The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000260.4(MYO7A):c.6326C>T (p.Thr2109Ile)

CA278724

164724 (ClinVar)

Gene: MYO7A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: a0970228-dea0-44d1-aa6d-d35746a8cff7
Approved on: 2023-01-18
Published on: 2023-02-06

HGVS expressions

NM_000260.4:c.6326C>T
NM_000260.4(MYO7A):c.6326C>T (p.Thr2109Ile)
NC_000011.10:g.77211909C>T
CM000673.2:g.77211909C>T
NC_000011.9:g.76922954C>T
CM000673.1:g.76922954C>T
NC_000011.8:g.76600602C>T
NG_009086.1:g.88645C>T
NG_009086.2:g.88664C>T
ENST00000409709.9:c.6326C>T
ENST00000670577.1:n.4127C>T
ENST00000409619.6:c.6179C>T
ENST00000409709.7:c.6326C>T
ENST00000458169.2:n.3752C>T
ENST00000458637.6:c.6212C>T
ENST00000481328.7:n.3862C>T
ENST00000526863.2:n.26-636C>T
ENST00000605744.1:n.1793C>T
NM_000260.3:c.6326C>T
NM_001127180.1:c.6212C>T
NM_001127180.2:c.6212C>T
NM_001369365.1:c.6179C>T

Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 5
PM2_Supporting PP1_Moderate PM3_Strong 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 variant NM_000260.4:c.6326C>T in MYO7A is a missense variant predicted to cause substitution of threonine by isoleucine at amino acid 2109 (p.Thr2109Ile). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00006 (8/128408 alleles, 0 homozygotes) for the European (Non-Finnish) population, which meets PM2_supporting criteria. The REVEL computational prediction analysis tool produced a score of 0.821, meeting PP3 criteria. This variant has been reported in two unrelated probands, both with Usher syndrome (PP4; SCV000199631.4). In addition, both probands had an additional MYO7A pathogenic or likely pathogenic variant in trans, meeting PM3_Strong criteria. Finally, the variant was shown to segregate with two affected family members (PP1_Moderate). In summary, the variant meets criteria to be classified as likely pathogenic for AR Usher syndrome. ACMG/AMP criteria met, as specified by the ClinGen Hearing Loss VCEP: PM2_supporting, PP3, PP4, PM3_Strong, PP1_Moderate (ClinGen Hearing Loss VCEP specifications version 2; 1/18/2023).
Met criteria codes
PM2_Supporting
The MAF in GnomAD is 0.00006 (8/128408 alleles), which is below the threshold of 0.00007 set by the HL VCEP to met PM2_Supporting criteria.
PP1_Moderate
Variant and likely path/path variant (VCV000043313.2 ) segregated in two affecred family members (SCV000199631.4).
PM3_Strong
Two probands with clinical features of Usher syndrome carried the variant (VCV000043313.2) in trans with likely path/path variants (SCV000199631.4). (2 PM3 pts.) Proband with congenital progressive profound sensorineural hearing loss and retinitis pigmentosa also carried a variant of uncertain significance (VCV000178667.1) in trans (SCV000199631.4). (.25 PM3 pts.)
PP4
Proband with congenital progressive profound sensorineural hearing loss and retinitis pigmentosa (SCV000199631.4).
PP3
REVEL: .821
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