2-1634302-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_012293.3(PXDN):c.4342G>C(p.Val1448Leu) 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1448M) has been classified as Uncertain significance.
Frequency
Consequence
NM_012293.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PXDN | NM_012293.3 | c.4342G>C | p.Val1448Leu | missense_variant | 23/23 | ENST00000252804.9 | |
LOC124907723 | XR_007086188.1 | n.272C>G | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PXDN | ENST00000252804.9 | c.4342G>C | p.Val1448Leu | missense_variant | 23/23 | 1 | NM_012293.3 | P1 | |
PXDN | ENST00000478155.5 | n.3430G>C | non_coding_transcript_exon_variant | 15/15 | 2 | ||||
PXDN | ENST00000493654.1 | n.1679G>C | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
PXDN | ENST00000453308.1 | c.*132G>C | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at