rs142890313
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PP2PP3BP6
The NM_080680.3(COL11A2):c.4040C>T(p.Pro1347Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000298 in 1,612,610 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P1347Q) has been classified as Likely benign.
Frequency
Consequence
NM_080680.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL11A2 | NM_080680.3 | c.4040C>T | p.Pro1347Leu | missense_variant | 56/66 | ENST00000341947.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL11A2 | ENST00000341947.7 | c.4040C>T | p.Pro1347Leu | missense_variant | 56/66 | 5 | NM_080680.3 | P4 | |
COL11A2 | ENST00000374708.8 | c.3782C>T | p.Pro1261Leu | missense_variant | 54/64 | 5 | A1 | ||
COL11A2 | ENST00000683572.1 | n.7C>T | non_coding_transcript_exon_variant | 1/9 | |||||
COL11A2 | ENST00000477772.1 | n.273-1692C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000827 AC: 20AN: 241766Hom.: 0 AF XY: 0.0000529 AC XY: 7AN XY: 132250
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1460504Hom.: 0 Cov.: 40 AF XY: 0.0000234 AC XY: 17AN XY: 726552
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74314
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Occurs in the triple helical domain at the Y position in the canonical Gly-X-Y repeat; although this variant may have an effect on normal protein folding and function, missense substitution at the Y position is not a common mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge - |
Connective tissue disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Human Genetics, Inc, Center for Human Genetics, Inc | Nov 01, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at