rs114092230
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015967.8(PTPN22):c.1627A>T(p.Ser543Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,632 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S543G) has been classified as Likely benign.
Frequency
Consequence
NM_015967.8 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPN22 | NM_015967.8 | c.1627A>T | p.Ser543Cys | missense_variant | Exon 13 of 21 | NP_057051.4 | ||
PTPN22 | NM_001308297.2 | c.1555A>T | p.Ser519Cys | missense_variant | Exon 12 of 20 | NP_001295226.2 | ||
PTPN22 | NM_001193431.3 | c.1627A>T | p.Ser543Cys | missense_variant | Exon 13 of 21 | NP_001180360.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPN22 | ENST00000359785.10 | c.1627A>T | p.Ser543Cys | missense_variant | Exon 13 of 21 | 1 | ENSP00000352833.5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251394Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135870
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461632Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727138
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at