10-20001841-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032812.9(PLXDC2):c.179C>T(p.Ala60Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,613,908 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032812.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLXDC2 | NM_032812.9 | c.179C>T | p.Ala60Val | missense_variant | 2/14 | ENST00000377252.5 | NP_116201.7 | |
PLXDC2 | NM_001282736.2 | c.179C>T | p.Ala60Val | missense_variant | 2/13 | NP_001269665.1 | ||
PLXDC2 | XM_011519750.3 | c.179C>T | p.Ala60Val | missense_variant | 2/14 | XP_011518052.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLXDC2 | ENST00000377252.5 | c.179C>T | p.Ala60Val | missense_variant | 2/14 | 1 | NM_032812.9 | ENSP00000366460.3 | ||
PLXDC2 | ENST00000377242.7 | c.179C>T | p.Ala60Val | missense_variant | 2/13 | 1 | ENSP00000366450.3 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 251040Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135668
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461790Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727194
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2022 | The c.179C>T (p.A60V) alteration is located in exon 2 (coding exon 2) of the PLXDC2 gene. This alteration results from a C to T substitution at nucleotide position 179, causing the alanine (A) at amino acid position 60 to be replaced by a valine (V). 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