NM_000090.4:c.3202-2A>G

Variant names:

• chr2-189006935-A-G
• rs587779682
• NM_000090.4:c.3202-2A>G

Variant summary

Our verdict is Likely pathogenic. The variant received 6 ACMG points: 6P and 0B. PVS1_Moderate PM2 PP5_Moderate

The NM_000090.4(COL3A1):​c.3202-2A>G variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: COL3A1 NM_000090.4 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 3.34
• Publications: 0 publications found

Genes affected

COL3A1 (HGNC:2201): (collagen type III alpha 1 chain) This gene encodes the pro-alpha1 chains of type III collagen, a fibrillar collagen that is found in extensible connective tissues such as skin, lung, uterus, intestine and the vascular system, frequently in association with type I collagen. Mutations in this gene are associated with Ehlers-Danlos syndrome type IV, and with aortic and arterial aneurysms. [provided by R. Dalgleish, Feb 2008]

COL3A1 Gene-Disease associations (from GenCC):

• autosomal dominant Ehlers-Danlos syndrome, vascular type

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, PanelApp Australia, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, Genomics England PanelApp
• Ehlers-Danlos syndrome, vascular type

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
• polymicrogyria with or without vascular-type Ehlers-Danlos syndrome

  Inheritance: AR Classification: STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae)

ENSG00000295704 (HGNC:):

ACMG classification

Our verdict: Likely_pathogenic. The variant received 6 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.012269938 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 2-189006935-A-G is Pathogenic according to our data. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-189006935-A-G is described in CliVar as Pathogenic. Clinvar id is 101440.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL3A1	NM_000090.4	c.3202-2A>G		splice_acceptor_variant, intron_variant	Intron 43 of 50	ENST00000304636.9	NP_000081.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL3A1	ENST00000304636.9	c.3202-2A>G		splice_acceptor_variant, intron_variant	Intron 43 of 50	1	NM_000090.4	ENSP00000304408.4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

Ehlers-Danlos syndrome, type 4 Pathogenic:2

Jul 17, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 101440). This variant is also known as IVS44-2A>G. Disruption of this splice site has been observed in individuals with clinical features of autosomal dominant COL3A1-related conditions (PMID: 17224388; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 43 of the COL3A1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in COL3A1 are known to be pathogenic (PMID: 24922459). -

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Collagen Diagnostic Laboratory, University of Washington

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.19
CADD	Pathogenic	26
DANN	Uncertain	0.99
Eigen	Pathogenic	0.96
Eigen_PC	Pathogenic	0.76
FATHMM_MKL	Pathogenic	0.99	D
PhyloP100		3.3
GERP RS		5.0
Mutation Taster		=1/99	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.99		Position offset: 2

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

Other links and lift over

dbSNP: rs587779682; hg19: chr2-189871661;