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Intellectual disability

Gene: VIPAS39

Amber List (moderate evidence)
VIPAS39 (VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog)
EnsemblGeneIds (GRCh38): ENSG00000151445
EnsemblGeneIds (GRCh37): ENSG00000151445
OMIM: 613401, Gene2Phenotype
VIPAS39 is in 17 panels

4 reviews

Arina Puzriakova (Genomics England Curator)

I don't know

Comment on publications: PMID: 39736737 was identified by the Genomics England Applied Machine Learning (ML) team in a Biocuration-ML project for identifying new gene-disease associations using Natural Language Processing (NLP) and Generative AI techniques.
Created: 27 Mar 2025, 12:13 p.m. | Last Modified: 27 Mar 2025, 12:13 p.m.
Panel Version: 8.227
PMID: 39736737 (2024) - two sisters with compound heterozygous variants in VIPAS39 (c.762G>A and c.1064_1082delinsAGTG) presented with severe or profound intellectual disability as part of ARC syndrome. Both patients exhibited global developmental delay and intellectual disability, along with other features of ARC syndrome. The study also reviewed 8 other reported cases of VIPAS39-related ARC, finding intellectual disability in 6/10 patients.

Review of references of the 4 cases reported in other publications showed: 1 had 'mental retardation' (PMID: 35151346), 3 had global developmental delay (PMID: 26019847) (patient II in Table 2 of PMID:39736737 is indicated to have ID but this was not confirmed by the primary source (PMID: 37202112))

Overall, ID is not a consistent feature and not severe enough in most cases to justify inclusion on this panel. Patients are more likely to be picked up via other panels for which this gene is Green. Therefore maintaining the current Amber rating on ID panel.
Created: 27 Mar 2025, 12:12 p.m. | Last Modified: 27 Mar 2025, 12:12 p.m.
Panel Version: 8.226

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Arthrogryposis, renal dysfunction, and cholestasis 2, OMIM:613404

Publications

Created: 27 Mar 2025, 12:12 p.m.
Last Modified: 27 Mar 2025, 12:12 p.m.
Panel version: 8.226

Helen Brittain (Genomics England Curator)

Comment when marking as ready: Unlikely to present primarily as ID. Gene causes Arthrogryposis, renal dysfunction and cholestasis.
Created: 21 Dec 2017, 2:54 p.m.
Comment on list classification: Unlikely to present primarily as ID. Gene causes Arthrogryposis, renal dysfunction and cholestasis.
Created: 21 Dec 2017, 2:54 p.m.
Created: 21 Dec 2017, 2:54 p.m.

Panel version: Imported from Intellectual disability update Dec 2017 panel version 0.105

BRIDGE consortium (NIHRBR-RD)

Green List (high evidence)

This is a pertinent gene from the NIHR BioResource - Rare Diseases Study (NIHRBR-RD) BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene is on the SPEED_NEURO_20170705 gene list. Evidences used for SPEED NEURO gene list: in_ddg2p_20141118_conf;in_ddg2p_20141118_conf;in_ddg2p_201507;in_ddg2p_201507_conf;in_ddg2p_2_4_2017;in_ddg2p_2_4_2017_conf . Main mutation mechanism : Loss of function
Created: 27 Jul 2017, 8:52 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; neuro_20160418_strict; Loss of function. This is a pertinent gene from the BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene comes from the SPEED_NEURO_v3.0_20170404 gene list. The following experts from the BRIDGE consortium NIHRBR-RD contributed to this panel: - Professor F. Lucy Raymond, Cambridge Institute for Medical Research, University of Cambridge - Manju Kurian, Paediatric neurologist, Great Ormond Street Hosptial - Keren Carss, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Alba Sanchis-Juan, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Marie Erwood NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Louise Daugherty, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust
Created: 19 Jul 2017, 1:40 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

Created: 2 Aug 2017, 11:24 p.m.

Panel version: 1.354

Louise Daugherty (Genomics England Curator)

Comment on list classification: This gene is from an expert list and needs further assessment by the Genomics England curation team to assess inclusion and pertinence to this panel.
Created: 20 Jul 2017, 2:17 p.m.
Created: 20 Jul 2017, 2:17 p.m.

Panel version: 1.245

History Filter Activity

27 Mar 2025, Gel status: 2

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: VIPAS39 were set to

27 Mar 2025, Gel status: 2

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: VIPAS39 were changed from Gene2Phenotype confirmed gene with ID HPO to Arthrogryposis, renal dysfunction, and cholestasis 2, OMIM:613404

12 Mar 2018, Gel status: 2

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

20 Jul 2017, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

19 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

VIPAS39 was created by BRIDGE

19 Jul 2017, Gel status: 0

Added New Source

BRIDGE consortium (NIHRBR-RD)

VIPAS39 was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene