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Intellectual disability

Gene: NPHP3

Amber List (moderate evidence)

NPHP3 (nephrocystin 3)
EnsemblGeneIds (GRCh38): ENSG00000113971
EnsemblGeneIds (GRCh37): ENSG00000113971
OMIM: 608002, Gene2Phenotype
NPHP3 is in 26 panels

4 reviews

Arina Puzriakova (Genomics England Curator)

Comment on list classification: Kept rating Amber as affected individuals are more likely to be assessed under renal and ciliopathy panels, for which this gene is already Green.
Created: 28 Oct 2020, 12:52 p.m. | Last Modified: 28 Oct 2020, 12:52 p.m.
Panel Version: 3.493
Variants in NPHP3 cause a variety of phenotypes primarily characterised by renal pathology. Patients may also exhibit other variable features such as CNS malformations which can be associated with intellectual impairment. However, in the context of the wider phenotype it is unlikely that inclusion on the ID panel will be of diagnostic benefit, particularly when applying to a cohort of patients with non-syndromic ID.
Created: 28 Oct 2020, 12:51 p.m. | Last Modified: 28 Oct 2020, 12:51 p.m.
Panel Version: 3.492

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Nephronophthisis 3, 604387; Renal-hepatic-pancreatic dysplasia 1, 208540; Meckel syndrome 7, 267010

Zornitza Stark (Australian Genomics)

Green List (high evidence)

The spectrum of this ciliopathy includes brain malformations.
Created: 5 Mar 2020, 11:42 p.m. | Last Modified: 5 Mar 2020, 11:42 p.m.
Panel Version: 3.3

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Meckel syndrome 7, MIM# 267010

Publications

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, 7:50 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

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 access inclusion and pertinence to this panel.
Created: 28 Jul 2017, 3:01 p.m.

History Filter Activity

28 Oct 2020, Gel status: 2

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: NPHP3 were set to

28 Oct 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: nphp3 has been classified as Amber List (Moderate Evidence).

29 Sep 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to NPHP3.

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.

28 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).

27 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

NPHP3 was created by BRIDGE

27 Jul 2017, Gel status: 0

Added New Source

BRIDGE consortium (NIHRBR-RD)

NPHP3 was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene