rs1060501410

chr9-127824800-C-T

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2 PP3_Strong PP5_Very_Strong

The NM_001114753.3(ENG):c.991G>A(p.Gly331Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000142 in 1,404,106 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G331V) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 28)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: ENG NM_001114753.3 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:12
• Conservation: PhyloP100: 1.37

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 14 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.
• PP5: Variant 9-127824800-C-T is Pathogenic according to our data. Variant chr9-127824800-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 407115.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr9-127824800-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENG	NM_001114753.3	c.991G>A	p.Gly331Ser	missense_variant, splice_region_variant	7/15	ENST00000373203.9
ENG	NM_000118.4	c.991G>A	p.Gly331Ser	missense_variant, splice_region_variant	7/14
ENG	NM_001278138.2	c.445G>A	p.Gly149Ser	missense_variant, splice_region_variant	7/15
ENG	NM_001406715.1	c.991G>A	p.Gly331Ser	missense_variant, splice_region_variant	7/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENG	ENST00000373203.9	c.991G>A	p.Gly331Ser	missense_variant, splice_region_variant	7/15	1	NM_001114753.3	P2
ENG	ENST00000344849.4	c.991G>A	p.Gly331Ser	missense_variant, splice_region_variant	7/14	1		A2
ENG	ENST00000480266.6	c.445G>A	p.Gly149Ser	missense_variant, splice_region_variant	7/15	2

Frequencies

GnomAD3 genomes Cov.: 28

GnomAD4 exome AF: 0.00000142 AC: 2 AN: 1404106 Hom.: 0 Cov.: 33 AF XY: 0.00000289 AC XY: 2 AN XY: 692252

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: 0.00000185

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 28

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:12

Revision: reviewed by expert panel

Submissions by phenotype

Telangiectasia, hereditary hemorrhagic, type 1 Pathogenic:7

Likely pathogenic, criteria provided, single submitter	research	NIHR Bioresource Rare Diseases, University of Cambridge	Jan 01, 2018	PM2+PP3+PP4+PP5 -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	May 06, 2021	Based on the classification scheme VCGS_Germline_v1.3.3, this variant is classified as Pathogenic. Following criteria are met: 0103 - Dominant negative and loss of function are known mechanisms of disease in this gene and are associated with Hereditary Hemorrhagic Telangiectasia type 1 (MIM#187300). Loss-of-function variants have been reported, while missense variants have been demonstrated to have both loss of function and dominant negative effects on protein activity (PMID: 25312062). (I). 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from glycine to serine. (I) 0212 - Non-canonical splice site variant without proven consequence on splicing (no functional evidence available). This variant affects the last nucleotide of exon 7 and it was said that RT-PCR of a patient’s RNA showed splicing defect leading to exon skipping. However, data was not shown in the manuscript for independent confirmation (PMID: 16690726). (SP) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0503 - Missense variant consistently predicted to be tolerated by multiple in silico tools or not conserved in placental mammals with a minor amino acid change. (SB) 0505 - Abnormal splicing is predicted by in silico tools but affected nucleotide is moderately conserved. (I) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0801 - This variant has strong previous evidence of pathogenicity in at least 10 unrelated individuals with Hereditary Hemorrhagic Telangiectasia type 1 (MIM#187300) (ClinVar; PMIDs: 15517393, 17384219, 19767588, 24196379, 25970827, 29171923). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Oct 31, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München	Jan 25, 2018	- -
Pathogenic, reviewed by expert panel	curation	ClinGen Hereditary Hemorrhagic Telangiectasia Variant Curation Expert Panel, ClinGen	Mar 15, 2024	The NM_001114753.3: c.991G>A variant in ENG is a missense variant predicted to cause substitution of glycine by serine at amino acid 331 (p.Gly331Ser). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant has been reported in >10 probands with a phenotype consistent with HHT (PS4; PMID: 19767588, 34872578, 16690726, 34880085, 15517393, 25970827, 29171923, 32573726, 21158752, Internal lab contributors). At least one patient's phenotype meets Curacao Criteria for HHT, and sequencing and large deletion/duplication analysis was performed for ENG and ACVRL1, which is highly specific for HHT (PP4_Moderate; PMID: 19767588, 21158752). The variant has been reported to segregate with HHT in 3 affected meioses from 2 families (PP1; PMID: 19767588, 34872578). The computational predictor REVEL gives a score of 0.202, which is neither above nor below the thresholds predicting a damaging or benign impact on ENG function. However, RT-PCR analysis of cDNA demonstrated that the variant impacts splicing by leading to exon 7 skipping (PS3; PMID: 16690726). In summary, this variant meets the criteria to be classified as pathogenic for autosomal dominant hereditary hemorrhagic telangiectasia based on the ACMG/AMP criteria applied, as specified by the ClinGen Hereditary Hemorrhagic Telangiectasia Variant Curation Expert Panel: PS3, PS4, PP4_Moderate, PP1, PM2_Supporting (specification version 1.0.0; 1/4/2024). -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Apr 03, 2020	The ENG c.991G>A; p.Gly331Ser variant (rs1060501410) is published in the literature in individuals and families diagnosed with HHT (Bossler 2006, Gedge 2007, Letteboer 2005, McDonald 2009, Nishida 2012), and is reported as pathogenic in ClinVar (Variation ID: 407115). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. This variant occurs in the last nucleotide of the exon, which is a highly conserved nucleotide, and computational algorithms (Alamut v.2.11) predict this variant results in altered mRNA splicing. In support of these predictions, a functional study shows this alteration leads to exon 7 skipping (Prigoda 2006). Based on available information, this variant is considered to be pathogenic. REFERENCES Bossler AD et al. Novel mutations in ENG and ACVRL1 identified in a series of 200 individuals undergoing clinical genetic testing for hereditary hemorrhagic telangiectasia (HHT): correlation of genotype with phenotype. Hum Mutat. 2006 Jul;27(7):667-75. Gedge F et al. Clinical and analytical sensitivities in hereditary hemorrhagic telangiectasia testing and a report of de novo mutations. J Mol Diagn. 2007 Apr;9(2):258-65. Letteboer TG et al. Hereditary hemorrhagic telangiectasia: ENG and ALK-1 mutations in Dutch patients. Hum Genet. 2005 Jan;116(1-2):8-16. McDonald J et al. Multiple sequence variants in hereditary hemorrhagic telangiectasia cases: illustration of complexity in molecular diagnostic interpretation. J Mol Diagn. 2009 Nov;11(6):569-75. Nishida T et al. Brain arteriovenous malformations associated with hereditary hemorrhagic telangiectasia: gene-phenotype correlations. Am J Med Genet A. 2012 Nov;158A(11):2829-34. Prigoda NL et al. Hereditary haemorrhagic telangiectasia: mutation detection, test sensitivity and novel mutations. J Med Genet. 2006 Sep;43(9):722-8. -
Likely pathogenic, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Jul 22, 2021	- -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jun 26, 2023	Not observed in large population cohorts (gnomAD); Functional studies and in silico splice prediction algorithms suggest that the c.991 G>A variant, which affects the last nucleotide of exon 7, damages the natural splice donor site for intron 7 and leads to skipping of exon 7 (Prigoda et al., 2006); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24196379, 19767588, 15517393, 25970827, 16752392, 17384219, 29171923, 22991266, 16690726, 26582918, 34880085, 34872578, 32573726) -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Apr 27, 2023	PP3, PM2_supporting, PS3_moderate, PS4 -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jun 01, 2021	- -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

May 24, 2022

The c.991G>A pathogenic mutation (also known as p.G331S), located in coding exon 7 of the ENG gene, results from a G to A substitution at nucleotide position 991. The glycine at codon 331 is replaced by serine, an amino acid with similar properties. However, this change occurs in the last base pair of coding exon 7, which makes it likely to have some effect on normal mRNA splicing. A functional study demonstrated that this mutation results in the skipping of coding exon 7 (Prigoda NL et al. J. Med. Genet., 2006 Sep;43:722-8). This mutation has been reported in multiple individuals with a clinical diagnosis of hereditary hemorrhagic telangiectasia (Letteboer TG et al. Hum. Genet., 2005 Jan;116:8-16; McDonald J et al. J Mol Diagn, 2009 Nov;11:569-75). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Hereditary hemorrhagic telangiectasia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Dec 26, 2023

This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 331 of the ENG protein (p.Gly331Ser). This variant also falls at the last nucleotide of exon 7, which is part of the consensus splice site for this exon. This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with hereditary hemorrhagic telangiectasia (HHT) and brain arteriovenous malformations (BAVM) (PMID: 15517393, 16690726, 19767588, 22991266, 24196379, 25970827). ClinVar contains an entry for this variant (Variation ID: 407115). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.090
BayesDel_addAF	Benign	-0.031	T
BayesDel_noAF	Benign	-0.28
Cadd	Uncertain	26
Dann	Uncertain	1.0
DEOGEN2	Uncertain	0.46	T;T;.
Eigen	Uncertain	0.25
Eigen_PC	Benign	0.12
FATHMM_MKL	Benign	0.75	D
LIST_S2	Benign	0.70	T;T;T
M_CAP	Benign	0.053	D
MetaRNN	Uncertain	0.58	D;D;D
MetaSVM	Benign	-0.85	T
MutationAssessor	Uncertain	2.1	M;.;M
MutationTaster	Benign	0.90	N;N;N;N
PrimateAI	Benign	0.31	T
PROVEAN	Uncertain	-2.4	N;.;D
REVEL	Benign	0.20
Sift	Benign	0.11	T;.;T
Sift4G	Benign	0.42	T;T;T
Polyphen		1.0	D;.;.
Vest4		0.76
MutPred		0.40		Gain of disorder (P = 0.046);.;Gain of disorder (P = 0.046);
MVP		0.73
MPC		0.48
ClinPred		0.89	D
GERP RS		3.5
Varity_R		0.14
gMVP		0.64

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.99
SpliceAI score (max)		0.030		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: rs1060501410; hg19: chr9-130587079; COSMIC: COSV61228053; COSMIC: COSV61228053;