3-33114093-CGGGGGGCCGCGGCGCT-C
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_006371.5(CRTAP):c.18_33del(p.Gly7Ter) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000839 in 1,310,866 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. R6R) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 0.0000084 ( 0 hom. )
Consequence
CRTAP
NM_006371.5 frameshift
NM_006371.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.06
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 Pathogenic. Variant got 12 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 37 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 3-33114093-CGGGGGGCCGCGGCGCT-C is Pathogenic according to our data. Variant chr3-33114093-CGGGGGGCCGCGGCGCT-C is described in ClinVar as [Pathogenic]. Clinvar id is 1070167.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRTAP | NM_006371.5 | c.18_33del | p.Gly7Ter | frameshift_variant | 1/7 | ENST00000320954.11 | |
CRTAP | NM_001393363.1 | c.18_33del | p.Gly7Ter | frameshift_variant | 1/6 | ||
CRTAP | NM_001393364.1 | c.18_33del | p.Gly7Ter | frameshift_variant | 1/6 | ||
CRTAP | NM_001393365.1 | c.18_33del | p.Gly7Ter | frameshift_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRTAP | ENST00000320954.11 | c.18_33del | p.Gly7Ter | frameshift_variant | 1/7 | 1 | NM_006371.5 | P1 | |
CRTAP | ENST00000449224.1 | c.18_33del | p.Gly7Ter | frameshift_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 34
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GnomAD3 exomes AF: 0.000109 AC: 8AN: 73368Hom.: 0 AF XY: 0.0000233 AC XY: 1AN XY: 42892
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GnomAD4 exome AF: 0.00000839 AC: 11AN: 1310866Hom.: 0 AF XY: 0.00000464 AC XY: 3AN XY: 647122
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Osteogenesis imperfecta type 7 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Aug 29, 2023 | For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1070167). This variant has not been reported in the literature in individuals affected with CRTAP-related conditions. This variant is present in population databases (rs752412772, gnomAD 0.07%). This sequence change creates a premature translational stop signal (p.Gly7*) in the CRTAP gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CRTAP are known to be pathogenic (PMID: 17055431, 19862557, 24715559). - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at