rs121909254
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM5PP5_Moderate
The NM_005055.5(RAPSN):c.133G>T(p.Val45Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,576 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V45M) has been classified as Pathogenic.
Frequency
Consequence
NM_005055.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAPSN | NM_005055.5 | c.133G>T | p.Val45Leu | missense_variant | 1/8 | ENST00000298854.7 | NP_005046.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAPSN | ENST00000298854.7 | c.133G>T | p.Val45Leu | missense_variant | 1/8 | 1 | NM_005055.5 | ENSP00000298854.2 | ||
RAPSN | ENST00000352508.7 | c.133G>T | p.Val45Leu | missense_variant | 1/6 | 1 | ENSP00000298853.3 | |||
RAPSN | ENST00000529341.1 | c.133G>T | p.Val45Leu | missense_variant | 1/5 | 1 | ENSP00000431732.1 | |||
RAPSN | ENST00000524487.5 | c.133G>T | p.Val45Leu | missense_variant | 1/7 | 5 | ENSP00000435551.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461576Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727128
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Fetal akinesia deformation sequence 1;C4225367:Congenital myasthenic syndrome 11 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 13, 2023 | This sequence change replaces valine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 45 of the RAPSN protein (p.Val45Leu). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with RAPSN-related conditions. ClinVar contains an entry for this variant (Variation ID: 2175150). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt RAPSN protein function with a negative predictive value of 80%. This variant disrupts the p.Val45 amino acid residue in RAPSN. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17594401, 19620612). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at