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NM_014231.5(VAMP1):c.3-6C>T AND Myasthenic syndrome, congenital, 25, presynaptic

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 2, 2022
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:
RCV002272376.10

Allele description [Variation Report for NM_014231.5(VAMP1):c.3-6C>T]

NM_014231.5(VAMP1):c.3-6C>T

Genes:
TAPBPL:TAP binding protein like [Gene - OMIM - HGNC]
VAMP1:vesicle associated membrane protein 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12p13.31
Genomic location:
Preferred name:
NM_014231.5(VAMP1):c.3-6C>T
HGVS:
  • NC_000012.12:g.6466357G>A
  • NG_042188.2:g.9543C>T
  • NM_001297438.2:c.3-6C>T
  • NM_014231.5:c.3-6C>TMANE SELECT
  • NM_016830.4:c.3-6C>T
  • NM_199245.3:c.3-6C>T
  • NC_000012.11:g.6575523G>A
  • NC_000012.11:g.6575523G>A
  • NG_042188.1:g.9543C>T
  • NM_014231.3:c.3-6C>T
  • NM_014231.4:c.3-6C>T
Links:
dbSNP: rs749846681
NCBI 1000 Genomes Browser:
rs749846681
Molecular consequence:
  • NM_001297438.2:c.3-6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_014231.5:c.3-6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_016830.4:c.3-6C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_199245.3:c.3-6C>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Myasthenic syndrome, congenital, 25, presynaptic
Synonyms:
Myasthenic syndrome, congenital, 25
Identifiers:
MONDO: MONDO:0032675; MedGen: C5193027; OMIM: 618323

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002557640Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Sep 2, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot 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

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002557640.2

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

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3C. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with myasthenic syndrome, congenital (MIM# 618323). (I) 0106 - This gene is associated with autosomal recessive disease. It’s association with autosomal dominant spastic ataxia 1 (MIM#108600) is currently tenuous (PanelApp Australia). (I) 0212 - Non-canonical splice site variant without proven consequence on splicing (no functional evidence available). (SP) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 7 heterozygotes, 0 homozygotes). (SP) 0506 - Abnormal splicing is not predicted however, nucleotide is moderately conserved. (I) 0705 - No comparable splice site variants have previous evidence for pathogenicity. (I) 0806 - This variant has moderate previous evidence of being benign in unrelated individuals. It has been described as likely benign by a diagnostic laboratory in ClinVar. (SB) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

Last Updated: May 19, 2024