NM_018668.4(VPS33B):c.96+1G>T AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Jul 29, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000723216.2

Allele description [Variation Report for NM_018668.4(VPS33B):c.96+1G>T]

NM_018668.4(VPS33B):c.96+1G>T

Gene:
VPS33B:VPS33B late endosome and lysosome associated [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q26.1
Genomic location:
Preferred name:
NM_018668.4(VPS33B):c.96+1G>T
HGVS:
  • NC_000015.10:g.91022153C>A
  • NG_012162.1:g.5451G>T
  • NM_001289148.1:c.96+1G>T
  • NM_001289149.1:c.-116+1G>T
  • NM_018668.4:c.96+1G>T
  • LRG_884t1:c.96+1G>T
  • LRG_884:g.5451G>T
  • NC_000015.9:g.91565383C>A
Links:
dbSNP: rs1567232168
NCBI 1000 Genomes Browser:
rs1567232168
Molecular consequence:
  • NM_001289148.1:c.96+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001289149.1:c.-116+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_018668.4:c.96+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000854347Gharavi Laboratory,Columbia Universityno assertion criteria provided
Uncertain significance
(Sep 16, 2018)
germlineresearch

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

SCV001577726Invitaecriteria provided, single submitter
Likely pathogenic
(Jul 29, 2017)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedresearch
not providedgermlineunknownnot 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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933
See all PubMed Citations (4)

Details of each submission

From Gharavi Laboratory,Columbia University, SCV000854347.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001577726.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change affects a donor splice site in intron 1 of the VPS33B gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with VPS33B-related disease. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in VPS33B are known to be pathogenic (PMID: 16896922). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: Aug 27, 2021

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