3-142887764-A-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_013363.4(PCOLCE2):c.97T>A(p.Cys33Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000348 in 1,435,512 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 Uncertain significance (★).
Frequency
Consequence
NM_013363.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCOLCE2 | NM_013363.4 | c.97T>A | p.Cys33Ser | missense_variant | 2/9 | ENST00000295992.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCOLCE2 | ENST00000295992.8 | c.97T>A | p.Cys33Ser | missense_variant | 2/9 | 1 | NM_013363.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250424Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135588
GnomAD4 exome AF: 0.00000348 AC: 5AN: 1435512Hom.: 0 Cov.: 25 AF XY: 0.00000279 AC XY: 2AN XY: 716046
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 28, 2023 | The c.97T>A (p.C33S) alteration is located in exon 2 (coding exon 2) of the PCOLCE2 gene. This alteration results from a T to A substitution at nucleotide position 97, causing the cysteine (C) at amino acid position 33 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at