rs387906339
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PVS1_ModeratePP5
The NM_005807.6(PRG4):c.4190_4191delinsAG(p.Ser1397Ter) variant causes a stop gained change. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 33)
Consequence
PRG4
NM_005807.6 stop_gained
NM_005807.6 stop_gained
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.69
Genes affected
PRG4 (HGNC:9364): (proteoglycan 4) The protein encoded by this gene is a large proteoglycan that is synthesized by chondrocytes located at the surface of articular cartilage and by some synovial lining cells. This protein contains both chondroitin sulfate and keratan sulfate glycosaminoglycans. It functions as a boundary lubricant at the cartilage surface and contributes to the elastic absorption and energy dissipation of synovial fluid. Mutations in this gene result in camptodactyly-arthropathy-coxa vara-pericarditis syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
TPR (HGNC:12017): (translocated promoter region, nuclear basket protein) This gene encodes a large coiled-coil protein that forms intranuclear filaments attached to the inner surface of nuclear pore complexes (NPCs). The protein directly interacts with several components of the NPC. It is required for the nuclear export of mRNAs and some proteins. Oncogenic fusions of the 5' end of this gene with several different kinase genes occur in some neoplasias. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.00593 CDS is truncated, and there are 1 pathogenic variants in the truncated region.
PP5
?
Variant 1-186313753-CC-AG is Pathogenic according to our data. Variant chr1-186313753-CC-AG is described in ClinVar as [Pathogenic]. Clinvar id is 5655.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRG4 | NM_005807.6 | c.4190_4191delinsAG | p.Ser1397Ter | stop_gained | 13/13 | ENST00000445192.7 | |
TPR | NM_003292.3 | c.*217_*218delinsCT | 3_prime_UTR_variant | 51/51 | ENST00000367478.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRG4 | ENST00000445192.7 | c.4190_4191delinsAG | p.Ser1397Ter | stop_gained | 13/13 | 5 | NM_005807.6 | P2 | |
TPR | ENST00000367478.9 | c.*217_*218delinsCT | 3_prime_UTR_variant | 51/51 | 1 | NM_003292.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Camptodactyly-arthropathy-coxa vara-pericarditis syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 1999 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at