rs387907333
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PVS1PP5
The NM_006371.5(CRTAP):c.118_133delinsTACCC(p.Glu40TyrfsTer117) variant causes a frameshift change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 34)
Consequence
CRTAP
NM_006371.5 frameshift
NM_006371.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.38
Genes affected
CRTAP (HGNC:2379): (cartilage associated protein) The protein encoded by this gene is similar to the chicken and mouse CRTAP genes. The encoded protein is a scaffolding protein that may influence the activity of at least one member of the cytohesin/ARNO family in response to specific cellular stimuli. Defects in this gene are associated with osteogenesis imperfecta, a connective tissue disorder characterized by bone fragility and low bone mass. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PP5
?
Variant 3-33114195-GAGCTGATGCCGCTCG-TACCC is Pathogenic according to our data. Variant chr3-33114195-GAGCTGATGCCGCTCG-TACCC is described in ClinVar as [Pathogenic]. Clinvar id is 41922.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRTAP | NM_006371.5 | c.118_133delinsTACCC | p.Glu40TyrfsTer117 | frameshift_variant | 1/7 | ENST00000320954.11 | |
CRTAP | NM_001393363.1 | c.118_133delinsTACCC | p.Glu40TyrfsTer117 | frameshift_variant | 1/6 | ||
CRTAP | NM_001393364.1 | c.118_133delinsTACCC | p.Glu40TyrfsTer117 | frameshift_variant | 1/6 | ||
CRTAP | NM_001393365.1 | c.118_133delinsTACCC | p.Glu40TyrfsTer127 | frameshift_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRTAP | ENST00000320954.11 | c.118_133delinsTACCC | p.Glu40TyrfsTer117 | frameshift_variant | 1/7 | 1 | NM_006371.5 | P1 | |
CRTAP | ENST00000449224.1 | c.118_133delinsTACCC | p.Glu40TyrfsTer117 | frameshift_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD3 genomes
?
Cov.:
34
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 34
GnomAD4 genome
?
Cov.:
34
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Osteogenesis imperfecta type 7 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2012 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at