16-67390484-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015964.4(TPPP3):c.337G>A(p.Val113Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000465 in 1,613,592 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 (★).
Frequency
Consequence
NM_015964.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TPPP3 | NM_015964.4 | c.337G>A | p.Val113Ile | missense_variant | Exon 3 of 4 | ENST00000393957.7 | NP_057048.2 | |
TPPP3 | NM_016140.4 | c.337G>A | p.Val113Ile | missense_variant | Exon 4 of 5 | NP_057224.2 | ||
TPPP3 | XM_024450294.2 | c.337G>A | p.Val113Ile | missense_variant | Exon 3 of 4 | XP_024306062.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 250820Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135550
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461486Hom.: 0 Cov.: 32 AF XY: 0.0000358 AC XY: 26AN XY: 727056
GnomAD4 genome AF: 0.000158 AC: 24AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74278
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.337G>A (p.V113I) alteration is located in exon 4 (coding exon 2) of the TPPP3 gene. This alteration results from a G to A substitution at nucleotide position 337, causing the valine (V) at amino acid position 113 to be replaced by an isoleucine (I). 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