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Primary immunodeficiency

Gene: SEMA3E

Red List (low evidence)

SEMA3E (semaphorin 3E)
EnsemblGeneIds (GRCh38): ENSG00000170381
EnsemblGeneIds (GRCh37): ENSG00000170381
OMIM: 608166, Gene2Phenotype
SEMA3E is in 7 panels

3 reviews

Sophie Hambleton (Newcastle University)

Red List (low evidence)

Only 2 patients described
Created: 11 Jun 2018, 12:43 p.m.

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

Publications

Eleanor Williams (Genomics England Curator)

Red List (low evidence)

The following PubMed IDs were added to gene SEMA3E (OMIM gene MIM#608166): 11241468. These publications have been associated with the gene by the immunodeficiencies subgroup of the Human Phenotype Ontology Immune Mediated Disorders Consortium (https://hpo-immune-mediated-disorders.groups.io/g/update) in August 2020.
Created: 13 Oct 2020, 9:36 a.m. | Last Modified: 13 Oct 2020, 9:36 a.m.
Panel Version: 2.208
Comment on list classification: Rating this gene red as there is not enough evidence for its role in any immunodeficiency disorder.
Created: 9 May 2018, 4:03 p.m.
SEMA3E is provisionally associated with CHARGE Syndrome in OMIM and Orphanet. CHARGE syndrome is characterized by a pattern of congenital anomalies including choanal atresia and malformations of the heart, inner ear, and retina and is not a immunodeficiency related disorder. No entry for SEMA3E in Gene2Phenotype. In Genetics Home Reference it is linked to Hypogonadotropic hypogonadism 7 with or without anosmia (not an immunodecficiency related disorder). A PubMed search only brings up 1 related paper which shows that Sema3E plays an essential immunoregulatory role in experimental allergic asthma in mice (Movassagh et al 2017 (PMID:28634005)). Rating this gene red as there is not enough evidence for its role in any immunodeficiency disorder.
Created: 9 May 2018, 4:03 p.m.
Comment on phenotypes: Added the MIM number to the Charge syndrome phenotype
Created: 9 May 2018, 3:41 p.m.

Publications

Louise Daugherty (Genomics England Curator)

I don't know

OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): SEMA3E .PanelApp HGNC gene symbol check: SEMA3E . IUIS Disease: CHARGE syndrome due to SEMA3E deficiency . IUIS Inheritance: AD .T cells: Modestly decreased, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: Coloboma, heart anomaly, choanal atresia, intellectual retardation, genital and ear anomalies, CNS malformation, some are SCID-like and have low TRECs. IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: Thymic Defects with Additional Congenital Anomalies
Created: 2 Jul 2018, 10:35 a.m.
External expert review notes Red status, not enough evidence to date, I have kept this gene Red on this panel until further evidence
Created: 13 Jun 2018, 10:12 a.m.
Comment on publications: added further publications to support immune-mediated cerebellar ataxia
Created: 13 Jun 2018, 10:10 a.m.
Comment on phenotypes: added immune relevant phenotypes, not CHARGE syndrome, immune-mediated cerebellar ataxia
Created: 13 Jun 2018, 10:08 a.m.
Comment on publications: Added publications suggested from external expert review to support immunological association
Created: 13 Jun 2018, 10:05 a.m.
This gene was absent from the original PanelApp PID panel dataset (review April 2018). However it was listed in external expert immunodeficiency diagnostic gene list(s)
GOSH or GRID. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1.
Created: 19 Apr 2018, 3:28 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: SEMA3E, PanelApp HGNC gene symbol check: SEMA3E, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Other well defined PIDs / CHARGE syndrome / CHARGE syndrome
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: SEMA3E, GRID_Gene_Symbol: SEMA3E, GRID_Transcript_ENS_Community submitted: ENST00000307792, GRID_Transcript_RefSeq: NM_012431.2, GRID_Transcript_ENS_used_on_Production: ENST00000307792
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Other
  • IUIS Classification December 2019
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • Expert Review Red
  • ESID Registry 20171117
  • GRID V2.0
Phenotypes
  • CHARGE syndrome
  • immune-mediated cerebellar ataxia
  • Coloboma, heart anomaly, choanal atresia, intellectual retardation, genital and ear anomalies, CNS malformation, some are SCID-like and have low TRECs
  • Charge syndrome 214800
  • Combined immunodeficiencies with associated or syndromic features
OMIM
608166
Clinvar variants
Variants in SEMA3E
Penetrance
None
Publications
Panels with this gene

History Filter Activity

13 Oct 2020, Gel status: 1

Added New Source, Set publications

Eleanor Williams (Genomics England Curator)

Source Other was added to SEMA3E. Publications for gene SEMA3E were updated from 12144540; 1735828; 32048120; 21055784; 32086639 to 12144540; 1735828; 11241468; 32048120; 21055784; 32086639

28 Feb 2020, Gel status: 1

Added New Source, Set Phenotypes, Set publications

Louise Daugherty (Genomics England Curator)

Source IUIS Classification December 2019 was added to SEMA3E. Added phenotypes Coloboma, heart anomaly, choanal atresia, intellectual retardation, genital and ear anomalies, CNS malformation, some are SCID-like and have low TRECs; Combined immunodeficiencies with associated or syndromic features for gene: SEMA3E Publications for gene SEMA3E were updated from 1735828; 21055784; 12144540 to 12144540; 1735828; 32048120; 21055784; 32086639

12 Jul 2018, Gel status: 1

Panel promoted to version 1.0

Louise Daugherty (Genomics England Curator)

2018-07-12 Louise Daugherty (Genomics England Curator) promoted panel to v1.0. Reviews were assessed, and panel was revised according to expert reviews and further in-house curation based on PanelApp guidelines. Previous panels (A- or hypo-gammaglobulinaemia, Congenital neutropaenia, Agranulocytosis, Combined B and T cell defect, Inherited complement deficiency and SCID panels) that were merged with this panel, were checked again for any changes/new reviews prior to versioning of this panel, these merged panels are now retired/made internal.

1 Jul 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene SEMA3E were set to Charge syndrome 214800, CHARGE syndrome, immune-mediated cerebellar ataxia, Coloboma, heart anomaly, choanal atresia, intellectual retardation, genital and ear anomalies, CNS malformation, some are SCID-like and have low TRECs, Combined immunodeficiencies with associated or syndromic features

26 Jun 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to SEMA3E. Panel: Primary immunodeficiency disorders

26 Jun 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Victorian Clinical Genetics Services was added to SEMA3E. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: sema3e has been classified as Red List (Low Evidence).

13 Jun 2018, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: SEMA3E were set to 1735828; 21055784; 12144540

13 Jun 2018, Gel status: 1

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: SEMA3E were set to Charge syndrome 214800; CHARGE syndrome; immune-mediated cerebellar ataxia

13 Jun 2018, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: SEMA3E were set to 1735828

9 May 2018, Gel status: 1

Gene classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

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

9 May 2018, Gel status: 1

Gene classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

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

9 May 2018, Gel status: 2

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for SEMA3E were set to Charge syndrome 214800; CHARGE syndrome

19 Apr 2018, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

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

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to SEMA3E. Panel: Primary immunodeficiency disorders Phenotypes for gene SEMA3E were set to Charge syndrome, CHARGE syndrome

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene SEMA3E were set to Charge syndrome

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

SEMA3E was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

SEMA3E was created by Louise Daugherty