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SEMA4C

semaphorin 4C, the group of Immunoglobulin like domain containing|Semaphorins

Basic information

Region (hg38): 2:96859717-96870757

Previous symbols: [ "SEMAI" ]

Links

ENSG00000168758NCBI:54910OMIM:604462HGNC:10731Uniprot:Q9C0C4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEMA4C gene.

  • Inborn genetic diseases (39 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA4C 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
0
missense
38
clinvar
1
clinvar
39
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 38 1 0

Variants in SEMA4C

This is a list of pathogenic ClinVar variants found in the SEMA4C region.

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

Position Type Phenotype Significance ClinVar
2-96860696-T-C not specified Uncertain significance (Jan 09, 2024)3159794
2-96860730-C-T not specified Uncertain significance (Jan 05, 2022)2349314
2-96860784-G-A not specified Uncertain significance (Jun 22, 2023)2603022
2-96860840-G-A not specified Uncertain significance (Jul 30, 2023)2593845
2-96860876-C-G not specified Uncertain significance (Nov 03, 2023)3159793
2-96860876-C-T not specified Uncertain significance (Oct 14, 2023)3159792
2-96860903-G-C not specified Uncertain significance (Feb 16, 2023)2486480
2-96860925-C-T not specified Uncertain significance (Jan 26, 2022)2258836
2-96860976-G-C not specified Uncertain significance (Mar 29, 2022)2280755
2-96860976-G-T not specified Uncertain significance (Oct 17, 2023)3159790
2-96861030-C-T not specified Uncertain significance (Oct 04, 2022)2316777
2-96861056-C-T not specified Uncertain significance (Aug 22, 2023)2620735
2-96861062-C-T not specified Uncertain significance (Aug 08, 2023)2597445
2-96861248-C-T not specified Uncertain significance (Dec 18, 2023)3159789
2-96861320-A-T not specified Uncertain significance (Jan 26, 2023)3159788
2-96861321-A-G not specified Uncertain significance (Jan 16, 2024)3159787
2-96861350-C-T not specified Uncertain significance (Jun 30, 2022)2273748
2-96861368-C-T not specified Uncertain significance (Dec 12, 2023)3159785
2-96861369-G-A not specified Uncertain significance (Jan 17, 2023)2476098
2-96861401-G-C not specified Uncertain significance (Oct 26, 2022)2368836
2-96861449-G-T not specified Uncertain significance (Jul 20, 2022)2381406
2-96861608-C-G not specified Uncertain significance (Feb 09, 2023)2482646
2-96861765-G-A not specified Uncertain significance (Jun 28, 2023)2592877
2-96861791-T-C not specified Uncertain significance (Jun 14, 2023)2560267
2-96861837-T-C not specified Likely benign (Dec 21, 2023)3159784

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEMA4Cprotein_codingprotein_codingENST00000305476 1411042
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.0000045211914781557681257300.0265
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.393795340.7100.00003495303
Missense in Polyphen100207.390.482192159
Synonymous0.6222222340.9480.00001501800
Loss of Function5.63138.90.02570.00000185418

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.2090.208
Ashkenazi Jewish0.002110.00209
East Asian0.003870.00387
Finnish0.000.00
European (Non-Finnish)0.0001250.000123
Middle Eastern0.003870.00387
South Asian0.00009800.0000980
Other0.02300.0224

dbNSFP

Source: dbNSFP

Function
FUNCTION: Cell surface receptor for PLXNB2 that plays an important role in cell-cell signaling. PLXNB2 binding promotes downstream activation of RHOA and phosphorylation of ERBB2 at 'Tyr-1248'. Required for normal brain development, axon guidance and cell migration (By similarity). Probable signaling receptor which may play a role in myogenic differentiation through activation of the stress-activated MAPK cascade. {ECO:0000250, ECO:0000269|PubMed:17498836}.;
Pathway
Axon guidance - Homo sapiens (human) (Consensus)

Recessive Scores

pRec
0.156

Intolerance Scores

loftool
0.163
rvis_EVS
-0.78
rvis_percentile_EVS
13.05

Haploinsufficiency Scores

pHI
0.617
hipred
Y
hipred_score
0.662
ghis
0.573

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.813

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sema4c
Phenotype
pigmentation phenotype; 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); 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); 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); cellular phenotype;

Gene ontology

Biological process
neural crest cell migration;neural tube closure;cell migration in hindbrain;cerebellum development;positive regulation of cell migration;positive regulation of stress-activated MAPK cascade;muscle cell differentiation;negative regulation of axon extension involved in axon guidance;negative chemotaxis;semaphorin-plexin signaling pathway
Cellular component
extracellular space;integral component of plasma membrane;postsynaptic density;cell junction;synaptic vesicle membrane;postsynaptic membrane
Molecular function
protein binding;semaphorin receptor binding;neuropilin binding;chemorepellent activity