rs1060502250
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM4_SupportingPP3PP5_Moderate
The NM_000093.5(COL5A1):c.5141_5143del(p.Ser1714del) variant causes a inframe deletion, splice region change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. L1713L) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 33)
Consequence
COL5A1
NM_000093.5 inframe_deletion, splice_region
NM_000093.5 inframe_deletion, splice_region
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.85
Genes affected
COL5A1 (HGNC:2209): (collagen type V alpha 1 chain) This gene encodes an alpha chain for one of the low abundance fibrillar collagens. Fibrillar collagen molecules are trimers that can be composed of one or more types of alpha chains. Type V collagen is found in tissues containing type I collagen and appears to regulate the assembly of heterotypic fibers composed of both type I and type V collagen. This gene product is closely related to type XI collagen and it is possible that the collagen chains of types V and XI constitute a single collagen type with tissue-specific chain combinations. The encoded procollagen protein occurs commonly as the heterotrimer pro-alpha1(V)-pro-alpha1(V)-pro-alpha2(V). Mutations in this gene are associated with Ehlers-Danlos syndrome, types I and II. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_000093.5. Strenght limited to Supporting due to length of the change: 1aa.
PP3
?
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
PP5
?
Variant 9-134834972-TCTC-T is Pathogenic according to our data. Variant chr9-134834972-TCTC-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 409098.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL5A1 | NM_000093.5 | c.5141_5143del | p.Ser1714del | inframe_deletion, splice_region_variant | 65/66 | ENST00000371817.8 | |
LOC101448202 | NR_103451.2 | n.71-14766_71-14764del | intron_variant, non_coding_transcript_variant | ||||
COL5A1 | NM_001278074.1 | c.5141_5143del | p.Ser1714del | inframe_deletion, splice_region_variant | 65/66 | ||
COL5A1 | XM_017014266.3 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL5A1 | ENST00000371817.8 | c.5141_5143del | p.Ser1714del | inframe_deletion, splice_region_variant | 65/66 | 1 | NM_000093.5 | P4 | |
COL5A1 | ENST00000371820.4 | c.5141_5143del | p.Ser1714del | inframe_deletion, splice_region_variant | 65/66 | 2 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Ehlers-Danlos syndrome, classic type, 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Invitae | Nov 07, 2016 | Family studies have indicated that this variant was not present in the parents of an individual with classical Ehlers-Danlos syndrome, which suggests that it was de novo in that affected individual (Invitae). In summary, this variant is a novel in-frame deletion with uncertain impact on protein function. Because it has been observed as arising de novo in an affected individual, it has been classified as Likely Pathogenic. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acid is currently unknown. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a COL5A1-related disease. This sequence change deletes 3 nucleotides from exon 65 of the COL5A1 mRNA (c.5141_5143delCCT). This leads to the deletion of 1 amino acid residue in the COL5A1 protein (p.Ser1714del) but otherwise preserves the integrity of the reading frame. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at