rs72651640

Positions:

• chr17-50191841-CA-C

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000088.4(COL1A1):​c.2073del​(p.Gly692ValfsTer74) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: COL1A1 NM_000088.4 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:3
• Conservation: PhyloP100: -1.40

Genes affected

COL1A1 (HGNC:2197): (collagen type I alpha 1 chain) This gene encodes the pro-alpha1 chains of type I collagen whose triple helix comprises two alpha1 chains and one alpha2 chain. Type I is a fibril-forming collagen found in most connective tissues and is abundant in bone, cornea, dermis and tendon. Mutations in this gene are associated with osteogenesis imperfecta types I-IV, Ehlers-Danlos syndrome type VIIA, Ehlers-Danlos syndrome Classical type, Caffey Disease and idiopathic osteoporosis. Reciprocal translocations between chromosomes 17 and 22, where this gene and the gene for platelet-derived growth factor beta are located, are associated with a particular type of skin tumor called dermatofibrosarcoma protuberans, resulting from unregulated expression of the growth factor. Two transcripts, resulting from the use of alternate polyadenylation signals, have been identified for this gene. [provided by R. Dalgleish, Feb 2008]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 17-50191841-CA-C is Pathogenic according to our data. Variant chr17-50191841-CA-C is described in ClinVar as [Pathogenic]. Clinvar id is 503696.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-50191841-CA-C is described in Lovd as [Likely_pathogenic]. Variant chr17-50191841-CA-C is described in Lovd as [Pathogenic]. Variant chr17-50191841-CA-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL1A1	NM_000088.4	c.2073del	p.Gly692ValfsTer74	frameshift_variant	31/51	ENST00000225964.10	NP_000079.2
COL1A1	XM_011524341.2	c.1875del	p.Gly626ValfsTer74	frameshift_variant	28/48		XP_011522643.1
COL1A1	XM_005257058.5	c.2073del	p.Gly692ValfsTer74	frameshift_variant	31/49		XP_005257115.2
COL1A1	XM_005257059.5	c.1155del	p.Gly386ValfsTer74	frameshift_variant	18/38		XP_005257116.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL1A1	ENST00000225964.10	c.2073del	p.Gly692ValfsTer74	frameshift_variant	31/51	1	NM_000088.4	ENSP00000225964	P1
COL1A1	ENST00000476387.1	n.422del		non_coding_transcript_exon_variant	7/9	2
COL1A1	ENST00000504289.1			downstream_gene_variant		2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000432 AC: 1 AN: 231742 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 125182

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000304

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

COL1A1-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Aug 14, 2024

The COL1A1 c.2073delT variant is predicted to result in a frameshift and premature protein termination (p.Gly692Valfs*74). This variant was reported in individuals with osteogenesis imperfecta (OI) and OI/Ehlers-Danlos syndrome (Morlino et al 2019. PubMed ID: 31794058; Table S1, Lin et al 2023. PubMed ID: 37270749). This variant is reported in 0.0030% of alleles in individuals of Latino descent in gnomAD. Frameshift variants in COL1A1 are expected to be pathogenic. This variant is interpreted as pathogenic. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Jan 08, 2024

Identified in two affected family members with a clinical diagnosis of Ehlers-Danlos syndrome and minimal features of osteogenesis imperfecta in published literature (PMID: 31794058); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 37270749, 29946973, 35456387, 9443882, 31794058) -

Osteogenesis imperfecta type I Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 19, 2021

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 503696). This premature translational stop signal has been observed in individual(s) with osteogenesis imperfecta type I (PMID: 9443882). This variant is present in population databases (rs72651640, gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gly692Valfs*74) in the COL1A1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COL1A1 are known to be pathogenic (PMID: 7942841, 9295084, 9443882). -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs72651640; hg19: chr17-48269202;