rs113994158
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001039958.2(MESP2):c.500_503dup(p.Gly169ProfsTer199) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000764 in 1,308,722 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. P166P) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001039958.2 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MESP2 | NM_001039958.2 | c.500_503dup | p.Gly169ProfsTer199 | frameshift_variant | 1/2 | ENST00000341735.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MESP2 | ENST00000341735.5 | c.500_503dup | p.Gly169ProfsTer199 | frameshift_variant | 1/2 | 1 | NM_001039958.2 | P1 | |
MESP2 | ENST00000560219.2 | c.31-1208_31-1205dup | intron_variant | 1 | |||||
MESP2 | ENST00000558723.1 | n.39-1208_39-1205dup | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 7.64e-7 AC: 1AN: 1308722Hom.: 0 Cov.: 30 AF XY: 0.00000156 AC XY: 1AN XY: 638988
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Spondylocostal dysostosis 2, autosomal recessive Pathogenic:1Other:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2008 | - - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at