.
PM5
Another missense variant, c.2904G>C (p.E968D), in the same codon has been reported in a patient with Usher syndrome (PMID:27460420). However, this variant has not yet met the criteria to be classified as pathogenic or likely pathogenic by the ClinGen Hearing Loss VCEP (PM5 not met).
Curation History
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