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COVID-19 research

Gene: SEMA3E

Green List (high evidence)

SEMA3E (semaphorin 3E)
EnsemblGeneIds (GRCh38): ENSG00000170381
EnsemblGeneIds (GRCh37): ENSG00000170381
OMIM: 608166, Gene2Phenotype
SEMA3E is in 8 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)

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.

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
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

2 Apr 2020, Gel status: 3

Added New Source, Set Phenotypes, Status Update

Ellen McDonagh (Genomics England Curator)

Source Expert Review Green was added to SEMA3E. Added 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 for gene: SEMA3E Rating Changed from Red List (low evidence) to Green List (high evidence)

1 Apr 2020, Gel status: 1

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Ellen McDonagh (Genomics England Curator)

gene: SEMA3E was added gene: SEMA3E was added to Viral susceptibility. Sources: ESID Registry 20171117,Victorian Clinical Genetics Services,GRID V2.0,IUIS Classification December 2019,Expert Review Red,IUIS Classification February 2018 Mode of inheritance for gene: SEMA3E was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: SEMA3E were set to 21055784; 32086639; 1735828; 12144540; 32048120 Phenotypes for gene: SEMA3E were set to 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