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Intellectual disability

Gene: EFNB1

Amber List (moderate evidence)
EFNB1 (ephrin B1)
EnsemblGeneIds (GRCh38): ENSG00000090776
EnsemblGeneIds (GRCh37): ENSG00000090776
OMIM: 300035, Gene2Phenotype
EFNB1 is in 8 panels

4 reviews

Arina Puzriakova (Genomics England Curator)

I don't know

Comment on list classification: Upgrading from Red to Amber as a literature search did reveal evidence to suggest that some individuals may develop intellectual deficits. However, in most affected cases this was a mild presentation and there are more prominent and recognisable features observed in the general group of EFNB1-related cases which are more likely to inform diagnostic testing (e.g. craniosynostosis and clefting).
Created: 29 Feb 2024, 4:41 p.m. | Last Modified: 29 Feb 2024, 4:41 p.m.
Panel Version: 5.474
Comment on publications: PMID: 25679214 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: 29 Feb 2024, 2:28 p.m. | Last Modified: 29 Feb 2024, 2:28 p.m.
Panel Version: 5.473
This gene causes craniofrontonasal syndrome (CFNS) - a predominantly craniosynostosis phenotype with various limb features. Cognitive function is usually unaffected; however, some cases have been observed:

- PMID: 23335590 (2013) - describes six males with CFNS due to mosaic EFNB1 variants. Mild learning disability was reported for 5/6.

- PMID: 25679214 (2015) - EFNB1 variant (p.G290R) was found in an individual from a X-linked Intellectual Disability cohort. Limited information so it is unclear if this patient had additional features of CFNS.

- PMID: 27650623 (2016) - one patient with a c.451G>A (p.Gly151Ser) variant in EFNB1 showed borderline intellectual functioning (IQ = 76) along with other typical features such as unilateral coronal synostosis, cleft palate, and septate uterus. On the other hand, the other patient described in this paper had normal developmental milestones.

- PMID: 31088393 (2019) - a de novo heterozygous variant c.640C > T; p.(Gln214Ter) in EFNB1 was detected in a girl with severe ID, typical facial dysmorphia, ocular anomalies, short fifth finger, cerebellar vermis dysplasia and fourth ventricle deformity.

- PMID: 24520368 (2014) - EphrinB1 deficient mouse model of CFNS shows cortical abnormalities and impaired non-spatial learning and memory tasks
Created: 29 Feb 2024, 2:27 p.m. | Last Modified: 29 Feb 2024, 2:27 p.m.
Panel Version: 5.472

Mode of inheritance
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)

Phenotypes
Craniofrontonasal dysplasia, OMIM:304110

Publications

Created: 29 Feb 2024, 2:27 p.m.
Last Modified: 29 Feb 2024, 2:27 p.m.
Panel version: 5.472

Helen Brittain (Genomics England Curator)

Comment when marking as ready: Normal intellect expected.
Created: 19 Dec 2017, 3:09 p.m.
Comment on list classification: Normal intellect is expected in Craniofrontonasal syndrome.
Created: 19 Dec 2017, 3:08 p.m.
Created: 19 Dec 2017, 3:08 p.m.

Panel version: Imported from Intellectual disability update Dec 2017 panel version 0.53

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_UKGTN_v12 . Main mutation mechanism : Loss of function
Created: 27 Jul 2017, 5:37 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; UKGTN_v12; 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, 12:20 p.m.

Mode of inheritance
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)

Publications

Created: 2 Aug 2017, 5:08 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, 11:44 a.m.
Created: 20 Jul 2017, 11:44 a.m.

Panel version: 1.195

Details

Mode of Inheritance
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Sources
  • Expert Review Amber
  • Victorian Clinical Genetics Services
Phenotypes
  • Craniofrontonasal dysplasia, OMIM:304110
OMIM
300035
Clinvar variants
Variants in EFNB1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

29 Feb 2024, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: efnb1 has been classified as Amber List (Moderate Evidence).

29 Feb 2024, Gel status: 1

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: EFNB1 were set to 23335590

28 Feb 2024, Gel status: 1

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: EFNB1 were changed from Gene2Phenotype confirmed gene with ID HPO to Craniofrontonasal dysplasia, OMIM:304110

28 Feb 2024, Gel status: 1

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: EFNB1 were set to

28 Sep 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to EFNB1.

12 Mar 2018, Gel status: 1

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.

5 Jan 2018, Gel status: 1

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

This gene has been classified as Red List (Low Evidence).

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

Added New Source

BRIDGE consortium (NIHRBR-RD)

EFNB1 was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene

19 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

EFNB1 was created by BRIDGE