3-111707992-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000477665.2(PLCXD2):c.230C>T(p.Ala77Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000211 in 1,614,044 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000477665.2 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 | UniProt |
---|---|---|---|---|---|---|---|
PLCXD2 | NM_001413064.1 | c.230C>T | p.Ala77Val | missense_variant | 2/4 | ENST00000636933.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCXD2 | ENST00000636933.2 | c.230C>T | p.Ala77Val | missense_variant | 2/4 | 5 | NM_001413064.1 | P1 | |
PLCXD2 | ENST00000477665.2 | c.230C>T | p.Ala77Val | missense_variant | 2/5 | 1 | |||
PLCXD2 | ENST00000393934.7 | c.230C>T | p.Ala77Val | missense_variant | 2/4 | 1 | |||
PLCXD2 | ENST00000468174.1 | n.270C>T | non_coding_transcript_exon_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251236Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135778
GnomAD4 exome AF: 0.000223 AC: 326AN: 1461860Hom.: 1 Cov.: 31 AF XY: 0.000227 AC XY: 165AN XY: 727230
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2023 | The c.230C>T (p.A77V) alteration is located in exon 2 (coding exon 2) of the PLCXD2 gene. This alteration results from a C to T substitution at nucleotide position 230, causing the alanine (A) at amino acid position 77 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