NM_002890.3(RASA1):c.248G>A (p.Gly83Glu) AND Capillary malformation-arteriovenous malformation 1

Clinical significance:Uncertain significance (Last evaluated: Jun 16, 2016)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000280765.2

Allele description [Variation Report for NM_002890.3(RASA1):c.248G>A (p.Gly83Glu)]

NM_002890.3(RASA1):c.248G>A (p.Gly83Glu)

Gene:
RASA1:RAS p21 protein activator 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q14.3
Genomic location:
Preferred name:
NM_002890.3(RASA1):c.248G>A (p.Gly83Glu)
HGVS:
  • NC_000005.10:g.87268699G>A
  • NG_011650.1:g.5366G>A
  • NM_002890.3:c.248G>AMANE SELECT
  • NP_002881.1:p.Gly83Glu
  • NC_000005.9:g.86564516G>A
  • NM_002890.2:c.248G>A
Protein change:
G83E
Links:
dbSNP: rs755788420
NCBI 1000 Genomes Browser:
rs755788420
Molecular consequence:
  • NM_002890.3:c.248G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Capillary malformation-arteriovenous malformation 1 (CMAVM1)
Identifiers:
MONDO: MONDO:0020783; MedGen: C4747394; Orphanet: 137667; OMIM: 608354

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000458944Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Uncertain significance
(Jun 14, 2016)
germlineclinical testing

ICSL_Variant_Classification_20161018.pdf,

Citation Link,

SCV000552999Invitaecriteria provided, single submitter
Uncertain significance
(Jun 16, 2016)
germlineclinical testing

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

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV000458944.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV000552999.2

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

Description

This sequence change replaces glycine with glutamic acid at codon 83 of the RASA1 protein (p.Gly83Glu). The glycine residue is weakly conserved and there is a moderate physicochemical difference between glycine and glutamic acid. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a RASA1-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, this variant is a novel missense change with uncertain impact on protein function. 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: Nov 27, 2021

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