1-25800232-T-TGGGCC
Variant summary
Our verdict is Pathogenic. Variant got 20 ACMG points: 20P and 0B. PVS1PS1_ModeratePM2PP5_Very_Strong
The NM_020451.3(SELENON):c.8_12dup(p.Arg5_?4) variant causes a frameshift, start lost change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Genomes: not found (cov: 30)
Consequence
SELENON
NM_020451.3 frameshift, start_lost
NM_020451.3 frameshift, start_lost
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.342
Genes affected
SELENON (HGNC:15999): (selenoprotein N) This gene encodes a glycoprotein that is localized in the endoplasmic reticulum. It plays an important role in cell protection against oxidative stress, and in the regulation of redox-related calcium homeostasis. Mutations in this gene are associated with early onset muscle disorders, referred to as SEPN1-related myopathy. SEPN1-related myopathy consists of 4 autosomal recessive disorders, originally thought to be separate entities: rigid spine muscular dystrophy (RSMD1), the classical form of multiminicore disease, desmin related myopathy with Mallory-body like inclusions, and congenital fiber-type disproportion (CFTD). This protein is a selenoprotein, containing the rare amino acid selenocysteine (Sec). Sec is encoded by the UGA codon, which normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. A second stop-codon redefinition element (SRE) adjacent to the UGA codon has been identified in this gene (PMID:15791204). SRE is a phylogenetically conserved stem-loop structure that stimulates readthrough at the UGA codon, and augments the Sec insertion efficiency by SECIS. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2016]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 20 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 150 pathogenic variants in the truncated region.
PS1
?
Another start lost variant in NM_020451.3 (SELENON) was described as [Likely_pathogenic] in ClinVar as 4491
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 1-25800232-T-TGGGCC is Pathogenic according to our data. Variant chr1-25800232-T-TGGGCC is described in ClinVar as [Pathogenic]. Clinvar id is 623320.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELENON | NM_020451.3 | c.8_12dup | p.Arg5_?4 | frameshift_variant, start_lost | 1/13 | ENST00000361547.7 | |
SELENON | NM_206926.2 | c.8_12dup | p.Arg5_?4 | frameshift_variant, start_lost | 1/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELENON | ENST00000361547.7 | c.8_12dup | p.Arg5_?4 | frameshift_variant, start_lost | 1/13 | 1 | NM_020451.3 | ||
SELENON | ENST00000354177.9 | c.8_12dup | p.Arg5_?4 | frameshift_variant, start_lost | 1/12 | 5 | |||
SELENON | ENST00000374315.1 | c.8_12dup | p.Arg5_?4 | frameshift_variant, start_lost | 1/12 | 5 | P1 | ||
SELENON | ENST00000494537.2 | c.8_12dup | p.Arg5_?4 | frameshift_variant, start_lost, NMD_transcript_variant | 1/13 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 30
GnomAD3 genomes
?
Cov.:
30
GnomAD4 exome Cov.: 8
GnomAD4 exome
Cov.:
8
GnomAD4 genome ? Cov.: 30
GnomAD4 genome
?
Cov.:
30
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Eichsfeld type congenital muscular dystrophy Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Sep 07, 2022 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 623320). This premature translational stop signal has been observed in individual(s) with SELENON-related conditions (PMID: 19557870). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the gnomAD database. This sequence change creates a premature translational stop signal (p.Arg5Glyfs*63) in the SELENON gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SELENON are known to be pathogenic (PMID: 21131290, 21670436). - |
Pathogenic, criteria provided, single submitter | curation | Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University | Dec 30, 2017 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 20, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at