rs369268728
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4BS1_Supporting
The ENST00000442510.8(PTPRC):āc.3404A>Cā(p.Lys1135Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000843 in 1,612,896 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 (ā ā ). Synonymous variant affecting the same amino acid position (i.e. K1135K) has been classified as Likely benign.
Frequency
Consequence
ENST00000442510.8 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPRC | NM_002838.5 | c.3404A>C | p.Lys1135Thr | missense_variant | 31/33 | ENST00000442510.8 | NP_002829.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTPRC | ENST00000442510.8 | c.3404A>C | p.Lys1135Thr | missense_variant | 31/33 | 1 | NM_002838.5 | ENSP00000411355 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152064Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000719 AC: 18AN: 250342Hom.: 0 AF XY: 0.0000665 AC XY: 9AN XY: 135306
GnomAD4 exome AF: 0.0000842 AC: 123AN: 1460714Hom.: 0 Cov.: 31 AF XY: 0.0000839 AC XY: 61AN XY: 726666
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74384
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2022 | The c.3398A>C (p.K1133T) alteration is located in exon 31 (coding exon 30) of the PTPRC gene. This alteration results from a A to C substitution at nucleotide position 3398, causing the lysine (K) at amino acid position 1133 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Immunodeficiency 104 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 31, 2022 | This sequence change replaces lysine, which is basic and polar, with threonine, which is neutral and polar, at codon 1135 of the PTPRC protein (p.Lys1135Thr). This variant is present in population databases (rs369268728, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with PTPRC-related conditions. ClinVar contains an entry for this variant (Variation ID: 568894). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at