11-47980977-CGCTGCTGCT-CGCTGCTGCTGCTGCTGCT
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_002843.4(PTPRJ):c.77_85dupTGCTGCTGC(p.Leu26_Leu28dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000134 in 1,191,832 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000068 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
PTPRJ
NM_002843.4 disruptive_inframe_insertion
NM_002843.4 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.197
Publications
1 publications found
Genes affected
PTPRJ (HGNC:9673): (protein tyrosine phosphatase receptor type J) The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes, including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP possesses an extracellular region containing five fibronectin type III repeats, a single transmembrane region, and a single intracytoplasmic catalytic domain, and thus represents a receptor-type PTP. This protein is present in all hematopoietic lineages, and was shown to negatively regulate T cell receptor signaling possibly through interfering with the phosphorylation of Phospholipase C Gamma 1 and Linker for Activation of T Cells. This protein can also dephosphorylate the PDGF beta receptor, and may be involved in UV-induced signal transduction. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
PTPRJ Gene-Disease associations (from GenCC):
- 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
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PTPRJ | NM_002843.4 | c.77_85dupTGCTGCTGC | p.Leu26_Leu28dup | disruptive_inframe_insertion | Exon 1 of 25 | ENST00000418331.7 | NP_002834.3 | |
| PTPRJ | NM_001098503.2 | c.77_85dupTGCTGCTGC | p.Leu26_Leu28dup | disruptive_inframe_insertion | Exon 1 of 9 | NP_001091973.1 | ||
| PTPRJ | XM_047427374.1 | c.419_427dupTGCTGCTGC | p.Leu140_Leu142dup | disruptive_inframe_insertion | Exon 1 of 17 | XP_047283330.1 | ||
| PTPRJ | XM_017018085.2 | c.48+371_48+379dupTGCTGCTGC | intron_variant | Intron 1 of 24 | XP_016873574.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.00000681 AC: 1AN: 146754Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
146754
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000144 AC: 15AN: 1045078Hom.: 0 Cov.: 31 AF XY: 0.0000203 AC XY: 10AN XY: 492898 show subpopulations
GnomAD4 exome
AF:
AC:
15
AN:
1045078
Hom.:
Cov.:
31
AF XY:
AC XY:
10
AN XY:
492898
show subpopulations
African (AFR)
AF:
AC:
1
AN:
21680
American (AMR)
AF:
AC:
0
AN:
7142
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
12892
East Asian (EAS)
AF:
AC:
0
AN:
24360
South Asian (SAS)
AF:
AC:
1
AN:
19136
European-Finnish (FIN)
AF:
AC:
0
AN:
18714
Middle Eastern (MID)
AF:
AC:
0
AN:
2730
European-Non Finnish (NFE)
AF:
AC:
13
AN:
897270
Other (OTH)
AF:
AC:
0
AN:
41154
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.492
Heterozygous variant carriers
0
2
3
5
6
8
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000681 AC: 1AN: 146754Hom.: 0 Cov.: 32 AF XY: 0.0000140 AC XY: 1AN XY: 71394 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
146754
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
71394
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
40398
American (AMR)
AF:
AC:
0
AN:
14886
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3390
East Asian (EAS)
AF:
AC:
0
AN:
4744
South Asian (SAS)
AF:
AC:
0
AN:
4540
European-Finnish (FIN)
AF:
AC:
0
AN:
9284
Middle Eastern (MID)
AF:
AC:
0
AN:
298
European-Non Finnish (NFE)
AF:
AC:
0
AN:
66346
Other (OTH)
AF:
AC:
0
AN:
2006
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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