rs1554836048
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_017433.5(MYO3A):c.2890G>A(p.Asp964Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,820 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
MYO3A
NM_017433.5 missense
NM_017433.5 missense
Scores
2
9
8
Clinical Significance
Conservation
PhyloP100: 5.68
Genes affected
MYO3A (HGNC:7601): (myosin IIIA) The protein encoded by this gene belongs to the myosin superfamily. Myosins are actin-dependent motor proteins and are categorized into conventional myosins (class II) and unconventional myosins (classes I and III through XV) based on their variable C-terminal cargo-binding domains. Class III myosins, such as this one, have a kinase domain N-terminal to the conserved N-terminal motor domains and are expressed in photoreceptors. The protein encoded by this gene plays an important role in hearing in humans. Three different recessive, loss of function mutations in the encoded protein have been shown to cause nonsyndromic progressive hearing loss. Expression of this gene is highly restricted, with the strongest expression in retina and cochlea. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO3A | NM_017433.5 | c.2890G>A | p.Asp964Asn | missense_variant | 26/35 | ENST00000642920.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO3A | ENST00000642920.2 | c.2890G>A | p.Asp964Asn | missense_variant | 26/35 | NM_017433.5 | P1 | ||
MYO3A | ENST00000543632.5 | c.1777-54437G>A | intron_variant | 1 | |||||
MYO3A | ENST00000642197.1 | n.3094G>A | non_coding_transcript_exon_variant | 26/27 | |||||
MYO3A | ENST00000647478.1 | c.*885G>A | 3_prime_UTR_variant, NMD_transcript_variant | 24/30 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461820Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 727212
GnomAD4 exome
AF:
AC:
2
AN:
1461820
Hom.:
Cov.:
34
AF XY:
AC XY:
1
AN XY:
727212
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
Asia WGS
AF:
AC:
1
AN:
3478
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 28, 2017 | The p.Asp964Asn variant in MYO3A has not been previously reported in individuals with hearing loss, or in large population studies. Computational prediction too ls and conservation analysis suggest that the p.Asp964Asn variant may impact the protein, though this information is not predictive enough to determine pathogen icity. In summary, the clinical significance of the p.Asp964Asn variant is uncer tain. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Uncertain
T;T
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D
MetaSVM
Uncertain
D
MutationAssessor
Benign
L;L
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
.;D
REVEL
Uncertain
Sift
Benign
.;T
Sift4G
Benign
.;T
Polyphen
P;P
Vest4
0.73
MutPred
Gain of MoRF binding (P = 0.0269);Gain of MoRF binding (P = 0.0269);
MVP
0.92
MPC
0.27
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at