16-1486108-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001328608.2(PTX4):c.1268G>A(p.Ser423Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,614,104 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_001328608.2 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 |
---|---|---|---|---|---|---|---|
PTX4 | NM_001328608.2 | c.1268G>A | p.Ser423Asn | missense_variant | 3/3 | ENST00000447419.7 | |
PTX4 | NM_001013658.1 | c.1253G>A | p.Ser418Asn | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTX4 | ENST00000447419.7 | c.1268G>A | p.Ser423Asn | missense_variant | 3/3 | 5 | NM_001328608.2 | A2 | |
PTX4 | ENST00000293922.1 | c.1253G>A | p.Ser418Asn | missense_variant | 3/3 | 1 | P2 | ||
PTX4 | ENST00000440447.2 | c.*244G>A | 3_prime_UTR_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152266Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251332Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135872
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461838Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727220
GnomAD4 genome AF: 0.000131 AC: 20AN: 152266Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74400
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.1253G>A (p.S418N) alteration is located in exon 3 (coding exon 3) of the PTX4 gene. This alteration results from a G to A substitution at nucleotide position 1253, causing the serine (S) at amino acid position 418 to be replaced by an asparagine (N). 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