chr2-1644706-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_012293.3(PXDN):c.3655G>A(p.Val1219Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,447,450 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. V1219L) 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 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PXDN | NM_012293.3 | c.3655G>A | p.Val1219Met | missense_variant | 18/23 | ENST00000252804.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PXDN | ENST00000252804.9 | c.3655G>A | p.Val1219Met | missense_variant | 18/23 | 1 | NM_012293.3 | P1 | |
PXDN | ENST00000477093.1 | n.297G>A | non_coding_transcript_exon_variant | 2/3 | 4 | ||||
PXDN | ENST00000478155.5 | n.2743G>A | non_coding_transcript_exon_variant | 10/15 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000823 AC: 2AN: 243132Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132222
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1447450Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 719432
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at