SEMA4F

ssemaphorin 4F, the group of Semaphorins

Basic information

Region (hg38): 2:74654226-74690634

Previous symbols: [ "SEMAM" ]

Links

ENSG00000135622 ∙ NCBI:10505 ∙ OMIM:603706 ∙ HGNC:10734 ∙ Uniprot:O95754 ∙ 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 SEMA4F gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA4F 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		1
missense			47	4		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	5	0

Variants in SEMA4F

This is a list of pathogenic ClinVar variants found in the SEMA4F region.

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

Position	Type	Phenotype	Significance	ClinVar
2-74654381-C-T		not specified	Likely benign (Oct 05, 2023)
2-74654428-T-C		not specified	Uncertain significance (May 09, 2023)
2-74654437-C-G		not specified	Uncertain significance (Mar 07, 2023)
2-74654459-T-G		not specified	Uncertain significance (Aug 04, 2024)
2-74656561-C-G		not specified	Uncertain significance (Sep 16, 2021)
2-74656570-A-G		not specified	Uncertain significance (Apr 13, 2023)
2-74656612-A-G		not specified	Uncertain significance (Feb 17, 2024)
2-74656617-C-G		not specified	Uncertain significance (Aug 12, 2024)
2-74656623-G-A			Likely benign (Dec 01, 2022)
2-74656629-G-A		not specified	Uncertain significance (Apr 25, 2023)
2-74656647-G-A		not specified	Uncertain significance (Jun 28, 2024)
2-74656681-G-A		not specified	Uncertain significance (Mar 19, 2024)
2-74657599-A-G		not specified	Uncertain significance (Aug 08, 2023)
2-74657866-A-G		not specified	Uncertain significance (Jul 08, 2022)
2-74662749-G-C		not specified	Uncertain significance (Jun 07, 2024)
2-74662775-G-A		not specified	Uncertain significance (Oct 04, 2022)
2-74662778-G-A		not specified	Uncertain significance (Oct 03, 2022)
2-74662791-T-A		not specified	Uncertain significance (Sep 14, 2022)
2-74662803-G-T		not specified	Uncertain significance (Feb 26, 2024)
2-74673462-G-T		not specified	Uncertain significance (Aug 13, 2021)
2-74673499-C-T		not specified	Uncertain significance (Nov 08, 2024)
2-74673505-C-G		not specified	Uncertain significance (Nov 28, 2024)
2-74673522-G-A		not specified	Uncertain significance (Feb 28, 2023)
2-74673533-C-T			Likely benign (Dec 01, 2022)
2-74673570-C-A		not specified	Uncertain significance (Jun 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEMA4F	protein_coding	protein_coding	ENST00000357877	14	27832

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.15e-13	0.879	125575	0	173	125748	0.000688

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.322	451	471	0.958	0.0000293	4899
Missense in Polyphen		151	169.07	0.89311		1891
Synonymous	-0.261	190	185	1.02	0.0000107	1701
Loss of Function	1.96	25	38.0	0.658	0.00000240	373

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00228	0.00222
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000652	0.000653
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000846	0.000844
Middle Eastern	0.000652	0.000653
South Asian	0.000196	0.000196
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has growth cone collapse activity against retinal ganglion-cell axons. {ECO:0000250}.
• Pathway: Axon guidance - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0945

Intolerance Scores

• loftool: 0.860
• rvis_EVS: -1.06
• rvis_percentile_EVS: 7.52

Haploinsufficiency Scores

• pHI: 0.0811
• hipred: N
• hipred_score: 0.234
• ghis: 0.562

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.149

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sema4f

Gene ontology

• Biological process: neural crest cell migration;cell-cell signaling;nervous system development;axon guidance;positive regulation of cell migration;retinal ganglion cell axon guidance;negative regulation of axon extension involved in axon guidance;negative chemotaxis;semaphorin-plexin signaling pathway
• Cellular component: extracellular space;endoplasmic reticulum;plasma membrane;integral component of plasma membrane;membrane;postsynaptic membrane
• Molecular function: semaphorin receptor binding;neuropilin binding;chemorepellent activity