rs121912558

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

Scores

3
3
1

Clinical Significance

Pathogenic criteria provided, single submitter P:2

Conservation

PhyloP100: 3.80
Variant links:
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]

Genome browser will be placed here

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
MYO6NM_004999.4 linkuse as main transcriptc.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
MYO6ENST00000369977.8 linkuse as main transcriptc.3496C>T p.Arg1166Ter stop_gained 34/351 NM_004999.4 ENSP00000358994 A1Q9UM54-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000342
AC:
5
AN:
1461882
Hom.:
0
Cov.:
31
AF XY:
0.00000413
AC XY:
3
AN XY:
727242
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000450
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378

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 submitterclinical testingGeneDxJun 25, 2020Observed 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 providedliterature onlyOMIMMay 01, 2003- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.63
D
BayesDel_noAF
Pathogenic
0.62
CADD
Pathogenic
38
DANN
Uncertain
1.0
Eigen
Pathogenic
0.78
Eigen_PC
Uncertain
0.66
FATHMM_MKL
Uncertain
0.91
D
MutationTaster
Benign
1.0
A;A;A;A
Vest4
0.93
GERP RS
5.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs121912558; hg19: chr6-76623836; API