rs1131692247
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3PP5
The NM_001080483.3(MYMK):āc.553T>Cā(p.Cys185Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000889 in 1,461,742 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 (no stars).
Frequency
Genomes: not found (cov: 33)
Exomes š: 0.0000089 ( 0 hom. )
Consequence
MYMK
NM_001080483.3 missense
NM_001080483.3 missense
Scores
2
4
12
Clinical Significance
Conservation
PhyloP100: 4.58
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PM1
?
In a chain Protein myomaker (size 220) in uniprot entity MYMK_HUMAN there are 10 pathogenic changes around while only 1 benign (91%) in NM_001080483.3
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.756
PP5
?
Variant 9-133514749-A-G is Pathogenic according to our data. Variant chr9-133514749-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 430840.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr9-133514749-A-G is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYMK | NM_001080483.3 | c.553T>C | p.Cys185Arg | missense_variant | 5/5 | ENST00000339996.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYMK | ENST00000339996.4 | c.553T>C | p.Cys185Arg | missense_variant | 5/5 | 2 | NM_001080483.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251148Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135722
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GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461742Hom.: 0 Cov.: 29 AF XY: 0.00000825 AC XY: 6AN XY: 727196
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GnomAD4 genome ? Cov.: 33
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33
Bravo
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Congenital nonprogressive myopathy with Moebius and Robin sequences Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 07, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Pathogenic
D
MetaSVM
Benign
T
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
P
Vest4
MutPred
Loss of catalytic residue at C185 (P = 0.0915);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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