rs1554726245
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PM4PP3PP5_Moderate
The NM_000093.5(COL5A1):c.5150_5158del(p.Asp1717_Glu1719del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. V1716V) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 33)
Consequence
COL5A1
NM_000093.5 inframe_deletion
NM_000093.5 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.78
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_000093.5.
PP3
?
No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
PP5
?
Variant 9-134834981-TGGACGCCGA-T is Pathogenic according to our data. Variant chr9-134834981-TGGACGCCGA-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 523326.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.5150_5158del | p.Asp1717_Glu1719del | inframe_deletion | 65/66 | ENST00000371817.8 | |
LOC101448202 | NR_103451.2 | n.71-14781_71-14773del | intron_variant, non_coding_transcript_variant | ||||
COL5A1 | NM_001278074.1 | c.5150_5158del | p.Asp1717_Glu1719del | inframe_deletion | 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.5150_5158del | p.Asp1717_Glu1719del | inframe_deletion | 65/66 | 1 | NM_000093.5 | P4 | |
COL5A1 | ENST00000371820.4 | c.5150_5158del | p.Asp1717_Glu1719del | inframe_deletion | 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
Atrophic scars;C0241074:Hyperextensible skin;C1844820:Joint hypermobility;C1851828:Cigarette-paper scars;C4025260:Large joint dislocations Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at