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SEMA3E

semaphorin 3E, the group of Immunoglobulin like domain containing|Semaphorins

Basic information

Region (hg38): 7:83363237-83649139

Previous symbols: [ "SEMAH" ]

Links

ENSG00000170381NCBI:9723OMIM:608166HGNC:10727Uniprot:O15041AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • CHARGE syndrome (Limited), mode of inheritance: AD
  • Kallmann syndrome (Limited), mode of inheritance: AD
  • CHARGE syndrome (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
CHARGE syndromeADCardiovascularThe condition can involve congenital cardiac anomalies, and awareness may allow early managementCardiovascular; Craniofacial; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Ophthalmologic; Renal11241468; 15235037

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEMA3E gene.

  • CHARGE association (424 variants)
  • not provided (183 variants)
  • SEMA3E-related condition (32 variants)
  • CHARGE association;Hypogonadotropic hypogonadism 7 with or without anosmia (31 variants)
  • Inborn genetic diseases (28 variants)
  • Hypogonadotropic hypogonadism 7 with or without anosmia;CHARGE association (23 variants)
  • not specified (9 variants)
  • Amenorrhea (1 variants)
  • Hypogonadotropic hypogonadism 7 with or without anosmia (1 variants)
  • Isolated anophthalmia-microphthalmia syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA3E gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
3
clinvar
96
clinvar
5
clinvar
104
missense
234
clinvar
6
clinvar
2
clinvar
242
nonsense
6
clinvar
6
start loss
0
frameshift
1
clinvar
4
clinvar
5
inframe indel
0
splice donor/acceptor (+/-2bp)
3
clinvar
3
splice region
13
20
1
34
non coding
1
clinvar
86
clinvar
92
clinvar
179
Total 0 1 251 188 99

Variants in SEMA3E

This is a list of pathogenic ClinVar variants found in the SEMA3E region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
7-83367330-A-G Benign (Sep 22, 2018)1242507
7-83367359-A-G Likely benign (May 26, 2019)1198930
7-83367390-A-T Benign (Aug 09, 2018)1233803
7-83367515-A-T Benign (Oct 05, 2018)1291034
7-83367517-G-GATTT Benign (Sep 22, 2018)1236886
7-83367540-T-G Benign (Sep 22, 2018)1174248
7-83367594-C-A CHARGE association Uncertain significance (Jul 03, 2023)529136
7-83367598-C-T CHARGE association Likely benign (Sep 25, 2020)696607
7-83367599-G-A CHARGE association Uncertain significance (Oct 08, 2023)2714884
7-83367607-G-A CHARGE association Likely benign (Jun 18, 2020)738651
7-83367610-C-CA CHARGE association Uncertain significance (Feb 11, 2020)1059922
7-83367612-G-A CHARGE association Likely benign (Apr 08, 2020)1111717
7-83367614-C-A CHARGE association Uncertain significance (Apr 29, 2023)2713563
7-83367631-G-A CHARGE association Benign/Likely benign (Jan 28, 2024)695746
7-83367632-G-C CHARGE association Uncertain significance (Mar 21, 2023)2713659
7-83367635-C-T CHARGE association • CHARGE association;Hypogonadotropic hypogonadism 7 with or without anosmia Uncertain significance (Nov 07, 2023)1061205
7-83367661-A-G CHARGE association Likely benign (Oct 15, 2023)2795522
7-83367675-A-T CHARGE association Uncertain significance (Apr 29, 2022)1967543
7-83367680-G-A CHARGE association Uncertain significance (Apr 25, 2021)1513385
7-83367690-G-T CHARGE association Uncertain significance (Mar 14, 2023)2878641
7-83367691-C-T SEMA3E-related condition Likely benign (Jun 07, 2022)3044633
7-83367694-T-C CHARGE association • SEMA3E-related condition Conflicting classifications of pathogenicity (Nov 19, 2023)374661
7-83367698-C-T CHARGE association Uncertain significance (Jan 14, 2024)1387125
7-83367698-CTCTT-C CHARGE association Uncertain significance (Nov 01, 2022)1969993
7-83367703-T-C CHARGE association Benign (Feb 01, 2024)416920

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEMA3Eprotein_codingprotein_codingENST00000307792 17285105
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
8.71e-91.001257130351257480.000139
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4654084350.9370.00002355096
Missense in Polyphen137172.080.796122018
Synonymous-2.281891531.230.000008441426
Loss of Function3.272144.50.4720.00000252519

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002390.000239
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.0003240.000323
European (Non-Finnish)0.0001320.000132
Middle Eastern0.00005440.0000544
South Asian0.0001630.000163
Other0.0001640.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays an important role in signaling via the cell surface receptor PLXND1. Mediates reorganization of the actin cytoskeleton, leading to the retraction of cell projections. Promotes focal adhesion disassembly and inhibits adhesion of endothelial cells to the extracellular matrix. Regulates angiogenesis, both during embryogenesis and after birth. Can down- regulate sprouting angiogenesis. Required for normal vascular patterning during embryogenesis. Plays an important role in ensuring the specificity of synapse formation (By similarity). {ECO:0000250}.;
Pathway
Axon guidance - Homo sapiens (human);Developmental Biology;Other semaphorin interactions;Semaphorin interactions;Plexin-D1 Signaling;Axon guidance (Consensus)

Recessive Scores

pRec
0.112

Intolerance Scores

loftool
0.718
rvis_EVS
-0.8
rvis_percentile_EVS
12.49

Haploinsufficiency Scores

pHI
0.0926
hipred
Y
hipred_score
0.638
ghis
0.454

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.158

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sema3e
Phenotype
embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Zebrafish Information Network

Gene name
sema3e
Affected structure
axial vasculature
Phenotype tag
abnormal
Phenotype quality
has fewer parts of type

Gene ontology

Biological process
branching involved in blood vessel morphogenesis;neural crest cell migration;negative regulation of cell-matrix adhesion;sprouting angiogenesis;regulation of cell shape;negative regulation of angiogenesis;positive regulation of cell migration;negative regulation of axon extension involved in axon guidance;synapse organization;negative chemotaxis;semaphorin-plexin signaling pathway;regulation of actin cytoskeleton reorganization
Cellular component
extracellular region;extracellular space;integral component of plasma membrane
Molecular function
protein binding;semaphorin receptor binding;neuropilin binding;chemorepellent activity