NM_152564.5(VPS13B):c.11832dup (p.Ser3945fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: May 15, 2015
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:: RCV000058889.2

Allele description [Variation Report for NM_152564.5(VPS13B):c.11832dup (p.Ser3945fs)]

NM_152564.5(VPS13B):c.11832dup (p.Ser3945fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

8q22.2

Genomic location:

Preferred name:

NM_152564.5(VPS13B):c.11832dup (p.Ser3945fs)

HGVS:

NC_000008.11:g.99875504dup
NG_007098.2:g.867239dup
NM_017890.5:c.11907dup
NM_152564.5:c.11832dupMANE SELECT
NP_060360.3:p.Ser3970fs
NP_689777.3:p.Ser3945fs
LRG_351t1:c.11907_11908insC
LRG_351:g.867239dup
NC_000008.10:g.100887727_100887728insC
NC_000008.10:g.100887732dup
NM_017890.3:c.11907dupC
NM_017890.4:c.11907_11908insC
NM_017890.4:c.11907dupC
p.Ser3970GlnfsX22

Protein change:

S3945fs

Links:

dbSNP: rs180177374

NCBI 1000 Genomes Browser:

rs180177374

Molecular consequence:

NM_017890.5:c.11907dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_152564.5:c.11832dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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S41 family peptidase [Caldicellulosiruptor naganoensis]
S41 family peptidase [Caldicellulosiruptor naganoensis]
gi|2414069177|gnl|extdb|OTJ99_00091 WAM32376.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000090410	SNPedia	no assertion criteria provided	pathogenic	germline	not provided	PubMed (1) [See all records that cite this PMID]
SCV000329309	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (May 15, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000090410

SNPedia

no assertion criteria provided

pathogenic

germline

not provided

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

SCV000329309

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(May 15, 2015)

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
not provided	germline	not provided	not provided	not provided	not provided	1	not provided	literature only

Citations

PubMed

Mutational spectrum of COH1 and clinical heterogeneity in Cohen syndrome.

Seifert W, Holder-Espinasse M, Spranger S, Hoeltzenbein M, Rossier E, Dollfus H, Lacombe D, Verloes A, Chrzanowska KH, Maegawa GH, Chitayat D, Kotzot D, Huhle D, Meinecke P, Albrecht B, Mathijssen I, Leheup B, Raile K, Hennies HC, Horn D.

J Med Genet. 2006 May;43(5):e22.

PubMed [citation]

PMID:: 16648375
PMCID:: PMC2564527

Details of each submission

From SNPedia, SCV000090410.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	PubMed (1)

Description

Converted during submission to Pathogenic.

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

From GeneDx, SCV000329309.5

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

Description

The c.11907dupC pathogenic variant in the VPS13B gene has been reported previously in association with Cohen syndrome (Kolehmainen et al., 2004; Seifert et al., 2006). The c.11907dupC variant causes a frameshift starting with codon Serine 3970, changes this amino acid to a Glutamine residue, and creates a premature Stop codon at position 22 of the new reading frame, denoted p.Ser3970GlnfsX22. This variant is predicted to cause loss of normal protein function through protein truncation. Furthermore, c.11907dupC was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret c.11907dupC 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: Sep 29, 2024

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