NM_018668.5(VPS33B):c.1540G>A (p.Gly514Ser) AND not provided

Germline classification:: Benign (3 submissions)
Last evaluated:: Jan 31, 2024
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:: RCV001709550.7

Allele description [Variation Report for NM_018668.5(VPS33B):c.1540G>A (p.Gly514Ser)]

NM_018668.5(VPS33B):c.1540G>A (p.Gly514Ser)

Gene:

VPS33B:VPS33B late endosome and lysosome associated [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q26.1

Genomic location:

Preferred name:

NM_018668.5(VPS33B):c.1540G>A (p.Gly514Ser)

HGVS:

NC_000015.10:g.91000531C>T
NG_012162.1:g.27073G>A
NM_001289148.1:c.1459G>A
NM_001289149.1:c.1267G>A
NM_018668.5:c.1540G>AMANE SELECT
NP_001276077.1:p.Gly487Ser
NP_001276078.1:p.Gly423Ser
NP_061138.3:p.Gly514Ser
LRG_884:g.27073G>A
NC_000015.9:g.91543761C>T
NM_018668.3:c.1540G>A
Q9H267:p.Gly514Ser

Protein change:

G423S

Links:

UniProtKB: Q9H267#VAR_013828; dbSNP: rs11073964

NCBI 1000 Genomes Browser:

rs11073964

Molecular consequence:

NM_001289148.1:c.1459G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001289149.1:c.1267G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_018668.5:c.1540G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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ORF1 [Rattus sp.]
ORF1 [Rattus sp.]
gi|2462658|emb|CAA63695.1|

Protein
RecName: Full=Beta-secretase 1; AltName: Full=Aspartyl protease 2; Short=ASP2; S...
RecName: Full=Beta-secretase 1; AltName: Full=Aspartyl protease 2; Short=ASP2; Short=Asp 2; AltName: Full=Beta-site amyloid precursor protein cleaving enzyme 1; Short=Beta-site APP cleaving enzyme 1; AltName: Full=Memapsin-2; AltName: Full=Membrane-associated aspartic protease 2; Flags: Precursor
gi|18268203|sp|P56818.2|BACE1_MOUSE

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001937733	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Nov 12, 2018)	germline	clinical testing	Citation Link,
SCV002408372	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 31, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005295520	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001937733

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Nov 12, 2018)

germline

clinical testing

Citation Link,

SCV002408372

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 31, 2024)

germline

clinical testing

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

SCV005295520

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign

germline

not provided

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing, not provided

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

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 GeneDx, SCV001937733.1

#	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002408372.3

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005295520.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	not provided	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: Sep 29, 2024

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