Menu
GeneBe

SEMA6C

semaphorin 6C, the group of Semaphorins

Basic information

Region (hg38): 1:151131684-151146631

Links

ENSG00000143434NCBI:10500OMIM:609294HGNC:10740Uniprot:Q9H3T2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEMA6C gene.

  • Inborn genetic diseases (8 variants)
  • not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA6C 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
8
clinvar
1
clinvar
2
clinvar
11
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
2
2
non coding
0
Total 0 0 8 1 2

Variants in SEMA6C

This is a list of pathogenic ClinVar variants found in the SEMA6C region.

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

Position Type Phenotype Significance ClinVar
1-151132845-G-A not specified Uncertain significance (Oct 18, 2021)2378764
1-151132921-G-A not specified Uncertain significance (Sep 16, 2021)2250840
1-151133140-G-A not specified Uncertain significance (Aug 10, 2021)2349304
1-151133151-A-G not specified Uncertain significance (Aug 16, 2021)2372986
1-151133355-T-C Likely benign (Mar 01, 2024)3067221
1-151134828-C-G Benign (May 21, 2018)767698
1-151135315-G-A Benign (May 21, 2018)717809
1-151136113-C-T not specified Uncertain significance (Jul 14, 2021)2374447
1-151136850-T-G Benign (May 21, 2018)767699
1-151137041-G-A not specified Uncertain significance (Sep 16, 2021)2351079
1-151138034-G-A Likely benign (Dec 01, 2022)2639168
1-151138078-G-A not specified Uncertain significance (Nov 01, 2021)2355228
1-151139661-C-G not specified Uncertain significance (Sep 01, 2021)2247756
1-151142531-G-A Benign (Dec 05, 2017)770327

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEMA6Cprotein_codingprotein_codingENST00000368913 1814944
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000001241.0012563201161257480.000461
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.594275300.8050.00003345992
Missense in Polyphen7393.5770.7801959
Synonymous0.4212172250.9640.00001382169
Loss of Function3.381740.10.4240.00000230431

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001530.000152
Ashkenazi Jewish0.000.00
East Asian0.0001640.000109
Finnish0.003380.00338
European (Non-Finnish)0.0002470.000246
Middle Eastern0.0001640.000109
South Asian0.0002640.000261
Other0.0003260.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Shows growth cone collapsing activity on dorsal root ganglion (DRG) neurons in vitro. May be a stop signal for the DRG neurons in their target areas, and possibly also for other neurons. May also be involved in the maintenance and remodeling of neuronal connections. {ECO:0000269|PubMed:12110693}.;
Pathway
Axon guidance - Homo sapiens (human) (Consensus)

Recessive Scores

pRec
0.100

Haploinsufficiency Scores

pHI
0.158
hipred
Y
hipred_score
0.567
ghis
0.512

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.132

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sema6c
Phenotype
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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process
neural crest cell migration;axon guidance;positive regulation of cell migration;negative regulation of axon extension involved in axon guidance;negative chemotaxis;semaphorin-plexin signaling pathway
Cellular component
extracellular space;integral component of plasma membrane
Molecular function
semaphorin receptor binding;neuropilin binding;chemorepellent activity