rs1554810510

chr9-127826640-CG-C

Variant summary

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

The NM_001114753.3(ENG):c.392del(p.Pro131ArgfsTer32) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,746 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. P131P) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: ENG NM_001114753.3 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:3
• Conservation: PhyloP100: -0.0560

Genes affected

ENG (HGNC:3349): (endoglin) This gene encodes a homodimeric transmembrane protein which is a major glycoprotein of the vascular endothelium. This protein is a component of the transforming growth factor beta receptor complex and it binds to the beta1 and beta3 peptides with high affinity. Mutations in this gene cause hereditary hemorrhagic telangiectasia, also known as Osler-Rendu-Weber syndrome 1, an autosomal dominant multisystemic vascular dysplasia. This gene may also be involved in preeclampsia and several types of cancer. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2013]

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 9-127826640-CG-C is Pathogenic according to our data. Variant chr9-127826640-CG-C is described in ClinVar as [Pathogenic]. Clinvar id is 458347.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENG	NM_001114753.3	c.392del	p.Pro131ArgfsTer32	frameshift_variant	4/15	ENST00000373203.9
ENG	NM_000118.4	c.392del	p.Pro131ArgfsTer32	frameshift_variant	4/14
ENG	NM_001406715.1	c.392del	p.Pro131ArgfsTer32	frameshift_variant	4/8
ENG	NM_001278138.2	c.-155del		5_prime_UTR_variant	4/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENG	ENST00000373203.9	c.392del	p.Pro131ArgfsTer32	frameshift_variant	4/15	1	NM_001114753.3	P2
ENG	ENST00000344849.4	c.392del	p.Pro131ArgfsTer32	frameshift_variant	4/14	1		A2
ENG	ENST00000480266.6	c.-155del		5_prime_UTR_variant	4/15	2
ENG	ENST00000462196.1	n.292del		non_coding_transcript_exon_variant	3/4	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461746 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 727164

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Telangiectasia, hereditary hemorrhagic, type 1 Pathogenic:1

Pathogenic, no assertion criteria provided

research

Genomics And Bioinformatics Analysis Resource, Columbia University

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Spontaneous, recurrent epistaxis Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

New York Genome Center

Sep 13, 2019

The c.392del (p.Pro131ArgfsTer32) variant identified in the ENG gene is the deletion of a single nucleotide resulting in the frameshift of the protein at amino acid 131/659 (coding exon 4/15), which is predicted to lead to the premature termination of the protein approximately 32 amino acids downstream of the variant. This variant is absent from gnomAD and ExAC, suggesting it is not a common benign variant in the populations represented in these databases. This variant is classified as Pathogenic in ClinVar (VarID:458347), and has been identified in two individuals in the literature with hereditary haemorrhagic telangiectasia [PMID: 16542389; PMID: 30251589]. This variant was identified in a proband submitted for clinical testing, and found to be inherited from an affected parent. The c.392del (p.Pro131ArgfsTer32) variant is reported here as Pathogenic. -

Hereditary hemorrhagic telangiectasia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Nov 08, 2022

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 458347). This premature translational stop signal has been observed in individuals with epistaxis, telangiectasias and gastrointestinal bleeding (PMID: 16542389). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Pro131Argfs*32) in the ENG gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ENG are known to be pathogenic (PMID: 15879500). -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1554810510; hg19: chr9-130588919;