GeneBe

rs747484779

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_002843.4(PTPRJ):​c.77_85delTGCTGCTGC​(p.Leu26_Leu28del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000957 in 1,045,078 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: not found (cov: 32)
Exomes 𝑓: 9.6e-7 ( 0 hom. )

Consequence

PTPRJ
NM_002843.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.689
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PTPRJNM_002843.4 linkc.77_85delTGCTGCTGC p.Leu26_Leu28del disruptive_inframe_deletion Exon 1 of 25 ENST00000418331.7 NP_002834.3 Q12913-1Q9NPR5
PTPRJNM_001098503.2 linkc.77_85delTGCTGCTGC p.Leu26_Leu28del disruptive_inframe_deletion Exon 1 of 9 NP_001091973.1 Q12913-2
PTPRJXM_047427374.1 linkc.419_427delTGCTGCTGC p.Leu140_Leu142del disruptive_inframe_deletion Exon 1 of 17 XP_047283330.1
PTPRJXM_017018085.2 linkc.48+371_48+379delTGCTGCTGC intron_variant Intron 1 of 24 XP_016873574.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PTPRJENST00000418331.7 linkc.77_85delTGCTGCTGC p.Leu26_Leu28del disruptive_inframe_deletion Exon 1 of 25 1 NM_002843.4 ENSP00000400010.2 Q12913-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
9.57e-7
AC:
1
AN:
1045078
Hom.:
0
AF XY:
0.00000203
AC XY:
1
AN XY:
492898
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000111
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs747484779; hg19: chr11-48002529; API