chr4-101025893-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_000944.5(PPP3CA):āc.1538A>Gā(p.Asn513Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000182 in 1,591,828 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ). Synonymous variant affecting the same amino acid position (i.e. N513N) has been classified as Likely benign.
Frequency
Consequence
NM_000944.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP3CA | NM_000944.5 | c.1538A>G | p.Asn513Ser | missense_variant | 14/14 | ENST00000394854.8 | |
PPP3CA | NM_001130691.2 | c.1508A>G | p.Asn503Ser | missense_variant | 13/13 | ||
PPP3CA | NM_001130692.2 | c.1382A>G | p.Asn461Ser | missense_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP3CA | ENST00000394854.8 | c.1538A>G | p.Asn513Ser | missense_variant | 14/14 | 1 | NM_000944.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000134 AC: 2AN: 149808Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000327 AC: 8AN: 244530Hom.: 0 AF XY: 0.0000302 AC XY: 4AN XY: 132366
GnomAD4 exome AF: 0.0000187 AC: 27AN: 1442020Hom.: 0 Cov.: 35 AF XY: 0.0000223 AC XY: 16AN XY: 717126
GnomAD4 genome AF: 0.0000134 AC: 2AN: 149808Hom.: 0 Cov.: 30 AF XY: 0.0000137 AC XY: 1AN XY: 72988
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 29, 2023 | This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 513 of the PPP3CA protein (p.Asn513Ser). This variant is present in population databases (rs199874915, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with PPP3CA-related conditions. ClinVar contains an entry for this variant (Variation ID: 1474325). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Epileptic encephalopathy, infantile or early childhood, 1;C4748872:Arthrogryposis, cleft palate, craniosynostosis, and impaired intellectual development Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 14, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at