Nephrocalcinosis or nephrolithiasis
Gene: VIPAS39EnsemblGeneIds (GRCh38): ENSG00000151445
EnsemblGeneIds (GRCh37): ENSG00000151445
OMIM: 613401, Gene2Phenotype
VIPAS39 is in 17 panels
3 reviews
Eleanor Williams (Genomics England Curator)
The rating of this gene has been updated following NHS Genomic Medicine Service approval. The reviewers note that this is a key gene for ARC. >10 cases on HGMD for ARC (OMIM 208085) phenotype which has association with Nephrocalcinosis.Created: 7 Mar 2022, 11:09 p.m. | Last Modified: 7 Mar 2022, 11:09 p.m.
Panel Version: 2.27
Arina Puzriakova (Genomics England Curator)
Comment on list classification: Changed rating from Green to Amber so that Green genes on this panel reflect the NHS signed-off version. This will be reviewed at the next GMS panel update (added 'for-review' tag).Created: 20 Oct 2020, 3:33 p.m. | Last Modified: 20 Oct 2020, 3:33 p.m.
Panel Version: 2.16
Rebecca Foulger (Genomics England curator)
PMID:20190753 (Cullinane et al., 2010) identify biallelic (homozygous or compound het) variants in 7 probands from consanguineous families with ARC (MIM:613404) from various ethnic backgrounds (Turkish, Croation, Israeli Arab, Italian). Variants include Q179X, T250ArgfsX279, R220X, Q291X, M1R. The paper does not further discuss the kidney phenotype.Created: 21 Apr 2020, 3:50 p.m. | Last Modified: 21 Apr 2020, 3:50 p.m.
Panel Version: 2.10
Added to panel as Green following advice from Helen Brittain, Genomics England Clinical Team. Nephrocalcinosis is a feature of the phenotype. Other syndromes are on this panel (Lesch-Nyhan and Lowe syndrome) as Green, and therefore rated Green to match. This rating should be reviewed by GLHs at the date of next GMS panel update.
Sources: LiteratureCreated: 21 Apr 2020, 3:49 p.m.
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
Arthrogryposis, renal dysfunction, and cholestasis 2, 613404
Publications
Details
- Mode of Inheritance
- BIALLELIC, autosomal or pseudoautosomal
- Sources
-
- Expert Review Green
- Literature
- Phenotypes
-
- Arthrogryposis, renal dysfunction, and cholestasis 2, OMIM:613404
- OMIM
- 613401
- Clinvar variants
- Variants in VIPAS39
- Penetrance
- None
- Publications
- Panels with this gene
-
- Arthrogryposis
- Inherited bleeding disorders
- Neonatal cholestasis
- Fetal anomalies
- Proteinuric renal disease
- Undiagnosed metabolic disorders
- Childhood onset dystonia, chorea or related movement disorder
- CAKUT
- Nephrocalcinosis or nephrolithiasis
- Cholestasis
- Unexplained kidney failure in young people
- Bleeding and platelet disorders
- DDG2P
- Renal tubulopathies
- Intellectual disability
- Likely inborn error of metabolism
- Ichthyosis and erythrokeratoderma
History Filter Activity
Set Phenotypes
Eleanor Williams (Genomics England Curator)Phenotypes for gene: VIPAS39 were changed from Arthrogryposis, renal dysfunction, and cholestasis 2, 613404 to Arthrogryposis, renal dysfunction, and cholestasis 2, OMIM:613404
Removed Tag
Eleanor Williams (Genomics England Curator)Tag for-review was removed from gene: VIPAS39.
Added New Source, Status Update
Eleanor Williams (Genomics England Curator)Source Expert Review Green was added to VIPAS39. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
Entity classified by Genomics England curator
Arina Puzriakova (Genomics England Curator)Gene: vipas39 has been classified as Amber List (Moderate Evidence).
Added Tag
Arina Puzriakova (Genomics England Curator)Tag for-review tag was added to gene: VIPAS39.
Entity classified by Genomics England curator
Rebecca Foulger (Genomics England curator)Gene: vipas39 has been classified as Green List (High Evidence).
Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes
Rebecca Foulger (Genomics England curator)gene: VIPAS39 was added gene: VIPAS39 was added to Nephrocalcinosis or nephrolithiasis. Sources: Literature Mode of inheritance for gene: VIPAS39 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: VIPAS39 were set to 20190753 Phenotypes for gene: VIPAS39 were set to Arthrogryposis, renal dysfunction, and cholestasis 2, 613404