chr11-47449174-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 10P and 1B. PM2PP5_Very_StrongBP4
The NM_005055.5(RAPSN):c.-210A>G variant causes a upstream gene change. The variant allele was found at a frequency of 0.0000183 in 656,818 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 Likely pathogenic (★★).
Frequency
Consequence
NM_005055.5 upstream_gene
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAPSN | NM_005055.5 | c.-210A>G | upstream_gene_variant | ENST00000298854.7 | NP_005046.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAPSN | ENST00000298854.7 | c.-210A>G | upstream_gene_variant | 1 | NM_005055.5 | ENSP00000298854.2 | ||||
RAPSN | ENST00000352508.7 | c.-210A>G | upstream_gene_variant | 1 | ENSP00000298853.3 | |||||
RAPSN | ENST00000529341.1 | c.-210A>G | upstream_gene_variant | 1 | ENSP00000431732.1 | |||||
RAPSN | ENST00000524487.5 | c.-210A>G | upstream_gene_variant | 5 | ENSP00000435551.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152244Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000178 AC: 9AN: 504574Hom.: 0 Cov.: 5 AF XY: 0.0000149 AC XY: 4AN XY: 267610
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74384
ClinVar
Submissions by phenotype
Fetal akinesia deformation sequence 1;C4225367:Congenital myasthenic syndrome 11 Pathogenic:2
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This variant occurs in a non-coding region of the RAPSN gene. It does not change the encoded amino acid sequence of the RAPSN protein. This variant is present in population databases (rs786200905, gnomAD 0.06%). This variant has been observed in individual(s) with congenital myasthenic syndrome (PMID: 12651869, 15145336, 19620612, 22326364). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 8051). Studies have shown that this variant alters RAPSN gene expression (PMID: 12651869, 15282317). For these reasons, this variant has been classified as Pathogenic. -
Congenital myasthenic syndrome 11 Pathogenic:2
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Onset at age 6 years with poor feeding, weak cry, ptosis, facial weakness and long face, high arched palate. Slow RNS was in favor of a neuromuscular junction disorder. -
Congenital myasthenic syndrome 11;C4760576:Fetal akinesia deformation sequence 2 Pathogenic:1Other:1
Variant interpreted as Pathogenic and reported on 04-18-2019 by Lab or GTR ID 507240. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
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Congenital myasthenic syndrome Pathogenic:1Other:1
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Fetal akinesia deformation sequence 2 Pathogenic:1
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Abnormality of the musculature Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at