NM_018668.5(VPS33B):c.1509dup (p.Lys504fs) AND Cholestasis, progressive familial intrahepatic, 12

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 18, 2022
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV002276993.1

Allele description [Variation Report for NM_018668.5(VPS33B):c.1509dup (p.Lys504fs)]

NM_018668.5(VPS33B):c.1509dup (p.Lys504fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

15q26.1

Genomic location:

Preferred name:

NM_018668.5(VPS33B):c.1509dup (p.Lys504fs)

HGVS:

NC_000015.10:g.91000562dup
NG_012162.1:g.27042dup
NM_001289148.1:c.1428dup
NM_001289149.1:c.1236dup
NM_018668.5:c.1509dupMANE SELECT
NP_001276077.1:p.Lys477fs
NP_001276078.1:p.Lys413fs
NP_061138.3:p.Lys504fs
LRG_884:g.27042dup
NC_000015.9:g.91543792dup
NM_018668.4:c.109dupG

Protein change:

K413fs

Links:

OMIM: 608552.0012; dbSNP: rs1209349503

NCBI 1000 Genomes Browser:

rs1209349503

Molecular consequence:

NM_001289148.1:c.1428dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001289149.1:c.1236dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_018668.5:c.1509dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Cholestasis, progressive familial intrahepatic, 12 (PFIC12)
Synonyms:: CHOLESTASIS, ISOLATED LOW-GGT
Identifiers:: MONDO: MONDO:0031040; MedGen: C5774311; OMIM: 620010

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002564418	OMIM	no assertion criteria provided	Pathogenic (Aug 18, 2022)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002564418

OMIM

no assertion criteria provided

Pathogenic
(Aug 18, 2022)

germline

literature only

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	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Novel missense mutation in VPS33B is associated with isolated low gamma-glutamyltransferase cholestasis: Attenuated, incomplete phenotype of arthrogryposis, renal dysfunction, and cholestasis syndrome.

Qiu YL, Liu T, Abuduxikuer K, Hao CZ, Gong JY, Zhang MH, Li LT, Yan YY, Li JQ, Wang JS.

Hum Mutat. 2019 Dec;40(12):2247-2257. doi: 10.1002/humu.23770. Epub 2019 Sep 3.

PubMed [citation]

PMID:: 31479177

Details of each submission

From OMIM, SCV002564418.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

Progressive Familial Intrahepatic Cholestasis 12

For discussion of the 1-bp duplication (c.109dupG, NM_018668.4) in the VPS33B gene, causing a frameshift predicted to result in a premature termination codon (Lys504GlufsTer), that was found in compound heterozygous state in a Chinese brother (P2) and sister (P3) with isolated cholestasis (PFIC12; 610010) by Qiu et al. (2019), see 608552.0011.

Arthrogryposis, Renal Dysfunction, and Cholestasis 1

In a Chinese female infant (P4) who died at the age of 6 months with arthrogryposis, renal dysfunction, and cholestasis-1 (ARCS1; 208085), Qiu et al. (2019) identified compound heterozygosity for the c.109dupG mutation and a splice site mutation (c.403+2T-A; 608552.0013).

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

Last Updated: Dec 24, 2023

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