1-113814951-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015967.8(PTPN22):c.2378C>T(p.Ser793Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000311 in 1,606,806 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015967.8 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 |
---|---|---|---|---|---|---|---|---|
PTPN22 | NM_015967.8 | c.2378C>T | p.Ser793Leu | missense_variant | Exon 21 of 21 | NP_057051.4 | ||
PTPN22 | NM_001308297.2 | c.2306C>T | p.Ser769Leu | missense_variant | Exon 20 of 20 | NP_001295226.2 | ||
PTPN22 | NM_001193431.3 | c.2294C>T | p.Ser765Leu | missense_variant | Exon 21 of 21 | NP_001180360.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPN22 | ENST00000359785.10 | c.2378C>T | p.Ser793Leu | missense_variant | Exon 21 of 21 | 1 | ENSP00000352833.5 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152006Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000407 AC: 1AN: 245640Hom.: 0 AF XY: 0.00000754 AC XY: 1AN XY: 132616
GnomAD4 exome AF: 0.00000275 AC: 4AN: 1454800Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 723548
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152006Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2378C>T (p.S793L) alteration is located in exon 21 (coding exon 21) of the PTPN22 gene. This alteration results from a C to T substitution at nucleotide position 2378, causing the serine (S) at amino acid position 793 to be replaced by a leucine (L). 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