10-20177014-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_032812.9(PLXDC2):c.899C>A(p.Thr300Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000312 in 1,602,284 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032812.9 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLXDC2 | NM_032812.9 | c.899C>A | p.Thr300Lys | missense_variant | Exon 8 of 14 | ENST00000377252.5 | NP_116201.7 | |
PLXDC2 | NM_001282736.2 | c.752C>A | p.Thr251Lys | missense_variant | Exon 7 of 13 | NP_001269665.1 | ||
PLXDC2 | XM_011519750.3 | c.899C>A | p.Thr300Lys | missense_variant | Exon 8 of 14 | XP_011518052.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLXDC2 | ENST00000377252.5 | c.899C>A | p.Thr300Lys | missense_variant | Exon 8 of 14 | 1 | NM_032812.9 | ENSP00000366460.3 | ||
PLXDC2 | ENST00000377242.7 | c.752C>A | p.Thr251Lys | missense_variant | Exon 7 of 13 | 1 | ENSP00000366450.3 | |||
PLXDC2 | ENST00000377238.2 | n.674C>A | non_coding_transcript_exon_variant | Exon 7 of 13 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151332Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000826 AC: 2AN: 242154Hom.: 0 AF XY: 0.00000765 AC XY: 1AN XY: 130780
GnomAD4 exome AF: 0.00000207 AC: 3AN: 1450952Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1AN XY: 721648
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151332Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73792
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.899C>A (p.T300K) alteration is located in exon 8 (coding exon 8) of the PLXDC2 gene. This alteration results from a C to A substitution at nucleotide position 899, causing the threonine (T) at amino acid position 300 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at