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SEMA3F

semaphorin 3F, the group of Immunoglobulin like domain containing|Semaphorins|MicroRNA protein coding host genes

Basic information

Region (hg38): 3:50155044-50189075

Links

ENSG00000001617NCBI:6405OMIM:601124HGNC:10728Uniprot:Q13275AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEMA3F gene.

  • Inborn genetic diseases (31 variants)
  • SEMA3F-related condition (24 variants)
  • not provided (8 variants)
  • Hypogonadotropic hypogonadism (5 variants)
  • Hearing impairment (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA3F 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
1
clinvar
4
clinvar
5
missense
47
clinvar
2
clinvar
49
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
2
2
non coding
3
clinvar
3
Total 0 0 51 6 0

Variants in SEMA3F

This is a list of pathogenic ClinVar variants found in the SEMA3F region.

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

Position Type Phenotype Significance ClinVar
3-50159631-C-T SEMA3F-related condition Likely benign (Feb 15, 2023)3054789
3-50159632-G-A SEMA3F-related condition • not specified Conflicting classifications of pathogenicity (Aug 16, 2023)2367544
3-50159634-C-T SEMA3F-related condition Likely benign (Oct 10, 2021)3051108
3-50159659-C-T SEMA3F-related condition Benign (Sep 24, 2022)3060222
3-50159664-C-T SEMA3F-related condition Benign (Apr 11, 2022)3060562
3-50159665-G-C SEMA3F-related condition Benign (Nov 22, 2022)3057219
3-50159677-T-C SEMA3F-related condition Likely benign (Feb 15, 2022)3054991
3-50159678-C-T not specified Uncertain significance (Jul 19, 2022)2302177
3-50159702-C-T SEMA3F-related condition • not specified Uncertain significance (Nov 21, 2023)2631886
3-50159708-C-T Hypogonadotropic hypogonadism Uncertain significance (-)982047
3-50159709-G-A SEMA3F-related condition Likely benign (Dec 02, 2021)3046469
3-50159714-G-A not specified Uncertain significance (Mar 02, 2023)2493428
3-50159716-G-A not specified Uncertain significance (Jun 22, 2021)2234113
3-50159719-C-T SEMA3F-related condition Uncertain significance (Dec 05, 2023)3047908
3-50173787-C-T SEMA3F-related condition Benign (Nov 22, 2022)3038914
3-50173805-C-T not specified Uncertain significance (Jan 31, 2024)3159727
3-50173812-C-T SEMA3F-related condition Likely benign (Jan 19, 2022)3055104
3-50173820-T-A not specified Uncertain significance (Oct 30, 2023)3159728
3-50173821-C-A not specified Uncertain significance (Feb 15, 2023)2459054
3-50173882-C-T not specified Uncertain significance (Jun 12, 2023)2559459
3-50173883-G-A not specified Uncertain significance (Mar 31, 2023)2510380
3-50173891-G-A not specified Uncertain significance (Sep 27, 2021)2252184
3-50173908-C-T SEMA3F-related condition Likely benign (Jul 10, 2022)3054869
3-50173930-G-A not specified Uncertain significance (Dec 01, 2023)3159734
3-50173941-C-T SEMA3F-related condition Uncertain significance (Jan 13, 2023)2636641

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEMA3Fprotein_codingprotein_codingENST00000002829 1834031
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.000111125731081257390.0000318
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.473885510.7040.00003895061
Missense in Polyphen126249.360.50532240
Synonymous0.6082142260.9490.00001641621
Loss of Function5.75547.90.1040.00000293444

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004620.0000462
European (Non-Finnish)0.00006450.0000615
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: May play a role in cell motility and cell adhesion.;
Pathway
Axon guidance - Homo sapiens (human) (Consensus)

Recessive Scores

pRec
0.149

Intolerance Scores

loftool
0.158
rvis_EVS
-0.26
rvis_percentile_EVS
34.88

Haploinsufficiency Scores

pHI
0.400
hipred
Y
hipred_score
0.786
ghis
0.593

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.124

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sema3f
Phenotype
cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; vision/eye phenotype; hearing/vestibular/ear 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); skeleton phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process
neural crest cell migration;axon guidance;facial nerve structural organization;trigeminal nerve structural organization;nerve development;branchiomotor neuron axon guidance;positive regulation of cell migration;ventral trunk neural crest cell migration;negative regulation of axon extension involved in axon guidance;axon extension involved in axon guidance;negative chemotaxis;sympathetic ganglion development;semaphorin-plexin signaling pathway;sympathetic neuron projection extension;sympathetic neuron projection guidance;regulation of postsynapse organization;neural crest cell migration involved in autonomic nervous system development;semaphorin-plexin signaling pathway involved in neuron projection guidance;semaphorin-plexin signaling pathway involved in axon guidance
Cellular component
extracellular space;integral component of plasma membrane;glutamatergic synapse
Molecular function
semaphorin receptor binding;neuropilin binding;chemorepellent activity