2-1644706-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_012293.3(PXDN):āc.3655G>Cā(p.Val1219Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000691 in 1,447,450 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 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 nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1219E) has been classified as Uncertain significance.
Frequency
Consequence
NM_012293.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PXDN | NM_012293.3 | c.3655G>C | p.Val1219Leu | missense_variant | 18/23 | ENST00000252804.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PXDN | ENST00000252804.9 | c.3655G>C | p.Val1219Leu | missense_variant | 18/23 | 1 | NM_012293.3 | P1 | |
PXDN | ENST00000477093.1 | n.297G>C | non_coding_transcript_exon_variant | 2/3 | 4 | ||||
PXDN | ENST00000478155.5 | n.2743G>C | non_coding_transcript_exon_variant | 10/15 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243132Hom.: 0 AF XY: 0.00000756 AC XY: 1AN XY: 132222
GnomAD4 exome AF: 6.91e-7 AC: 1AN: 1447450Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1AN XY: 719432
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at