chr5-140795611-A-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_018905.3(PCDHA2):c.647A>T(p.Asp216Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018905.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCDHA2 | ENST00000526136.2 | c.647A>T | p.Asp216Val | missense_variant | Exon 1 of 4 | 1 | NM_018905.3 | ENSP00000431748.1 | ||
PCDHA1 | ENST00000504120.4 | c.2394+6927A>T | intron_variant | Intron 1 of 3 | 1 | NM_018900.4 | ENSP00000420840.3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 34
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.647A>T (p.D216V) alteration is located in exon 1 (coding exon 1) of the PCDHA2 gene. This alteration results from a A to T substitution at nucleotide position 647, causing the aspartic acid (D) at amino acid position 216 to be replaced by a valine (V). 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
Publications
No publications associated with this variant yet.