rs121912558
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Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The ENST00000369977.8(MYO6):c.3496C>T(p.Arg1166Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000342 in 1,461,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
MYO6
ENST00000369977.8 stop_gained
ENST00000369977.8 stop_gained
Scores
3
3
1
Clinical Significance
Conservation
PhyloP100: 3.80
Genes affected
MYO6 (HGNC:7605): (myosin VI) This gene encodes a reverse-direction motor protein that moves toward the minus end of actin filaments and plays a role in intracellular vesicle and organelle transport. The protein consists of a motor domain containing an ATP- and an actin-binding site and a globular tail which interacts with other proteins. This protein maintains the structural integrity of inner ear hair cells and mutations in this gene cause non-syndromic autosomal dominant and recessive hearing loss. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 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 6-75914119-C-T is Pathogenic according to our data. Variant chr6-75914119-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 8579.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr6-75914119-C-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYO6 | NM_004999.4 | c.3496C>T | p.Arg1166Ter | stop_gained | 34/35 | ENST00000369977.8 | NP_004990.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYO6 | ENST00000369977.8 | c.3496C>T | p.Arg1166Ter | stop_gained | 34/35 | 1 | NM_004999.4 | ENSP00000358994 | A1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727242
GnomAD4 exome
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31
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3
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727242
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
Bravo
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jun 25, 2020 | Observed in heterozygous state in five patients with mild hearing loss, including four cases with onset between 29-35 years of age and family histories consistent with autosomal dominant inheritance, and one sporadic case with unknown age of onset and inheritance pattern (Miyagawa et al., 2015; Oka et al., 2020); R1166X segregated in two other heterozygous affected relatives in one of these families; Published functional studies demonstrate a damging effect resulting in a truncated protein with aberrant binding and localization (Arden et al., 2016); Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 31589614, 25999546, 32143290, 12687499, 18348273, 27474411, 25525159, 18212818) - |
Autosomal recessive nonsyndromic hearing loss 37 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 2003 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
A;A;A;A
Vest4
GERP RS
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at