chr9-134834981-TGGACGCCGA-T

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 (★).

Frequency

Genomes: not found (cov: 33)

Consequence

COL5A1
NM_000093.5 inframe_deletion

Scores

Not classified

Clinical Significance

Likely pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 9.78
Variant links:
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 Protein UniProt
COL5A1NM_000093.5 linkuse as main transcriptc.5150_5158del p.Asp1717_Glu1719del inframe_deletion 65/66 ENST00000371817.8 NP_000084.3
LOC101448202NR_103451.2 linkuse as main transcriptn.71-14781_71-14773del intron_variant, non_coding_transcript_variant
COL5A1NM_001278074.1 linkuse as main transcriptc.5150_5158del p.Asp1717_Glu1719del inframe_deletion 65/66 NP_001265003.1
COL5A1XM_017014266.3 linkuse as main transcript downstream_gene_variant XP_016869755.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
COL5A1ENST00000371817.8 linkuse as main transcriptc.5150_5158del p.Asp1717_Glu1719del inframe_deletion 65/661 NM_000093.5 ENSP00000360882 P4P20908-1
COL5A1ENST00000371820.4 linkuse as main transcriptc.5150_5158del p.Asp1717_Glu1719del inframe_deletion 65/662 ENSP00000360885 A2P20908-2

Frequencies

GnomAD3 genomes
Cov.:
33
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
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 submitterclinical testingCentre for Mendelian Genomics, University Medical Centre LjubljanaJan 01, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1554726245; hg19: chr9-137726827; API