rs139767471
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM1BS2
The NM_001114753.3(ENG):c.698C>T(p.Thr233Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,610,338 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T233T) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 26)
Exomes 𝑓: 0.000016 ( 1 hom. )
Consequence
ENG
NM_001114753.3 missense
NM_001114753.3 missense
Scores
12
7
Clinical Significance
Conservation
PhyloP100: 1.74
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM1
?
In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 5 benign, 10 uncertain in NM_001114753.3
BS2
?
High AC in GnomAdExome4 at 24 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENG | NM_001114753.3 | c.698C>T | p.Thr233Met | missense_variant | 6/15 | ENST00000373203.9 | |
ENG | NM_000118.4 | c.698C>T | p.Thr233Met | missense_variant | 6/14 | ||
ENG | NM_001278138.2 | c.152C>T | p.Thr51Met | missense_variant | 6/15 | ||
ENG | NM_001406715.1 | c.698C>T | p.Thr233Met | missense_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENG | ENST00000373203.9 | c.698C>T | p.Thr233Met | missense_variant | 6/15 | 1 | NM_001114753.3 | P2 | |
ENG | ENST00000344849.4 | c.698C>T | p.Thr233Met | missense_variant | 6/14 | 1 | A2 | ||
ENG | ENST00000480266.6 | c.152C>T | p.Thr51Met | missense_variant | 6/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000667 AC: 1AN: 149926Hom.: 0 Cov.: 26
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000281 AC: 7AN: 248928Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134996
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GnomAD4 exome AF: 0.0000164 AC: 24AN: 1460412Hom.: 1 Cov.: 33 AF XY: 0.0000206 AC XY: 15AN XY: 726508
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GnomAD4 genome ? AF: 0.00000667 AC: 1AN: 149926Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 72978
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hereditary hemorrhagic telangiectasia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 21, 2021 | This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 233 of the ENG protein (p.Thr233Met). This variant is present in population databases (rs139767471, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with ENG-related conditions. ClinVar contains an entry for this variant (Variation ID: 528053). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
D;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;M
MutationTaster
Benign
N;N;N;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;.;D
REVEL
Benign
Sift
Uncertain
D;.;D
Sift4G
Uncertain
D;D;D
Polyphen
D;.;.
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at