rs1060501410

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PS4PS3PP4_ModeratePP1PM2_Supporting

This summary comes from the ClinGen Evidence Repository: 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). LINK:https://erepo.genome.network/evrepo/ui/classification/CA16612528/MONDO:0008535/136

Frequency

Genomes: not found (cov: 28)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

ENG
NM_001114753.3 missense, splice_region

Scores

6
13
Splicing: ADA: 1.000
2

Clinical Significance

Pathogenic reviewed by expert panel P:12

Conservation

PhyloP100: 1.37
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 ACMG points.

PS3
For more information check the summary or visit ClinGen Evidence Repository.
PS4
For more information check the summary or visit ClinGen Evidence Repository.
PM2
For more information check the summary or visit ClinGen Evidence Repository.
PP1
For more information check the summary or visit ClinGen Evidence Repository.
PP4
For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ENGNM_001114753.3 linkc.991G>A p.Gly331Ser missense_variant, splice_region_variant Exon 7 of 15 ENST00000373203.9 NP_001108225.1 P17813-1Q96CG0A0A024R878
ENGNM_000118.4 linkc.991G>A p.Gly331Ser missense_variant, splice_region_variant Exon 7 of 14 NP_000109.1 P17813-2Q5T9B9
ENGNM_001278138.2 linkc.445G>A p.Gly149Ser missense_variant, splice_region_variant Exon 7 of 15 NP_001265067.1 P17813Q96CG0F5GX88B7Z6Y5
ENGNM_001406715.1 linkc.991G>A p.Gly331Ser missense_variant, splice_region_variant Exon 7 of 8 NP_001393644.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENGENST00000373203.9 linkc.991G>A p.Gly331Ser missense_variant, splice_region_variant Exon 7 of 15 1 NM_001114753.3 ENSP00000362299.4 P17813-1
ENGENST00000344849.4 linkc.991G>A p.Gly331Ser missense_variant, splice_region_variant Exon 7 of 14 1 ENSP00000341917.3 P17813-2
ENGENST00000480266.6 linkc.445G>A p.Gly149Ser missense_variant, splice_region_variant Exon 7 of 15 2 ENSP00000479015.1 F5GX88

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
show subpopulations
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
LINK: link

Submissions by phenotype

Telangiectasia, hereditary hemorrhagic, type 1 Pathogenic:7
Jan 25, 2018
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Oct 31, 2018
Fulgent Genetics, Fulgent Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Sep 09, 2024
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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 in ClinVar (Variation ID: 407115), but is absent from the 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. PMID: 16752392. 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. PMID: 17384219. Letteboer TG et al. Hereditary hemorrhagic telangiectasia: ENG and ALK-1 mutations in Dutch patients. Hum Genet. 2005 Jan;116(1-2):8-16. PMID: 15517393. 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. PMID: 19767588. 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. PMID: 22991266. Prigoda NL et al. Hereditary haemorrhagic telangiectasia: mutation detection, test sensitivity and novel mutations. J Med Genet. 2006 Sep;43(9):722-8. PMID: 16690726. -

Mar 15, 2024
ClinGen Hereditary Hemorrhagic Telangiectasia Variant Curation Expert Panel, ClinGen
Significance: Pathogenic
Review Status: reviewed by expert panel
Collection Method: curation

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). -

Jul 22, 2021
MGZ Medical Genetics Center
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Jan 01, 2018
NIHR Bioresource Rare Diseases, University of Cambridge
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: research

PM2+PP3+PP4+PP5 -

May 06, 2021
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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 -

not provided Pathogenic:3
Jun 26, 2023
GeneDx
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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) -

Jun 01, 2021
CeGaT Center for Human Genetics Tuebingen
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Feb 29, 2024
Mayo Clinic Laboratories, Mayo Clinic
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

PP3, PM2, PS3_moderate, PS4 -

Cardiovascular phenotype Pathogenic:1
May 24, 2022
Ambry Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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
Jan 11, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1060501410; hg19: chr9-130587079; COSMIC: COSV61228053; COSMIC: COSV61228053; API