rs397514462
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PS1PM1PM5PP3_ModeratePP5
The NM_000451.4(SHOX):c.509C>A(p.Ala170Asp) variant causes a missense change. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A170P) has been classified as Pathogenic.
Frequency
Consequence
NM_000451.4 missense
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 |
---|---|---|---|---|---|---|---|
SHOX | NM_000451.4 | c.509C>A | p.Ala170Asp | missense_variant | 3/5 | ENST00000686671.1 | |
SHOX | NM_006883.2 | c.509C>A | p.Ala170Asp | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHOX | ENST00000686671.1 | c.509C>A | p.Ala170Asp | missense_variant | 3/5 | NM_000451.4 | P1 | ||
SHOX | ENST00000381575.6 | c.509C>A | p.Ala170Asp | missense_variant | 3/5 | 1 | |||
SHOX | ENST00000381578.6 | c.509C>A | p.Ala170Asp | missense_variant | 4/6 | 5 | P1 | ||
SHOX | ENST00000334060.8 | c.509C>A | p.Ala170Asp | missense_variant | 4/6 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1461668Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727146
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Leri-Weill dyschondrosteosis Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 01, 2011 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at