rs730882229
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_015466.4(PTPN23):c.3995G>A(p.Arg1332His) variant causes a missense change. The variant allele was found at a frequency of 0.0000143 in 1,613,156 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R1332L) has been classified as Likely pathogenic.
Frequency
Consequence
NM_015466.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPN23 | NM_015466.4 | c.3995G>A | p.Arg1332His | missense_variant | 21/25 | ENST00000265562.5 | |
PTPN23 | NM_001304482.2 | c.3617G>A | p.Arg1206His | missense_variant | 20/24 | ||
PTPN23 | XM_005265031.3 | c.3965G>A | p.Arg1322His | missense_variant | 21/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPN23 | ENST00000265562.5 | c.3995G>A | p.Arg1332His | missense_variant | 21/25 | 1 | NM_015466.4 | P1 | |
PTPN23 | ENST00000683708.1 | n.755G>A | non_coding_transcript_exon_variant | 2/5 | |||||
PTPN23 | ENST00000602307.5 | c.*3672G>A | 3_prime_UTR_variant, NMD_transcript_variant | 20/24 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151994Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250798Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135668
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461162Hom.: 0 Cov.: 39 AF XY: 0.0000124 AC XY: 9AN XY: 726884
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151994Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74232
ClinVar
Submissions by phenotype
Neurodevelopmental disorder and structural brain anomalies with or without seizures and spasticity Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Nov 08, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at