rs397516303

Variant names:

• chr11-77190083-AGAAGGACCTTT-A
• rs397516303
• NM_000260.4:c.3696_3706delAAGGACCTTTG

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000260.4(MYO7A):​c.3696_3706delAAGGACCTTTG​(p.Arg1232SerfsTer72) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MYO7A NM_000260.4 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:4
• Conservation: PhyloP100: 9.55

Genes affected

MYO7A (HGNC:7606): (myosin VIIA) This gene is a member of the myosin gene family. Myosins are mechanochemical proteins characterized by the presence of a motor domain, an actin-binding domain, a neck domain that interacts with other proteins, and a tail domain that serves as an anchor. This gene encodes an unconventional myosin with a very short tail. Defects in this gene are associated with the mouse shaker-1 phenotype and the human Usher syndrome 1B which are characterized by deafness, reduced vestibular function, and (in human) retinal degeneration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 11-77190083-AGAAGGACCTTT-A is Pathogenic according to our data. Variant chr11-77190083-AGAAGGACCTTT-A is described in ClinVar as [Pathogenic]. Clinvar id is 43217.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-77190083-AGAAGGACCTTT-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MYO7A	NM_000260.4	c.3696_3706delAAGGACCTTTG	p.Arg1232SerfsTer72	frameshift_variant	Exon 29 of 49	ENST00000409709.9	NP_000251.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MYO7A	ENST00000409709.9	c.3696_3706delAAGGACCTTTG	p.Arg1232SerfsTer72	frameshift_variant	Exon 29 of 49	1	NM_000260.4	ENSP00000386331.3
MYO7A	ENST00000458637.6	c.3696_3706delAAGGACCTTTG	p.Arg1232SerfsTer72	frameshift_variant	Exon 29 of 49	1		ENSP00000392185.2
MYO7A	ENST00000409619.6	c.3663_3673delAAGGACCTTTG	p.Arg1221SerfsTer72	frameshift_variant	Exon 30 of 50	1		ENSP00000386635.2
MYO7A	ENST00000458169.2	c.1239_1249delAAGGACCTTTG	p.Arg413SerfsTer72	frameshift_variant	Exon 9 of 29	1		ENSP00000417017.2
MYO7A	ENST00000670577.1	n.1536_1546delAAGGACCTTTG		non_coding_transcript_exon_variant	Exon 12 of 32			ENSP00000499323.1

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Usher syndrome type 1B Pathogenic:1

Jul 14, 2020

Natera, Inc.

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided Pathogenic:1

Oct 13, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Arg1232Serfs*72) in the MYO7A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MYO7A are known to be pathogenic (PMID: 8900236, 25404053). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This premature translational stop signal has been observed in individual(s) with autosomal recessive MYO7A-related conditions (PMID: 28731162, 30029497). ClinVar contains an entry for this variant (Variation ID: 43217). For these reasons, this variant has been classified as Pathogenic. -

Usher syndrome type 1;C1832475:Autosomal dominant nonsyndromic hearing loss 11;C1838701:Autosomal recessive nonsyndromic hearing loss 2 Pathogenic:1

-

Juno Genomics, Hangzhou Juno Genomics, Inc

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PVS1+PM2_Supporting+PM3_Supporting+PP1 -

Rare genetic deafness Pathogenic:1

Apr 23, 2010

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The 3696_3706del (Arg1232fs) variant in MYO7A has not been reported in the liter ature nor previously identified by our laboratory. However, the Arg1232fs varian t is predicted to cause a frameshift, which alters the protein's amino acid sequ ence beginning at codon 1232 and leads to a premature stop codon 72 codons downs tream. This alteration is then predicted to lead to a truncated or absent protei n. In summary, this variant is highly likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs397516303; hg19: chr11-76901128;