NM_001122955.4(BSCL2):c.455A>G (p.Asn152Ser) AND not provided

Germline classification:: Pathogenic (7 submissions)
Last evaluated:: May 29, 2023
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:: RCV000340485.35

Allele description [Variation Report for NM_001122955.4(BSCL2):c.455A>G (p.Asn152Ser)]

NM_001122955.4(BSCL2):c.455A>G (p.Asn152Ser)

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.455A>G (p.Asn152Ser)

Other names:

NM_001122955.3(BSCL2):c.455A>G(p.Asn152Ser); NM_001130702.2(BSCL2):c.263A>G(p.Asn88Ser); NM_032667.6(BSCL2):c.263A>G(p.Asn88Ser)

HGVS:

NC_000011.10:g.62702499T>C
NG_008461.1:g.12076A>G
NM_001122955.4:c.455A>GMANE SELECT
NM_001130702.2:c.263A>G
NM_001386027.1:c.455A>G
NM_001386028.1:c.455A>G
NM_032667.6:c.263A>G
NP_001116427.1:p.Asn152Ser
NP_001116427.1:p.Asn152Ser
NP_001124174.2:p.Asn88Ser
NP_001372956.1:p.Asn152Ser
NP_001372957.1:p.Asn152Ser
NP_116056.3:p.Asn88Ser
LRG_235t1:c.455A>G
LRG_235t2:c.263A>G
LRG_235:g.12076A>G
LRG_235p1:p.Asn152Ser
LRG_235p2:p.Asn88Ser
NC_000011.9:g.62469971T>C
NM_001122955.2:c.455A>G
NM_001122955.3:c.455A>G
NM_001122955.4:c.455A>G
NM_032667.5:c.263A>G
NR_037946.1:n.2975A>G
Q96G97:p.Asn88Ser

Protein change:

N152S; ASN88SER

Links:

UniProtKB: Q96G97#VAR_022375; OMIM: 606158.0013; dbSNP: rs137852972

NCBI 1000 Genomes Browser:

rs137852972

Molecular consequence:

NM_001122955.4:c.455A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001130702.2:c.263A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001386027.1:c.455A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001386028.1:c.455A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_032667.6:c.263A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_037946.1:n.2975A>G - 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
SCV000329928	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (May 29, 2023)	germline	clinical testing	Citation Link,
SCV000612493	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Pathogenic (Aug 17, 2015)	germline	clinical testing	PubMed (16) [See all records that cite these PMIDs] 16574104, 22474068, 14981520, 23553728, 21957196, 17387721, 22045697, 18585921, 25219579, 25454168, 16427281, 24345054, 21750110, 19396477, 20598714, 26467025
SCV001247774	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Mar 1, 2023)	germline	clinical testing	Citation Link,
SCV001446866	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 23, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001919334	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001928302	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV005196957	Clinical Genetics Laboratory, Skane University Hospital Lund	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 9, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	6	not provided	not provided	1	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Membrane topology of the human seipin protein.

Lundin C, Nordström R, Wagner K, Windpassinger C, Andersson H, von Heijne G, Nilsson I.

FEBS Lett. 2006 Apr 17;580(9):2281-4. Epub 2006 Mar 27.

PubMed [citation]

PMID:: 16574104

Seipin: from human disease to molecular mechanism.

Cartwright BR, Goodman JM.

J Lipid Res. 2012 Jun;53(6):1042-55. doi: 10.1194/jlr.R023754. Epub 2012 Apr 2. Review.

PubMed [citation]

PMID:: 22474068
PMCID:: PMC3351812

See all PubMed Citations (17)

Details of each submission

From GeneDx, SCV000329928.6

#	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 protein over-expression and impairment of synaptic neurotransmission (Windpassinger et al., 2004; Wei et al., 2014); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 17387721, 21750110, 22045697, 21957196, 18585921, 14981520, 18612770, 24345054, 16427281, 23553728, 19396477, 31589614, 31211173, 27549087, 29269637, 25219579, 27738760, 25454168, 20598714, 34085946, 32320108, 15732094)

#	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 Athena Diagnostics, SCV000612493.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (16)

#	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		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV001247774.26

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	6	not provided	not provided	clinical testing	not provided

Description

BSCL2: PP1:Strong, PM2, PS4:Moderate, PP4, PS3:Supporting

#	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		6	not provided	not provided	not provided

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001446866.1

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

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

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001919334.1

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

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001928302.1

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

From Clinical Genetics Laboratory, Skane University Hospital Lund, SCV005196957.1

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

#	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 20, 2024

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