rs3215098
Positions:
- chr9-8331574-A-AAACTTACCATTCATGAACTGT
- chr9-8331574-A-AAACTTACCATTCCTGAACTGTAACT
- chr9-8331574-A-AAACTTACCATTCCTGAACTGTAACTT
- chr9-8331574-A-AAACTTACCATTCCTGAACTGT
- chr9-8331574-A-AAACTTACCATTCCTGAACTGTAACTTACCTGCAAGT
- chr9-8331574-A-AAACTTACCATTCTCGAACTGT
- chr9-8331574-A-AAACTTACCATTCTTGAACTAT
- chr9-8331574-A-AAACTTACCATTCTTGAACTGAAACTTACCATTCTTGAACTGT
- chr9-8331574-A-AAACTTACCATTCTTGAACTGTAACTAACT
- chr9-8331574-A-AAACTTACCATTCTTGAACTGTAACT
- chr9-8331574-A-AAACTTACCATTCTTGAACTGT
- chr9-8331574-A-AAACTTACCATTGTTGAACTGT
- chr9-8331574-A-AAACTTACCCTTCTTGAACTGTAACT
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002839.4(PTPRD):c.5534+7_5534+8insACAGTTCATGAATGGTAAGTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 0)
Consequence
PTPRD
NM_002839.4 splice_region, intron
NM_002839.4 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.111
Genes affected
PTPRD (HGNC:9668): (protein tyrosine phosphatase receptor type D) 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 contains an extracellular region, a single transmembrane segment and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. The extracellular region of this protein is composed of three Ig-like and eight fibronectin type III-like domains. Studies of the similar genes in chicken and fly suggest the role of this PTP is in promoting neurite growth, and regulating neurons axon guidance. Multiple alternatively spliced transcript variants of this gene have been reported. A related pseudogene has been identified on chromosome 5. [provided by RefSeq, Jan 2010]
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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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTPRD | NM_002839.4 | c.5534+7_5534+8insACAGTTCATGAATGGTAAGTT | splice_region_variant, intron_variant | ENST00000381196.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTPRD | ENST00000381196.9 | c.5534+7_5534+8insACAGTTCATGAATGGTAAGTT | splice_region_variant, intron_variant | 5 | NM_002839.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 0
GnomAD3 genomes
Cov.:
0
GnomAD4 exome Cov.: 35
GnomAD4 exome
Cov.:
35
GnomAD4 genome Cov.: 0
GnomAD4 genome
Cov.:
0
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at