rs1555062984
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PM4PP3PP5
The NM_000260.4(MYO7A):c.652_657del(p.Asp218_Ile219del) variant causes a inframe deletion 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 (no stars).
Frequency
Genomes: not found (cov: 33)
Consequence
MYO7A
NM_000260.4 inframe_deletion
NM_000260.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.92
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
PM1
?
In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 8 uncertain in NM_000260.4
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_000260.4.
PP3
?
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
PP5
?
Variant 11-77156915-TACATCG-T is Pathogenic according to our data. Variant chr11-77156915-TACATCG-T is described in ClinVar as [Pathogenic]. Clinvar id is 11849.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr11-77156915-TACATCG-T is described in Lovd as [Pathogenic]. Variant chr11-77156915-TACATCG-T is described in Lovd as [Likely_pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO7A | NM_000260.4 | c.652_657del | p.Asp218_Ile219del | inframe_deletion | 7/49 | ENST00000409709.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO7A | ENST00000409709.9 | c.652_657del | p.Asp218_Ile219del | inframe_deletion | 7/49 | 1 | NM_000260.4 | ||
MYO7A | ENST00000409619.6 | c.619_624del | p.Asp207_Ile208del | inframe_deletion | 8/50 | 1 | |||
MYO7A | ENST00000458637.6 | c.652_657del | p.Asp218_Ile219del | inframe_deletion | 7/49 | 1 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Usher syndrome type 1B Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 10, 1995 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at