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NM_006267.5(RANBP2):c.3384T>G (p.Ser1128Arg) AND Familial acute necrotizing encephalopathy

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 26, 2022
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:
RCV001068306.7

Allele description [Variation Report for NM_006267.5(RANBP2):c.3384T>G (p.Ser1128Arg)]

NM_006267.5(RANBP2):c.3384T>G (p.Ser1128Arg)

Gene:
RANBP2:RAN binding protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q13
Genomic location:
Preferred name:
NM_006267.5(RANBP2):c.3384T>G (p.Ser1128Arg)
HGVS:
  • NC_000002.12:g.108763923T>G
  • NG_012210.1:g.49443T>G
  • NM_006267.5:c.3384T>GMANE SELECT
  • NP_006258.3:p.Ser1128Arg
  • NC_000002.11:g.109380379T>G
  • NM_006267.4:c.3384T>G
Protein change:
S1128R
Links:
dbSNP: rs771199260
NCBI 1000 Genomes Browser:
rs771199260
Molecular consequence:
  • NM_006267.5:c.3384T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Familial acute necrotizing encephalopathy
Synonyms:
Encephalopathy, acute, infection-induced, 3, suceptibility to; Susceptibility to Acute Necrotizing Encephalopathy 1
Identifiers:
MONDO: MONDO:0011953; MedGen: C2675556; Orphanet: 88619; OMIM: 608033

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001233411Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 26, 2022) 		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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001233411.5

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

Description

This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 1128 of the RANBP2 protein (p.Ser1128Arg). 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. 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: "Benign"; Align-GVGD: "Class C25"). ClinVar contains an entry for this variant (Variation ID: 861725). This variant has not been reported in the literature in individuals affected with RANBP2-related conditions. This variant is present in population databases (rs771199260, gnomAD 0.02%).

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

Last Updated: Feb 14, 2024