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Intellectual disability

Gene: FGFR1

Red List (low evidence)

FGFR1 (fibroblast growth factor receptor 1)
EnsemblGeneIds (GRCh38): ENSG00000077782
EnsemblGeneIds (GRCh37): ENSG00000077782
OMIM: 136350, Gene2Phenotype
FGFR1 is in 21 panels

7 reviews

Louise Daugherty (Genomics England Curator)

Red List (low evidence)

In view of recent external expert Green review this gene was reaccessed by curation and internal clinical team. It was decided to keep this gene Red on our Intellectual disability (ID) panel. The reason for not promoting this gene to Green: Encephalocraniocutaneous lipomatosis (ECCL) has been identified on testing affected tissue in view of the somatic mosaic nature. The pick up from germline analysis is untested, our current pipeline is not optimised for mosaicism, so it is unlikely to high. In view of the large range of disorders associated with this gene, and ID not being a feature of the majority, there would seem to be a greater chance of extraneous findings wrt this panel than diagnostic findings if it were rated green.
Created: 12 Sep 2018, 2:52 p.m.

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Gene causes several phenotypes but this specific phenotype caused by germline variants is associated with significant ID.
Created: 3 Feb 2020, 2:13 a.m. | Last Modified: 3 Feb 2020, 2:13 a.m.
Panel Version: 3.0
Please note that somatic mutations in this gene cause ECCL, MIM#613001, which is associated with intellectual disability PMID 26942290
Created: 17 Jun 2018, 7:49 p.m.

Mode of inheritance
Other

Phenotypes
Hartsfield syndrome, MIM# 615465

Publications

Variants in this GENE are reported as part of current diagnostic practice

Helen Brittain (Genomics England Curator)

Comment when marking as ready: Causation is clear for Pfeiffer syndrome, Kallman and Osteoglophonic dysplasia. Although ID is a reported feature of Pfeiffer syndrome, it is not universal and the condition would be expected to present in a syndromic manner with craniosynostosis prior to ID. This, along with the fact that it is caused by a recurrent missense variant, means that the utility of calling all variants in this gene in a cohort that includes non-syndromic ID is unlikely to be of benefit.
Created: 21 Dec 2017, 10:20 a.m.
Comment on list classification: Causation is clear for Pfeiffer syndrome, Kallman and Osteoglophonic dysplasia. Although ID is a reported feature of Pfeiffer syndrome, it is not universal and the condition would be expected to present in a syndromic manner with craniosynostosis prior to ID. This, along with the fact that it is caused by a recurrent missense variant, means that the utility of calling all variants in this gene in a cohort that includes non-syndromic ID is unlikely to be of benefit.
Created: 21 Dec 2017, 10:20 a.m.

Ellen McDonagh (Genomics England Curator)

Green List (high evidence)

This is a confirmed DD gene for Kallmann syndrome type 2 and Pfeiffer syndrome, which include the HPO term intellectual disability. It is a confirmed DD gene for Osteoglophonic dysplasia, which has delayed speech and language development as a phenotype.
Created: 13 Dec 2017, 9:46 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
KALLMANN SYNDROME TYPE 2; Pfeiffer syndrome 101600

Publications

Caroline Wright (Sanger)

Red List (low evidence)

Phenotypes
OSTEOGLOPHONIC DYSPLASIA (OGD)

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 : Activating; Loss of function
Created: 27 Jul 2017, 5:49 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; Nijmegen_ID_diagnostic; Nijmegen_ID_candidates; GEL_ID_red_20160217; neuro_20160418_strict; Activating; 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, 12:27 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Publications

Mode of pathogenicity
Other

Lu Raymond (university of cambridge )

Red List (low evidence)

Details

History Filter Activity

28 Sep 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to FGFR1.

15 Aug 2018, Gel status: 1

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: FGFR1 were set to Encephalocraniocutaneous lipomatosis, 613001; KALLMANN SYNDROME TYPE 2; Pfeiffer syndrome,101600

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

Set mode of inheritance, Set publications

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene FGFR1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene FGFR1 was set to ['28825856']

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)

FGFR1 was added to Intellectual disabilitypanel. Source: Expert Review Red

24 Jun 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

FGFR1 was added to Intellectual disabilitypanel. Sources: Radboud University Medical Center, Nijmegen