rs1311636142
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4BP6
The NM_005592.4(MUSK):c.481C>T(p.Leu161Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,554,896 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
MUSK
NM_005592.4 missense
NM_005592.4 missense
Scores
1
10
8
Clinical Significance
Conservation
PhyloP100: 1.64
Genes affected
MUSK (HGNC:7525): (muscle associated receptor tyrosine kinase) This gene encodes a muscle-specific tyrosine kinase receptor. The encoded protein may play a role in clustering of the acetylcholine receptor in the postsynaptic neuromuscular junction. Mutations in this gene have been associated with congenital myasthenic syndrome. Alternatively spliced transcript variants have been described.[provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.30504328).
BP6
Variant 9-110695525-C-T is Benign according to our data. Variant chr9-110695525-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 476146.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=2, Likely_benign=1}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MUSK | NM_005592.4 | c.481C>T | p.Leu161Phe | missense_variant | 4/15 | ENST00000374448.9 | NP_005583.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MUSK | ENST00000374448.9 | c.481C>T | p.Leu161Phe | missense_variant | 4/15 | 5 | NM_005592.4 | ENSP00000363571 | P4 | |
MUSK | ENST00000416899.7 | c.481C>T | p.Leu161Phe | missense_variant | 4/14 | 5 | ENSP00000393608 | A1 | ||
MUSK | ENST00000189978.10 | c.481C>T | p.Leu161Phe | missense_variant | 4/14 | 5 | ENSP00000189978 | |||
MUSK | ENST00000374439.1 | c.175C>T | p.Leu59Phe | missense_variant | 2/4 | 5 | ENSP00000363562 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152148Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000925 AC: 16AN: 172992Hom.: 0 AF XY: 0.000120 AC XY: 11AN XY: 91424
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GnomAD4 exome AF: 0.0000178 AC: 25AN: 1402748Hom.: 0 Cov.: 29 AF XY: 0.0000202 AC XY: 14AN XY: 693010
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74314
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:2Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Fetal akinesia deformation sequence 1;C4225368:Congenital myasthenic syndrome 9 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 07, 2022 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jun 04, 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
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M;.;M;.;.
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;.;.
REVEL
Uncertain
Sift
Uncertain
D;D;D;.;.
Sift4G
Benign
T;T;T;T;D
Polyphen
D;.;.;.;.
Vest4
MutPred
Loss of ubiquitination at K156 (P = 0.1372);Loss of ubiquitination at K156 (P = 0.1372);Loss of ubiquitination at K156 (P = 0.1372);Loss of ubiquitination at K156 (P = 0.1372);.;
MVP
MPC
ClinPred
T
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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