Submissions for variant NM_000260.4(MYO7A):c.6439-2A>G

gnomAD frequency: 0.00003  dbSNP: rs397516330

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000036235	SCV000059887	pathogenic	Rare genetic deafness	2011-07-07	criteria provided, single submitter	clinical testing	The 6439-2A>G variant in MYO7A has not been reported in the literature nor previ ously identified by our laboratory in any other families. The 6439-2A>G variant is predicted to cause abnormal splicing because the nucleotide substitution occu rs in the invariant region of the splice consensus sequence. In summary, this va riant meets our criteria to be classified as pathogenic.
Counsyl	RCV000664694	SCV000788697	pathogenic	Autosomal recessive nonsyndromic hearing loss 2; Usher syndrome type 1	2017-01-05	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000778156	SCV000914289	likely pathogenic	MYO7A-Related Disorders	2019-04-05	criteria provided, single submitter	clinical testing	The MYO7A c.6439-2A>G occurs in a canonical splice site (acceptor) and is therefore predicted to disrupt or distort the normal gene product. The c.6439-2A>G variant has been reported in three studies in which it was identified in a compound heterozygous state in four individuals with Usher syndrome, including in a pair of siblings (Glockle et al. 2014; Kletke et al. 2017; Neuhaus et al. 2017). The variant was also identified in a compound heterozygous state in two-year-old dizygotic twins with congenital severe, non-progressive hearing loss and likely vestibular dysfunction (Mutai et al. 2013). Whether they later developed retinitis pigmentosa was not reported. In these individuals, each of the identified variants was shown to be inherited from an unaffected heterozygous parent, consistent with autosomal recessive inheritance. The c.6439-2A>G variant has not been reported in association with autosomal dominant hearing loss. It was absent from 192 normal hearing control individuals and is reported at a frequency of 0.000067 in the European (Non-Finnish) population of the Genome Aggregation Database. This frequency is based on one allele only in a region of good sequence coverage, suggesting the variant is rare. Functional studies of the c.6439-2A>G variant have not been reported, but it is predicted to result in aberrant splicing. Based on the collective evidence, the c.6439-2A>G variant is classified as likely pathogenic for MYO7A-related disorders.
Invitae	RCV001208546	SCV001379940	pathogenic	not provided	2023-12-10	criteria provided, single submitter	clinical testing	This sequence change affects an acceptor splice site in intron 47 of the MYO7A gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in MYO7A are known to be pathogenic (PMID: 8900236, 25404053). This variant is present in population databases (rs397516330, gnomAD 0.007%). Disruption of this splice site has been observed in individual(s) with autosomal recessive deafness (PMID: 24164807). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 43329). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	RCV001208546	SCV001446975	pathogenic	not provided	2020-10-23	criteria provided, single submitter	clinical testing
Natera, Inc.	RCV001275537	SCV001460752	pathogenic	Usher syndrome type 1B	2020-09-16	no assertion criteria provided	clinical testing