NM_152564.5(VPS13B):c.9634C>T (p.Gln3212Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 11, 2018
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:: RCV000760308.1

Allele description [Variation Report for NM_152564.5(VPS13B):c.9634C>T (p.Gln3212Ter)]

NM_152564.5(VPS13B):c.9634C>T (p.Gln3212Ter)

Gene:

VPS13B:vacuolar protein sorting 13 homolog B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q22.2

Genomic location:

Preferred name:

NM_152564.5(VPS13B):c.9634C>T (p.Gln3212Ter)

HGVS:

NC_000008.11:g.99835216C>T
NG_007098.2:g.826951C>T
NM_017890.4:c.9709C>T
NM_017890.5:c.9709C>T
NM_152564.5:c.9634C>TMANE SELECT
NP_060360.3:p.Gln3237Ter
NP_689777.3:p.Gln3212Ter
LRG_351t1:c.9709C>T
LRG_351:g.826951C>T
NC_000008.10:g.100847444C>T
NM_017890.3:c.9709C>T

Protein change:

Q3212*

Links:

dbSNP: rs1563499381

NCBI 1000 Genomes Browser:

rs1563499381

Molecular consequence:

NM_017890.5:c.9709C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_152564.5:c.9634C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000890161	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Jul 11, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000890161

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Jul 11, 2018)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000890161.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The Q3237X variant in the VPS13B gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The Q3237X variant is not observed in large population cohorts (Lek et al., 2016). We interpret Q3237X as a pathogenic variant.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 7, 2025

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