NM_001032221.6(STXBP1):c.36G>C (p.Glu12Asp) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 27, 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:: RCV000189628.3

Allele description [Variation Report for NM_001032221.6(STXBP1):c.36G>C (p.Glu12Asp)]

NM_001032221.6(STXBP1):c.36G>C (p.Glu12Asp)

Genes:

LOC130002651:ATAC-STARR-seq lymphoblastoid silent region 20307 [Gene]
STXBP1:syntaxin binding protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.11

Genomic location:

Preferred name:

NM_001032221.6(STXBP1):c.36G>C (p.Glu12Asp)

Other names:

p.E12D:GAG>GAC

HGVS:

NC_000009.12:g.127612439G>C
NG_016623.1:g.5233G>C
NM_001032221.6:c.36G>CMANE SELECT
NM_001374306.2:c.36G>C
NM_001374307.2:c.-102G>C
NM_001374308.2:c.-197G>C
NM_001374309.2:c.-6+392G>C
NM_001374310.2:c.-197G>C
NM_001374311.2:c.-102G>C
NM_001374312.2:c.-109G>C
NM_001374313.2:c.36G>C
NM_001374314.1:c.36G>C
NM_001374315.2:c.36G>C
NM_003165.6:c.36G>C
NP_001027392.1:p.Glu12Asp
NP_001361235.1:p.Glu12Asp
NP_001361242.1:p.Glu12Asp
NP_001361243.1:p.Glu12Asp
NP_001361244.1:p.Glu12Asp
NP_003156.1:p.Glu12Asp
NC_000009.11:g.130374718G>C
NM_003165.2:c.36G>C
NM_003165.3:c.36G>C

Protein change:

E12D

Links:

dbSNP: rs796053378

NCBI 1000 Genomes Browser:

rs796053378

Molecular consequence:

NM_001374307.2:c.-102G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374308.2:c.-197G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374310.2:c.-197G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374311.2:c.-102G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374312.2:c.-109G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001374309.2:c.-6+392G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001032221.6:c.36G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374306.2:c.36G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374313.2:c.36G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374314.1:c.36G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001374315.2:c.36G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003165.6:c.36G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Fistularia commersonii mitochondrial gene for 12S rRNA, partial sequence, specim...
Fistularia commersonii mitochondrial gene for 12S rRNA, partial sequence, specimen_voucher: OCF(Okinawa Churashima Foundation)-P20140421-8
gi|906357734|dbj|AB974594.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000243273	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Oct 27, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000243273

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Oct 27, 2017)

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, SCV000243273.11

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

Description

p.Glu12Asp (GAG>GAC):c.36 G>C in exon 1 of the STXBP1 gene (NM_003165.2)The Glu12Asp missense change has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. The NHLBI ESP Exome Variant Project has not identified Glu12Asp in approximately 6,500 individuals of European or African American ethnicity, indicating that it is not a common benign variant in these populations. The amino acid substitution is conservative as both Glutamic acid and Aspartic acid are negatively charged, polar amino acid residues. Glu12Asp alters a conserved position in the STXBP1 protein. However, while several in silico algorithms predict Glu12Asp may be benign, another model predicts it is damaging to the structure/function of the protein. Therefore, based on the currently available information, it is unclear whether Glu12Asp is a disease-causing mutation or a rare benign variant. The variant is found in EPILEPSY panel(s).

#	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: Feb 28, 2024

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