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Intellectual disability

Gene: HAX1

Amber List (moderate evidence)

HAX1 (HCLS1 associated protein X-1)
EnsemblGeneIds (GRCh38): ENSG00000143575
EnsemblGeneIds (GRCh37): ENSG00000143575
OMIM: 605998, Gene2Phenotype
HAX1 is in 10 panels

6 reviews

Louise Daugherty (Genomics England Curator)

Comment on publications: Added publications from Sarah Leigh (Genomics England), 5 Mar 2018 review
Created: 14 Mar 2018, 12:52 p.m.

Helen Brittain (Genomics England Curator)

Comment when marking as ready: Majority have not had ID, further evidence needed as to frequency of ID / seizures and perhaps mutational spectrum.
Created: 8 Mar 2018, 2:15 p.m.
Comment on list classification: To date, a minority of cases have had ID or seizures, although there is some evidence emerging about the possibility of alternative transcripts. At present all cases have presented with severe congenital neutropaenia and infectious complications and would therefore be expected to present in this manner. Therefore there is a question regarding the clinical utility in isolated ID / seizure presentation
Created: 8 Mar 2018, 2:14 p.m.

Sarah Leigh (Genomics England Curator)

Associated with phenotype in OMIM and as a confirmed G2P association. At least 8 variants have been reported in Neutropenia, severe congenital 3, autosomal recessive (610738), three of these were Japanese cases carrying with p.Arg86* who also displayed mental retardation (PMID18611981).

Reported as a gene linked to isolated ID and associated disorders (Vissers 2016 PMID 26503795) and as an ID candidate gene (Gilessen 2014 PMID 24896178).
Created: 6 Mar 2018, 7:11 p.m.

Caroline Wright (Sanger)

Red List (low evidence)

Phenotypes
NEUTROPENIA, SEVERE CONGENITAL 3, AUTOSOMAL RECESSIVE

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;in_gilissen_2014_known . Main mutation mechanism : Loss of function
Created: 27 Jul 2017, 6:31 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; gilissen_2014_known; Nijmegen_ID_diagnostic; Nijmegen_ID_candidates; GEL_ID_red_20160217; 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, 12:35 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

Lu Raymond (university of cambridge )

Red List (low evidence)

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Victorian Clinical Genetics Services
  • Expert Review Amber
  • Expert Review Red
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Neutropenia, severe congenital 3, autosomal recessive, 610738
Tags
watchlist
OMIM
605998
Clinvar variants
Variants in HAX1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

28 Sep 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to HAX1.

14 Mar 2018, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for HAX1 were set to Neutropenia, severe congenital 3, autosomal recessive, 610738

14 Mar 2018, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for HAX1 were set to 18611981; 24896178; 26503795; 25529582

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.

12 Mar 2018, Gel status: 2

Added New Source, Set mode of inheritance

Ellen McDonagh (Genomics England Curator)

Expert Review Amber was added to HAX1. Panel: Intellectual disability Model of inheritance for gene HAX1 was set to BIALLELIC, autosomal or pseudoautosomal

13 Nov 2015, Gel status: 1

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 2

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

HAX1 was added to Intellectual disabilitypanel. Source: Expert Review Red

24 Jun 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

HAX1 was added to Intellectual disabilitypanel. Sources: Radboud University Medical Center, Nijmegen