NM_014231.5(VAMP1):c.340del (p.Ile114fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 27, 2023
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:: RCV001549899.3

Allele description [Variation Report for NM_014231.5(VAMP1):c.340del (p.Ile114fs)]

NM_014231.5(VAMP1):c.340del (p.Ile114fs)

Genes:

TAPBPL:TAP binding protein like [Gene - OMIM - HGNC]
VAMP1:vesicle associated membrane protein 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12p13.31

Genomic location:

Preferred name:

NM_014231.5(VAMP1):c.340del (p.Ile114fs)

HGVS:

NC_000012.12:g.6464891del
NG_042188.2:g.11010del
NM_001297438.2:c.340del
NM_014231.5:c.340delMANE SELECT
NM_016830.4:c.340del
NM_199245.3:c.340del
NP_001284367.1:p.Arg114fs
NP_055046.1:p.Ile114fs
NP_058439.1:p.Arg114fs
NP_954740.1:p.Ser114fs
NC_000012.11:g.6574057del
NG_042188.1:g.11010del
NM_014231.3:c.340del
NM_014231.3:c.340delA
NM_014231.4:c.340del
NM_014231.5:c.340delAMANE SELECT
NR_123717.2:n.359del

Protein change:

I114fs

Links:

OMIM: 185880.0002; dbSNP: rs746220436

NCBI 1000 Genomes Browser:

rs746220436

Molecular consequence:

NM_001297438.2:c.340del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_014231.5:c.340del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_016830.4:c.340del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_199245.3:c.340del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_123717.2:n.359del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001770135	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Jul 27, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001770135

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Jul 27, 2023)

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, SCV001770135.2

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

Description

Published functional studies demonstrate a damaging effect with inhibition of depolarization-evoked exocytosis (Shen et al., 2017); Frameshift variant predicted to result in protein truncation as the last 5 amino acids are replaced with 71 different amino acids, although loss-of-function variants have not been reported downstream of this position in the protein; This variant is associated with the following publications: (PMID: 28168212, 32616363)

#	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: Oct 26, 2024

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