The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: MYO7A vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: MYO7A CSPEC Genes: [ 'CDH23', 'COCH', 'GJB2', 'KCNQ4', 'MYO6', 'MYO7A', 'SLC26A4', 'TECTA', 'USH2A' ] * Message MONDOs: MONDO:0700087 CSPEC MONDO: [ 'MONDO:0019501', 'MONDO:0019497', 'MONDO:0019497', 'MONDO:0019497', 'MONDO:0019497', 'MONDO:0019497', 'MONDO:0019501', 'MONDO:0019497', 'MONDO:0010134', 'MONDO:0019497', 'MONDO:0019501' ]
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000260.4(MYO7A):c.983T>C (p.Leu328Pro)

CA381933255

1308583 (ClinVar)

Gene: MYO7A (HGNC:4647)
Condition: Usher syndrome type 1B (MONDO:0700087)
Inheritance Mode: Autosomal recessive inheritance
UUID: 7cdf2c5e-e1ab-4248-b4a4-ff015e04deb2
Approved on: 2024-12-18
Published on: 2025-03-28

HGVS expressions

NM_000260.4:c.983T>C
NM_000260.4(MYO7A):c.983T>C (p.Leu328Pro)
NC_000011.10:g.77158410T>C
CM000673.2:g.77158410T>C
NC_000011.9:g.76869456T>C
CM000673.1:g.76869456T>C
NC_000011.8:g.76547104T>C
NG_009086.1:g.35147T>C
NG_009086.2:g.35165T>C
ENST00000409709.9:c.983T>C
ENST00000409619.6:c.950T>C
ENST00000409709.7:c.983T>C
ENST00000409893.5:c.983T>C
ENST00000458637.6:c.983T>C
ENST00000620575.4:c.983T>C
NM_000260.3:c.983T>C
NM_001127179.2:c.983T>C
NM_001127180.1:c.983T>C
NM_001127180.2:c.983T>C
NM_001369365.1:c.950T>C
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Uncertain Significance

Met criteria codes 4
PM3_Supporting PM2_Supporting PP4 PP3
Not Met criteria codes 2
BS1 BA1

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.983T>C in MYO7A is a missense variant predicted to cause substitution of leucine by proline at amino acid 328 (p.Leu328Pro). The variant is absent from gnomAD v4.1.0 (PM2_Supporting). The variant p.Leu328Pro variant was identified by multigene panel testing in a three year old male proband with congenital bilateral profound sensorineural hearing loss and pigmentary retinopathy, delayed motor milestones, blonde fundus, and a diagnosis of Usher Syndrome 1B (PP4, PMID: 32281467). The proband also harbored a likely pathogenic variant NM_000260(MYO7A):c.471-2A>C, however the phase of the variants was not confirmed (0.5 PM3 points, PM3_Supporting; PMID: 32281467). The computational predictor REVEL gives a score of 0.877, which is above the threshold necessary to apply PP3 (PP3). There is a ClinVar entry for this variant (Variation ID: 1308583, one star review status), with one submitter classifying the variant as uncertain significance. In summary, this variant has been classified as a variant of uncertain significance for autosomal recessive Usher syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen Hearing Loss VCEP: PM2_Supporting, PP3, PP4, PM3_Supporting (ClinGen Hearing Loss VCEP specifications version 2; 12/18/2024).
Met criteria codes
PM3_Supporting
The variant p.Leu328Pro variant was identified by multigene panel testing in a three year old male proband with congenital bilateral profound sensorineural hearing loss and pigmentary retinopathy, delayed motor milestones, blonde fundus, and a diagnosis of Usher Syndrome 1B (PMID: 32281467). The proband also harbored a likely pathogenic variant NM_000260(MYO7A):c.471-2A>C, however the phase of the variants was not confirmed (0.5 PM3 points, PM3_Supporting; PMID: 32281467).
PM2_Supporting
The variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PP4
The variant p.Leu328Pro variant was identified by multigene panel testing in a three year old male proband with congenital bilateral profound sensorineural hearing loss and pigmentary retinopathy, delayed motor milestones, blonde fundus, and a diagnosis of Usher Syndrome 1B (PP4, PMID: 32281467).
PP3
The computational predictor REVEL gives a score of 0.877, which is above the threshold necessary to apply PP3 (PP3).
Not Met criteria codes
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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