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SEMA3C

semaphorin 3C, the group of I-set domain containing|Semaphorins

Basic information

Region (hg38): 7:80742537-80922359

Previous symbols: [ "SEMAE" ]

Links

ENSG00000075223NCBI:10512OMIM:602645HGNC:10725Uniprot:Q99985AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEMA3C gene.

  • Inborn genetic diseases (26 variants)
  • not provided (24 variants)
  • SEMA3C-related condition (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA3C 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
8
clinvar
2
clinvar
10
missense
42
clinvar
2
clinvar
3
clinvar
47
nonsense
0
start loss
0
frameshift
0
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
3
1
4
non coding
2
clinvar
2
Total 0 0 44 10 7

Variants in SEMA3C

This is a list of pathogenic ClinVar variants found in the SEMA3C region.

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

Position Type Phenotype Significance ClinVar
7-80744885-A-G SEMA3C-related condition Likely benign (Apr 19, 2022)3031781
7-80744914-T-C SEMA3C-related condition • not specified Uncertain significance (Nov 29, 2023)2207722
7-80744934-C-T SEMA3C-related condition Uncertain significance (Sep 27, 2022)2634557
7-80744940-T-C SEMA3C-related condition Uncertain significance (Oct 20, 2023)3054046
7-80744964-T-C not specified Uncertain significance (Dec 26, 2023)3159709
7-80745012-C-T SEMA3C-related condition Uncertain significance (Jan 27, 2023)2629299
7-80745026-A-G SEMA3C-related condition Benign (Jul 19, 2022)3060435
7-80745029-T-C SEMA3C-related condition Likely benign (May 21, 2021)783002
7-80745064-C-T not specified Uncertain significance (Feb 28, 2023)2490982
7-80745085-G-T SEMA3C-related condition • not specified Uncertain significance (Feb 15, 2024)2216058
7-80745122-T-C SEMA3C-related condition Benign (Jul 19, 2022)3058982
7-80745135-T-C SEMA3C-related condition • not specified Conflicting classifications of pathogenicity (Oct 14, 2023)718913
7-80745137-C-T SEMA3C-related condition Likely benign (Jun 16, 2023)3036368
7-80745212-T-C SEMA3C-related condition Likely benign (Aug 19, 2021)792861
7-80745216-G-C Benign (Dec 31, 2019)768166
7-80745220-T-C SEMA3C-related condition Uncertain significance (Oct 02, 2023)2636065
7-80745255-G-A SEMA3C-related condition Uncertain significance (May 22, 2023)2629081
7-80745265-G-C SEMA3C-related condition Uncertain significance (Feb 22, 2024)3056756
7-80748901-T-C SEMA3C-related condition Likely benign (Apr 13, 2022)3051955
7-80748909-T-C not specified Uncertain significance (May 27, 2022)2393784
7-80748934-C-T SEMA3C-related condition Likely benign (May 11, 2023)3046178
7-80748939-T-C Benign (Dec 31, 2019)708481
7-80748945-C-A SEMA3C-related condition Uncertain significance (Sep 28, 2022)2636100
7-80748949-C-T SEMA3C-related condition Benign/Likely benign (May 19, 2021)733120
7-80748978-T-C SEMA3C-related condition • not specified Uncertain significance (Dec 14, 2023)2378173

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEMA3Cprotein_codingprotein_codingENST00000265361 17179822
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0008740.9991257170311257480.000123
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9943624190.8630.00002274945
Missense in Polyphen148206.940.715182347
Synonymous0.6471381480.9320.000007921409
Loss of Function3.961340.00.3250.00000223477

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004000.000396
Ashkenazi Jewish0.000.00
East Asian0.0001640.000163
Finnish0.0002320.000231
European (Non-Finnish)0.0001240.000123
Middle Eastern0.0001640.000163
South Asian0.00003280.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Binds to plexin family members and plays an important role in the regulation of developmental processes. Required for normal cardiovascular development during embryogenesis. Functions as attractant for growing axons, and thereby plays an important role in axon growth and axon guidance (By similarity). {ECO:0000250}.;
Pathway
Axon guidance - Homo sapiens (human);Plexin-D1 Signaling (Consensus)

Recessive Scores

pRec
0.188

Intolerance Scores

loftool
0.653
rvis_EVS
-0.62
rvis_percentile_EVS
17.4

Haploinsufficiency Scores

pHI
0.233
hipred
Y
hipred_score
0.605
ghis
0.558

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.507

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sema3c
Phenotype
cellular 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype;

Zebrafish Information Network

Gene name
sema3c
Affected structure
enteric neuron
Phenotype tag
abnormal
Phenotype quality
decreased amount

Gene ontology

Biological process
neural crest cell migration;somitogenesis;blood vessel remodeling;outflow tract septum morphogenesis;cardiac right ventricle morphogenesis;pulmonary myocardium development;immune response;axon guidance;post-embryonic development;neural tube development;positive regulation of cell migration;response to drug;negative regulation of axon extension involved in axon guidance;negative chemotaxis;limb bud formation;dichotomous subdivision of terminal units involved in salivary gland branching;semaphorin-plexin signaling pathway;cardiac endothelial to mesenchymal transition;positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis
Cellular component
extracellular space;integral component of plasma membrane;extracellular exosome
Molecular function
semaphorin receptor binding;neuropilin binding;chemorepellent activity