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GeneBe

SEMA4F

ssemaphorin 4F, the group of Semaphorins

Basic information

Region (hg38): 2:74654227-74683853

Previous symbols: [ "SEMAM" ]

Links

ENSG00000135622NCBI:10505OMIM:603706HGNC:10734Uniprot:O95754AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEMA4F gene.

  • Inborn genetic diseases (37 variants)
  • not provided (2 variants)

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
clinvar
1
missense
36
clinvar
2
clinvar
38
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 36 3 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)3159830
2-74654428-T-C not specified Uncertain significance (May 09, 2023)2545640
2-74654437-C-G not specified Uncertain significance (Mar 07, 2023)2470488
2-74656561-C-G not specified Uncertain significance (Sep 16, 2021)2250479
2-74656570-A-G not specified Uncertain significance (Apr 13, 2023)2536911
2-74656612-A-G not specified Uncertain significance (Feb 17, 2024)3159828
2-74656623-G-A Likely benign (Dec 01, 2022)2651079
2-74656629-G-A not specified Uncertain significance (Apr 25, 2023)2519815
2-74657599-A-G not specified Uncertain significance (Aug 08, 2023)2617404
2-74657866-A-G not specified Uncertain significance (Jul 08, 2022)2300339
2-74662775-G-A not specified Uncertain significance (Oct 04, 2022)2316540
2-74662778-G-A not specified Uncertain significance (Oct 03, 2022)2214252
2-74662791-T-A not specified Uncertain significance (Sep 14, 2022)2312345
2-74662803-G-T not specified Uncertain significance (Feb 26, 2024)3159829
2-74673462-G-T not specified Uncertain significance (Aug 13, 2021)2382586
2-74673505-C-G not specified Uncertain significance (Sep 07, 2022)2384707
2-74673522-G-A not specified Uncertain significance (Feb 28, 2023)2491642
2-74673533-C-T Likely benign (Dec 01, 2022)2651080
2-74673697-G-A not specified Likely benign (Jan 03, 2024)3159831
2-74673724-G-A not specified Uncertain significance (Nov 08, 2022)2216359
2-74673778-T-C not specified Uncertain significance (Sep 26, 2023)3159832
2-74673806-C-T not specified Uncertain significance (Feb 23, 2023)2488980
2-74674510-G-A not specified Uncertain significance (Jun 11, 2021)2210012
2-74674622-G-A not specified Uncertain significance (Oct 27, 2022)2321121
2-74674646-C-T not specified Uncertain significance (Mar 21, 2023)2508258

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEMA4Fprotein_codingprotein_codingENST00000357877 1427832
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
9.15e-130.87912557501731257480.000688
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3224514710.9580.00002934899
Missense in Polyphen151169.070.893111891
Synonymous-0.2611901851.020.00001071701
Loss of Function1.962538.00.6580.00000240373

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002280.00222
Ashkenazi Jewish0.00009920.0000992
East Asian0.0006520.000653
Finnish0.00009270.0000924
European (Non-Finnish)0.0008460.000844
Middle Eastern0.0006520.000653
South Asian0.0001960.000196
Other0.0004890.000489

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sema4f
Phenotype

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