SEMA3C
Basic information
Region (hg38): 7:80742538-80922359
Previous symbols: [ "SEMAE" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- SEMA3C-related_disorder (172 variants)
- not_specified (71 variants)
- not_provided (24 variants)
- High_myopia (1 variants)
- See_cases (1 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. These statistics are base on transcript: NM_000006379.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 47 | 49 | ||||
| missense | 131 | 140 | ||||
| nonsense | 3 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 136 | 53 | 5 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SEMA3C | protein_coding | protein_coding | ENST00000265361 | 17 | 179822 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000874 | 0.999 | 125717 | 0 | 31 | 125748 | 0.000123 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.994 | 362 | 419 | 0.863 | 0.0000227 | 4945 |
| Missense in Polyphen | 148 | 206.94 | 0.71518 | 2347 | ||
| Synonymous | 0.647 | 138 | 148 | 0.932 | 0.00000792 | 1409 |
| Loss of Function | 3.96 | 13 | 40.0 | 0.325 | 0.00000223 | 477 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000400 | 0.000396 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000164 | 0.000163 |
| Finnish | 0.000232 | 0.000231 |
| European (Non-Finnish) | 0.000124 | 0.000123 |
| Middle Eastern | 0.000164 | 0.000163 |
| South Asian | 0.0000328 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
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