SEMA3F

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

Basic information

Region (hg38): 3:50155044-50189075

Links

ENSG00000001617 ∙ NCBI:6405 ∙ OMIM:601124 ∙ HGNC:10728 ∙ Uniprot:Q13275 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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	38	2	41
missense			69	8	2	79
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				7	1	8
non coding			4	5		9
Total	0	0	74	51	4

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 disorder	Likely benign (Feb 15, 2023)
3-50159632-G-A		SEMA3F-related disorder • not specified	Conflicting classifications of pathogenicity (Aug 16, 2023)
3-50159634-C-T		SEMA3F-related disorder	Likely benign (Oct 10, 2021)
3-50159659-C-T		SEMA3F-related disorder	Benign (Sep 24, 2022)
3-50159664-C-T		SEMA3F-related disorder	Benign (Apr 11, 2022)
3-50159665-G-C		SEMA3F-related disorder	Benign (Nov 22, 2022)
3-50159677-T-C		SEMA3F-related disorder	Likely benign (Feb 15, 2022)
3-50159678-C-T		not specified	Uncertain significance (Jul 19, 2022)
3-50159702-C-T		SEMA3F-related disorder • not specified	Uncertain significance (Nov 21, 2023)
3-50159708-C-T		Hypogonadotropic hypogonadism	Uncertain significance (-)
3-50159709-G-A		SEMA3F-related disorder	Likely benign (Dec 02, 2021)
3-50159714-G-A		not specified	Uncertain significance (Mar 02, 2023)
3-50159716-G-A		not specified	Uncertain significance (Jun 22, 2021)
3-50159719-C-T		SEMA3F-related disorder	Uncertain significance (Dec 05, 2023)
3-50173787-C-T		SEMA3F-related disorder	Benign (Nov 22, 2022)
3-50173805-C-T		not specified	Uncertain significance (Jan 31, 2024)
3-50173812-C-T		SEMA3F-related disorder	Likely benign (Jan 19, 2022)
3-50173820-T-A		not specified	Uncertain significance (Oct 30, 2023)
3-50173821-C-A		not specified	Uncertain significance (Feb 15, 2023)
3-50173882-C-T		not specified	Uncertain significance (Jun 12, 2023)
3-50173883-G-A		not specified	Uncertain significance (Mar 31, 2023)
3-50173891-G-A		not specified	Uncertain significance (Sep 27, 2021)
3-50173908-C-T		SEMA3F-related disorder	Likely benign (Jul 10, 2022)
3-50173930-G-A		not specified	Uncertain significance (Dec 01, 2023)
3-50173941-C-T		SEMA3F-related disorder	Uncertain significance (Jan 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEMA3F	protein_coding	protein_coding	ENST00000002829	18	34031

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000111	125731	0	8	125739	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.47	388	551	0.704	0.0000389	5061
Missense in Polyphen		126	249.36	0.5053		2240
Synonymous	0.608	214	226	0.949	0.0000164	1621
Loss of Function	5.75	5	47.9	0.104	0.00000293	444

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000645	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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