10-69802473-CTGGGGAGT-C
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_001368882.1(COL13A1):c.55_62delGAGTTGGG(p.Glu19ArgfsTer97) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_001368882.1 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL13A1 | NM_001368882.1 | c.55_62delGAGTTGGG | p.Glu19ArgfsTer97 | frameshift_variant | Exon 1 of 41 | ENST00000645393.2 | NP_001355811.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL13A1 | ENST00000645393.2 | c.55_62delGAGTTGGG | p.Glu19ArgfsTer97 | frameshift_variant | Exon 1 of 41 | NM_001368882.1 | ENSP00000496051.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Pathogenic:1
This sequence change creates a premature translational stop signal (p.Glu19Argfs*97) in the COL13A1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COL13A1 are known to be pathogenic (PMID: 26626625). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with COL13A1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1444676). For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at