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
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000260.3(MYO7A):c.1007G>A (p.Arg336His)

CA132194

43134 (ClinVar)

Gene: MYO7A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: 63bd6cea-9e2a-4ad6-a8c4-5a0d13f28c7e
Approved on: 2024-11-20
Published on: 2025-03-18

HGVS expressions

NM_000260.3:c.1007G>A
NM_000260.3(MYO7A):c.1007G>A (p.Arg336His)
NC_000011.10:g.77159450G>A
CM000673.2:g.77159450G>A
NC_000011.9:g.76870496G>A
CM000673.1:g.76870496G>A
NC_000011.8:g.76548144G>A
NG_009086.1:g.36187G>A
NG_009086.2:g.36205G>A
ENST00000409709.9:c.1007G>A
ENST00000409619.6:c.974G>A
ENST00000409709.7:c.1007G>A
ENST00000409893.5:c.1007G>A
ENST00000458637.6:c.1007G>A
ENST00000620575.4:c.1007G>A
NM_001127179.2:c.1007G>A
NM_001127180.1:c.1007G>A
NM_000260.4:c.1007G>A
NM_001127180.2:c.1007G>A
NM_001369365.1:c.974G>A
More

Likely Benign

Met criteria codes 2
BP2 BS1_Supporting
Not Met criteria codes 1
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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.1007G>A (p.Arg336His) variant in MYO7A is a missense variant predicted to cause a substitution of arginine by histidine at amino acid 336. The highest population minor allele frequency in gnomAD v4.1.0 is 0.00286 (2854/996858) in the non-Finnish European population, including 4 homozygous individuals, at least two of whom were beyond the average age of onset for MYO7A-related Usher syndrome. This frequency is higher than would be expected for an autosomal recessive condition based on the thresholds defined by the ClinGen Hearing Loss Expert Panel (BS1_Supporting). This variant has been reported in individuals with nonsyndromic, mild-moderate hearing loss in whom a second variant was not detected (PMID: 23804846) as well as an individual with Usher syndrome but lacking a second variant (PMID: 16470552). A patient with Usher syndrome was homozygous for both p.Arg336His and a likely pathogenic/pathogenic variant (BP2; PMID: 33363762, ClinVar IDs: 551533). The REVEL computational prediction tool produced a score of 0.734, which is above the threshold necessary to apply PP3. However, after discussion the expert panel decided not to apply PP3 based upon case level and frequency data. In summary, this variant meets criteria to be classified as likely benign for both Usher syndrome and nonsyndromic hearing loss. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BS1_Supporting, BP2. (ClinGen Hearing Loss VCEP specifications version 2; 11.20.2024).
Met criteria codes
BP2
A patient with Usher syndrome was homozygous for both p.Arg336His and a likely pathogenic/pathogenic variant (BP2; PMID: 33363762, ClinVar IDs: 551533).
BS1_Supporting
The highest population minor allele frequency in gnomAD v4.1.0 is 0.00286 (2854/996858) in the non-Finnish European population, including 4 homozygous individuals, at least two of whom were beyond the average age of onset for MYO7A-related Usher syndrome. This frequency is higher than would be expected for an autosomal recessive condition based on the thresholds defined by the ClinGen Hearing Loss Expert Panel.
Not Met criteria codes
PP3
REVEL score is 0.734, which is >0.7 threshold. After expert discussion, not applied because it is conflicting with case level and frequency data.
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.