2-1638928-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012293.3(PXDN):āc.4124C>Gā(p.Thr1375Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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. T1375I) has been classified as Likely benign.
Frequency
Consequence
NM_012293.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PXDN | NM_012293.3 | c.4124C>G | p.Thr1375Arg | missense_variant | 21/23 | ENST00000252804.9 | NP_036425.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PXDN | ENST00000252804.9 | c.4124C>G | p.Thr1375Arg | missense_variant | 21/23 | 1 | NM_012293.3 | ENSP00000252804.4 | ||
PXDN | ENST00000478155.5 | n.3212C>G | non_coding_transcript_exon_variant | 13/15 | 2 | |||||
PXDN | ENST00000453308.1 | n.224+374C>G | intron_variant | 3 | ENSP00000414098.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 249300Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135252
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461662Hom.: 0 Cov.: 35 AF XY: 0.0000193 AC XY: 14AN XY: 727118
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at