11-48112911-G-A
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002843.4(PTPRJ):c.280G>A(p.Asp94Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,614,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. D94D) has been classified as Likely benign.
Frequency
Consequence
NM_002843.4 missense
Scores
Clinical Significance
Conservation
Publications
- hereditary nonpolyposis colon cancerInheritance: AD Classification: LIMITED Submitted by: ClinGen
- thrombocytopenia 10Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
- colorectal cancerInheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTPRJ | NM_002843.4 | c.280G>A | p.Asp94Asn | missense_variant | Exon 3 of 25 | ENST00000418331.7 | NP_002834.3 | |
PTPRJ | NM_001098503.2 | c.280G>A | p.Asp94Asn | missense_variant | Exon 3 of 9 | NP_001091973.1 | ||
PTPRJ | XM_017018085.2 | c.232G>A | p.Asp78Asn | missense_variant | Exon 3 of 25 | XP_016873574.1 | ||
PTPRJ | XM_047427374.1 | c.622G>A | p.Asp208Asn | missense_variant | Exon 3 of 17 | XP_047283330.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000199 AC: 5AN: 251336 AF XY: 0.0000221 show subpopulations
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461880Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727242 show subpopulations
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.280G>A (p.D94N) alteration is located in exon 3 (coding exon 3) of the PTPRJ gene. This alteration results from a G to A substitution at nucleotide position 280, causing the aspartic acid (D) at amino acid position 94 to be replaced by an asparagine (N). 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