NM_001122955.4(BSCL2):c.409G>A (p.Asp137Asn) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jan 23, 2017
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000727086.5

Allele description [Variation Report for NM_001122955.4(BSCL2):c.409G>A (p.Asp137Asn)]

NM_001122955.4(BSCL2):c.409G>A (p.Asp137Asn)

Genes:

BSCL2:BSCL2 lipid droplet biogenesis associated, seipin [Gene - OMIM - HGNC]
HNRNPUL2-BSCL2:HNRNPUL2-BSCL2 readthrough (NMD candidate) [Gene - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q12.3

Genomic location:

Preferred name:

NM_001122955.4(BSCL2):c.409G>A (p.Asp137Asn)

HGVS:

NC_000011.10:g.62702545C>T
NG_008461.1:g.12030G>A
NM_001122955.4:c.409G>AMANE SELECT
NM_001130702.2:c.217G>A
NM_001386027.1:c.409G>A
NM_001386028.1:c.409G>A
NM_032667.6:c.217G>A
NP_001116427.1:p.Asp137Asn
NP_001124174.2:p.Asp73Asn
NP_001372956.1:p.Asp137Asn
NP_001372957.1:p.Asp137Asn
NP_116056.3:p.Asp73Asn
LRG_235t2:c.217G>A
LRG_235:g.12030G>A
LRG_235p2:p.Asp73Asn
NC_000011.9:g.62470017C>T
NR_037946.1:n.2929G>A

Protein change:

D137N

Links:

dbSNP: rs879253900

NCBI 1000 Genomes Browser:

rs879253900

Molecular consequence:

NM_001122955.4:c.409G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001130702.2:c.217G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386027.1:c.409G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001386028.1:c.409G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_032667.6:c.217G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_037946.1:n.2929G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

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
SCV000292730	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Jan 21, 2016)	germline	clinical testing	Citation Link,
SCV000705510	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (Jan 23, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000292730

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Jan 21, 2016)

germline

clinical testing

Citation Link,

SCV000705510

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Uncertain significance
(Jan 23, 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
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000292730.10

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

Description

The D73N variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. It 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. The D73N variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved in mammals; however, Asparagine is observed at this position in one species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign 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

From Eurofins Ntd Llc (ga), SCV000705510.2

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

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

Last Updated: Feb 20, 2024

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