rs1553303203

Variant names:

• chr1-218436106-CCGGCGGAAGA-C
• rs1553303203
• NM_003238.6:c.892_901delCGGCGGAAGA

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_003238.6(TGFB2):​c.892_901delCGGCGGAAGA​(p.Arg298SerfsTer30) variant causes a frameshift 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 Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. R298R) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TGFB2 NM_003238.6 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 9.55

Genes affected

TGFB2 (HGNC:11768): (transforming growth factor beta 2) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate a latency-associated peptide (LAP) and a mature peptide, and is found in either a latent form composed of a mature peptide homodimer, a LAP homodimer, and a latent TGF-beta binding protein, or in an active form consisting solely of the mature peptide homodimer. The mature peptide may also form heterodimers with other TGF-beta family members. Disruption of the TGF-beta/SMAD pathway has been implicated in a variety of human cancers. A chromosomal translocation that includes this gene is associated with Peters' anomaly, a congenital defect of the anterior chamber of the eye. Mutations in this gene may be associated with Loeys-Dietz syndrome. This gene encodes multiple isoforms that may undergo similar proteolytic processing. [provided by RefSeq, Aug 2016]

ACMG classification

Our verdict: Pathogenic. The variant received 12 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 1-218436106-CCGGCGGAAGA-C is Pathogenic according to our data. Variant chr1-218436106-CCGGCGGAAGA-C is described in ClinVar as [Pathogenic]. Clinvar id is 459270.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TGFB2	NM_003238.6	c.892_901delCGGCGGAAGA	p.Arg298SerfsTer30	frameshift_variant	Exon 5 of 7	ENST00000366930.9	NP_003229.1
TGFB2	NM_001135599.4	c.976_985delCGGCGGAAGA	p.Arg326SerfsTer30	frameshift_variant	Exon 6 of 8		NP_001129071.1
TGFB2	NR_138148.2	n.2143_2152delCGGCGGAAGA		non_coding_transcript_exon_variant	Exon 5 of 7
TGFB2	NR_138149.2	n.2227_2236delCGGCGGAAGA		non_coding_transcript_exon_variant	Exon 6 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TGFB2	ENST00000366930.9	c.892_901delCGGCGGAAGA	p.Arg298SerfsTer30	frameshift_variant	Exon 5 of 7	1	NM_003238.6	ENSP00000355897.4
TGFB2	ENST00000366929.4	c.976_985delCGGCGGAAGA	p.Arg326SerfsTer30	frameshift_variant	Exon 6 of 8	1		ENSP00000355896.4
TGFB2	ENST00000479322.1	n.376_385delCGGCGGAAGA		non_coding_transcript_exon_variant	Exon 3 of 5	3

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Loeys-Dietz syndrome 4 Pathogenic:1

Apr 11, 2017

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. While this particular variant has not been reported in the literature, loss-of-function variants in TGFB2 are known to be pathogenic (PMID: 22772368). This sequence change deletes 10 nucleotides from exon 5 of the TGFB2 mRNA (c.892_901del10), causing a frameshift at codon 298. This creates a premature translational stop signal (p.Arg298Serfs*30) and is expected to result in an absent or disrupted protein product. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1553303203; hg19: chr1-218609448;