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NM_018668.5(VPS33B):c.1602G>A (p.Trp534Ter) AND Arthrogryposis, renal dysfunction, and cholestasis 1

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 22, 2022
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:
RCV002052230.1

Allele description [Variation Report for NM_018668.5(VPS33B):c.1602G>A (p.Trp534Ter)]

NM_018668.5(VPS33B):c.1602G>A (p.Trp534Ter)

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.1602G>A (p.Trp534Ter)
HGVS:
  • NC_000015.10:g.90999955C>T
  • NG_012162.1:g.27649G>A
  • NM_001289148.1:c.1521G>A
  • NM_001289149.1:c.1329G>A
  • NM_018668.5:c.1602G>AMANE SELECT
  • NP_001276077.1:p.Trp507Ter
  • NP_001276078.1:p.Trp443Ter
  • NP_061138.3:p.Trp534Ter
  • LRG_884:g.27649G>A
  • NC_000015.9:g.91543185C>T
Protein change:
W443*
Links:
dbSNP: rs2151662496
NCBI 1000 Genomes Browser:
rs2151662496
Molecular consequence:
  • NM_001289148.1:c.1521G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001289149.1:c.1329G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_018668.5:c.1602G>A - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0023188123billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Mar 22, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical 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 3billion, SCV002318812.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

Stop-gained (nonsense): predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant.It is not observed in the gnomAD v2.1.1 dataset. Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Dec 24, 2023