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NM_152564.5(VPS13B):c.11831_11841delinsG (p.Pro3944fs) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Sep 25, 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:
RCV000521388.2

Allele description [Variation Report for NM_152564.5(VPS13B):c.11831_11841delinsG (p.Pro3944fs)]

NM_152564.5(VPS13B):c.11831_11841delinsG (p.Pro3944fs)

Gene:
VPS13B:vacuolar protein sorting 13 homolog B [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
8q22.2
Genomic location:
Preferred name:
NM_152564.5(VPS13B):c.11831_11841delinsG (p.Pro3944fs)
HGVS:
  • NC_000008.11:g.99875503_99875513delinsG
  • NG_007098.2:g.867238_867248delinsG
  • NM_017890.5:c.11906_11916delinsG
  • NM_152564.5:c.11831_11841delinsGMANE SELECT
  • NP_060360.3:p.Pro3969fs
  • NP_060360.3:p.Pro3969fs
  • NP_689777.3:p.Pro3944fs
  • LRG_351t1:c.11906_11916delinsG
  • LRG_351:g.867238_867248delinsG
  • LRG_351p1:p.Pro3969fs
  • NC_000008.10:g.100887731_100887741delinsG
  • NM_017890.3:c.11906_11916delCCAGCTGTTCTinsG
  • NM_017890.4:c.11906_11916delCCAGCTGTTCTinsG
  • NM_017890.4:c.11906_11916delinsG
  • NM_152564.5:c.11831_11841delinsG
Protein change:
P3944fs
Links:
dbSNP: rs786204456
NCBI 1000 Genomes Browser:
rs786204456
Molecular consequence:
  • NM_017890.5:c.11906_11916delinsG - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_152564.5:c.11831_11841delinsG - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000621232GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Sep 25, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000621232.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.11906_11916del11insG variant in the VPS13B gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.11906_11916del11insG variant causes a frameshift starting with codon Proline 3969, changes this amino acid to an Arginine residue, and creates a premature Stop codon at position 41 of the new reading frame, denoted p.Pro3969ArgfsX41. This variant is predicted to cause loss of normal protein function through protein truncation. The c.11906_11916del11insG variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.11906_11916del11insG as a likely pathogenic variant.

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

Last Updated: Oct 28, 2023