rs863223451
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP2BP6
The NM_000093.5(COL5A1):c.3868G>A(p.Ala1290Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,550,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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. A1290G) has been classified as Likely benign.
Frequency
Consequence
NM_000093.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.3868G>A | p.Ala1290Thr | missense_variant | 49/66 | ENST00000371817.8 | |
COL5A1 | NM_001278074.1 | c.3868G>A | p.Ala1290Thr | missense_variant | 49/66 | ||
COL5A1 | XM_017014266.3 | c.3868G>A | p.Ala1290Thr | missense_variant | 49/65 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.3868G>A | p.Ala1290Thr | missense_variant | 49/66 | 1 | NM_000093.5 | P4 | |
COL5A1 | ENST00000371820.4 | c.3868G>A | p.Ala1290Thr | missense_variant | 49/66 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000193 AC: 3AN: 155416Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 82232
GnomAD4 exome AF: 0.0000150 AC: 21AN: 1398744Hom.: 0 Cov.: 32 AF XY: 0.0000101 AC XY: 7AN XY: 689956
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74368
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2015 | The p.A1290T variant (also known as c.3868G>A), located in coding exon 49 of the COL5A1 gene, results from a G to A substitution at nucleotide position 3868. The alanine at codon 1290 is replaced by threonine, an amino acid with similar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6049 samples (12098 alleles) with coverage at this position. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this variant remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Aug 13, 2014 | The A1290T variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. The A1290T variant was not observed in approximately 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The A1290T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved in mammals. Moreover, a missense mutations in a nearby residue (E1292K) has been reported in association with EDS, supporting the functional importance of this region of the protein. Nevertheless, in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Based on the currently available clinical and molecular information, it is unclear whether this variant is a pathogenic mutation or a rare benign variant.This variant was found in COL5A1,TAAD - |
Ehlers-Danlos syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Apr 20, 2022 | - - |
Ehlers-Danlos syndrome, classic type, 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 26, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at