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NM_012414.4(RAB3GAP2):c.1153C>T (p.Arg385Cys) AND Warburg micro syndrome 2

Germline classification:
Uncertain significance (1 submission)
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:
RCV003339745.2

Allele description [Variation Report for NM_012414.4(RAB3GAP2):c.1153C>T (p.Arg385Cys)]

NM_012414.4(RAB3GAP2):c.1153C>T (p.Arg385Cys)

Gene:
RAB3GAP2:RAB3 GTPase activating non-catalytic protein subunit 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q41
Genomic location:
Preferred name:
NM_012414.4(RAB3GAP2):c.1153C>T (p.Arg385Cys)
HGVS:
  • NC_000001.11:g.220193357G>A
  • NG_015837.2:g.84145C>T
  • NM_012414.4:c.1153C>TMANE SELECT
  • NP_036546.2:p.Arg385Cys
  • NC_000001.10:g.220366699G>A
Protein change:
R385C
Links:
dbSNP: rs755157552
NCBI 1000 Genomes Browser:
rs755157552
Molecular consequence:
  • NM_012414.4:c.1153C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Warburg micro syndrome 2 (WARBM2)
Synonyms:
MICRO SYNDROME 2
Identifiers:
MONDO: MONDO:0013641; MedGen: C3280214; Orphanet: 2510; OMIM: 614225

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004047628Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significancegermlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV004047628.1

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

Description

The c.1153C>T (p.Arg385Cys) missense variant in RAB3GAP2 gene has been submitted to ClinVar as a Variant of Uncertain Significance, but no details are available for independent assessment. It has not been reported in affected individuals. This variant is reported with the allele frequency (0.0007%) in the gnomAD and novel in 1000 genome database. The amino acid Arg at position 385 is changed to a Cys changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Arg385Cys in RAB3GAP2 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Variant of Uncertain Significance (VUS).

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

Last Updated: Apr 6, 2024