NM_018668.5(VPS33B):c.1540G>A (p.Gly514Ser) AND Arthrogryposis, renal dysfunction, and cholestasis 1

Germline classification:: Benign (3 submissions)
Last evaluated:: Dec 5, 2021
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:: RCV000989400.6

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)

Name:: Arthrogryposis, renal dysfunction, and cholestasis 1 (ARCS1)
Identifiers:: MONDO: MONDO:0008822; MedGen: C1859722; Orphanet: 2697; OMIM: 208085

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
SCV000394445	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Jan 12, 2018)	germline	clinical testing	Citation Link,
SCV001139718	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Benign (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV002514508	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Dec 5, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000394445

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Jan 12, 2018)

germline

clinical testing

Citation Link,

SCV001139718

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Benign
(May 28, 2019)

unknown

clinical testing

Citation Link,

SCV002514508

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Dec 5, 2021)

germline

clinical testing

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

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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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical 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 Illumina Laboratory Services, Illumina, SCV000394445.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#	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 Mendelics, SCV001139718.1

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

From Genome-Nilou Lab, SCV002514508.1

#	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	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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