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NM_001114753.3(ENG):c.539C>T (p.Ser180Phe) AND Telangiectasia, hereditary hemorrhagic, type 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 11, 2017
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000633134.1

Allele description

NM_001114753.3(ENG):c.539C>T (p.Ser180Phe)

Gene:
ENG:endoglin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.11
Genomic location:
Preferred name:
NM_001114753.3(ENG):c.539C>T (p.Ser180Phe)
HGVS:
  • NC_000009.12:g.127825845G>A
  • NG_009551.1:g.33924C>T
  • NM_000118.3:c.539C>T
  • NM_001114753.3:c.539C>TMANE SELECT
  • NM_001278138.2:c.-8C>T
  • NP_000109.1:p.Ser180Phe
  • NP_001108225.1:p.Ser180Phe
  • LRG_589t1:c.539C>T
  • LRG_589:g.33924C>T
  • LRG_589p1:p.Ser180Phe
  • NC_000009.11:g.130588124G>A
Protein change:
S180F
Links:
dbSNP: rs375025857
NCBI 1000 Genomes Browser:
rs375025857
Molecular consequence:
  • NM_001278138.2:c.-8C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000118.3:c.539C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001114753.3:c.539C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Telangiectasia, hereditary hemorrhagic, type 1
Synonyms:
Osler Weber Rendu syndrome type 1
Identifiers:
MONDO: MONDO:0008535; MedGen: C4551861; Orphanet: 774; OMIM: 187300

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000754348Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 11, 2017) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000754348.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces serine with phenylalanine at codon 180 of the ENG protein (p.Ser180Phe). The serine residue is weakly conserved and there is a large physicochemical difference between serine and phenylalanine. This variant is present in population databases (rs375025857, ExAC 0.004%). This variant has not been reported in the literature in individuals with ENG-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The phenylalanine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 23, 2022