chr10-27399240-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001034842.5(PTCHD3):c.1358G>A(p.Gly453Asp) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000000808 in 1,237,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001034842.5 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
PTCHD3 | NM_001034842.5 | c.1358G>A | p.Gly453Asp | missense_variant, splice_region_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCHD3 | ENST00000642324.1 | c.1358G>A | p.Gly453Asp | missense_variant, splice_region_variant | 4/4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 27
GnomAD4 exome AF: 8.08e-7 AC: 1AN: 1237216Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 611194
GnomAD4 genome ? Cov.: 27
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.1358G>A (p.G453D) alteration is located in exon 4 (coding exon 4) of the PTCHD3 gene. This alteration results from a G to A substitution at nucleotide position 1358, causing the glycine (G) at amino acid position 453 to be replaced by an aspartic acid (D). 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