rs778921118
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM1PM2PP5BP4
The NM_000451.4(SHOX):c.528G>C(p.Glu176Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign 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 Uncertain significancein ClinVar.
Frequency
Consequence
NM_000451.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHOX | NM_000451.4 | c.528G>C | p.Glu176Asp | missense_variant | 3/5 | ENST00000686671.1 | |
SHOX | NM_006883.2 | c.528G>C | p.Glu176Asp | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHOX | ENST00000686671.1 | c.528G>C | p.Glu176Asp | missense_variant | 3/5 | NM_000451.4 | P1 | ||
SHOX | ENST00000381575.6 | c.528G>C | p.Glu176Asp | missense_variant | 3/5 | 1 | |||
SHOX | ENST00000381578.6 | c.528G>C | p.Glu176Asp | missense_variant | 4/6 | 5 | P1 | ||
SHOX | ENST00000334060.8 | c.528G>C | p.Glu176Asp | missense_variant | 4/6 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 33
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
SHOX-related short stature Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Human Genetics Disease in Children – Taif University, Taif University | Mar 03, 2016 | Clinical investigation included measurement of weight (kg), standing height (cm), arm span (cm), sitting height (cm), calculation of subischeal leg length (cm) [height-sitting height], growth hormone deficiency test, and measurement of father’s height (cm) and mother’s height (cm). There is no family history. THis mutation is in the homeodomain DNA binding site of SHOX gene in exon 4 (c. 528G>C), which plays an important role in DNA binding, protein transactivation, cell cycle and growth regulation. Clement et al. (2000) stated that the homeodomain proteins have important physiological functions in regulating embryonic development in vertebrates, suggesting that the mutations in SHOX gene especially in homeodomain region may lead to developmental abnormalities. According to the PolyPhen-2 prediction program this mutation is predicted to be probably damaging and considered to be pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at