2-130356160-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014369.4(PTPN18):c.53G>A(p.Arg18Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000701 in 1,312,568 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R18L) has been classified as Uncertain significance.
Frequency
Consequence
NM_014369.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPN18 | NM_014369.4 | c.53G>A | p.Arg18Gln | missense_variant | 1/15 | ENST00000175756.10 | |
PTPN18 | NM_001142370.2 | c.53G>A | p.Arg18Gln | missense_variant | 1/11 | ||
PTPN18 | XM_006712417.2 | c.53G>A | p.Arg18Gln | missense_variant | 1/16 | ||
PTPN18 | XM_006712416.5 | c.53G>A | p.Arg18Gln | missense_variant | 1/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN18 | ENST00000175756.10 | c.53G>A | p.Arg18Gln | missense_variant | 1/15 | 1 | NM_014369.4 | P1 | |
PTPN18 | ENST00000347849.7 | c.53G>A | p.Arg18Gln | missense_variant | 1/11 | 1 | |||
PTPN18 | ENST00000489215.5 | n.106G>A | non_coding_transcript_exon_variant | 1/4 | 4 | ||||
PTPN18 | ENST00000428843.5 | c.53G>A | p.Arg18Gln | missense_variant, NMD_transcript_variant | 1/9 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000856 AC: 13AN: 151920Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000681 AC: 79AN: 1160648Hom.: 0 Cov.: 30 AF XY: 0.0000858 AC XY: 48AN XY: 559122
GnomAD4 genome AF: 0.0000856 AC: 13AN: 151920Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74208
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 20, 2023 | The c.53G>A (p.R18Q) alteration is located in exon 1 (coding exon 1) of the PTPN18 gene. This alteration results from a G to A substitution at nucleotide position 53, causing the arginine (R) at amino acid position 18 to be replaced by a glutamine (Q). 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