rs200818171
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001145809.2(MYH14):c.565C>A(p.Arg189Ser) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MYH14
NM_001145809.2 missense, splice_region
NM_001145809.2 missense, splice_region
Scores
7
11
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.82
Genes affected
MYH14 (HGNC:23212): (myosin heavy chain 14) This gene encodes a member of the myosin superfamily. The protein represents a conventional non-muscle myosin; it should not be confused with the unconventional myosin-14 (MYO14). Myosins are actin-dependent motor proteins with diverse functions including regulation of cytokinesis, cell motility, and cell polarity. Mutations in this gene result in one form of autosomal dominant hearing impairment. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.819
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYH14 | NM_001145809.2 | c.565C>A | p.Arg189Ser | missense_variant, splice_region_variant | 4/43 | ENST00000642316.2 | NP_001139281.1 | |
MYH14 | NM_001077186.2 | c.565C>A | p.Arg189Ser | missense_variant, splice_region_variant | 4/42 | NP_001070654.1 | ||
MYH14 | NM_024729.4 | c.565C>A | p.Arg189Ser | missense_variant, splice_region_variant | 4/41 | NP_079005.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYH14 | ENST00000642316.2 | c.565C>A | p.Arg189Ser | missense_variant, splice_region_variant | 4/43 | NM_001145809.2 | ENSP00000493594 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1461252Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 726946
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1461252
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
726946
Gnomad4 AFR exome
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Gnomad4 AMR exome
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Gnomad4 ASJ exome
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Gnomad4 EAS exome
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Gnomad4 SAS exome
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Gnomad4 FIN exome
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Gnomad4 OTH exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
.;.;D;.;D;.;D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;D;D;.;D;D;.
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;M;M;M;.;M;M
MutationTaster
Benign
D;D;D;D
PrimateAI
Pathogenic
T
PROVEAN
Pathogenic
.;D;D;.;.;.;.
REVEL
Pathogenic
Sift
Pathogenic
.;D;D;.;.;.;.
Sift4G
Uncertain
D;D;D;.;D;D;D
Polyphen
D;D;D;D;.;D;D
Vest4
MutPred
Gain of phosphorylation at R189 (P = 0.0637);Gain of phosphorylation at R189 (P = 0.0637);Gain of phosphorylation at R189 (P = 0.0637);Gain of phosphorylation at R189 (P = 0.0637);Gain of phosphorylation at R189 (P = 0.0637);Gain of phosphorylation at R189 (P = 0.0637);Gain of phosphorylation at R189 (P = 0.0637);
MVP
MPC
1.4
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
DS_AL_spliceai
Position offset: -2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at