chr10-72007522-C-T
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PP3_StrongPP5_Moderate
The NM_004273.5(CHST3):c.491C>T(p.Pro164Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000276 in 1,451,634 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. P164P) has been classified as Likely benign.
Frequency
Consequence
NM_004273.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHST3 | NM_004273.5 | c.491C>T | p.Pro164Leu | missense_variant | 3/3 | ENST00000373115.5 | |
CHST3 | XM_006718075.5 | c.491C>T | p.Pro164Leu | missense_variant | 3/3 | ||
CHST3 | XM_011540369.3 | c.491C>T | p.Pro164Leu | missense_variant | 3/3 | ||
CHST3 | XM_047426022.1 | c.491C>T | p.Pro164Leu | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHST3 | ENST00000373115.5 | c.491C>T | p.Pro164Leu | missense_variant | 3/3 | 1 | NM_004273.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000423 AC: 1AN: 236198Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 129766
GnomAD4 exome AF: 0.00000276 AC: 4AN: 1451634Hom.: 0 Cov.: 31 AF XY: 0.00000277 AC XY: 2AN XY: 722542
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Spondyloepiphyseal dysplasia with congenital joint dislocations Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences | - | This missense variant was found to be pathogenic by various in silico tools, including MutationTaster, SIFT, and PolyPhen. Parents were found to be carriers. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at