rs193920949
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_014982.3(PCNX1):c.3049G>A(p.Ala1017Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,460,960 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. A1017S) has been classified as Uncertain significance.
Frequency
Consequence
NM_014982.3 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 |
---|---|---|---|---|---|---|---|
PCNX1 | NM_014982.3 | c.3049G>A | p.Ala1017Thr | missense_variant | 12/36 | ENST00000304743.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCNX1 | ENST00000304743.7 | c.3049G>A | p.Ala1017Thr | missense_variant | 12/36 | 1 | NM_014982.3 | P4 | |
PCNX1 | ENST00000439984.7 | c.2716G>A | p.Ala906Thr | missense_variant | 10/34 | 1 | A1 | ||
PCNX1 | ENST00000554691.5 | c.226G>A | p.Ala76Thr | missense_variant | 2/25 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250560Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135444
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1460960Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726764
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at