SEMA6C

semaphorin 6C, the group of Semaphorins

Basic information

Region (hg38): 1:151131684-151146631

Links

ENSG00000143434 ∙ NCBI:10500 ∙ OMIM:609294 ∙ HGNC:10740 ∙ Uniprot:Q9H3T2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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	2	2	12
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	2	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)
1-151132921-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-151133140-G-A		not specified	Uncertain significance (Aug 10, 2021)
1-151133151-A-G		not specified	Uncertain significance (Aug 16, 2021)
1-151133355-T-C			Likely benign (Mar 01, 2024)
1-151134828-C-G			Benign (May 21, 2018)
1-151135315-G-A			Benign (May 21, 2018)
1-151136113-C-T		not specified	Uncertain significance (Jul 14, 2021)
1-151136850-T-G			Benign (May 21, 2018)
1-151137041-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-151138034-G-A			Likely benign (Dec 01, 2022)
1-151138078-G-A		not specified	Uncertain significance (Nov 01, 2021)
1-151139661-C-G		not specified	Uncertain significance (Sep 01, 2021)
1-151142531-G-A			Benign (Dec 05, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEMA6C	protein_coding	protein_coding	ENST00000368913	18	14944

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000124	1.00	125632	0	116	125748	0.000461

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	427	530	0.805	0.0000334	5992
Missense in Polyphen		73	93.577	0.7801		959
Synonymous	0.421	217	225	0.964	0.0000138	2169
Loss of Function	3.38	17	40.1	0.424	0.00000230	431

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000109
Finnish	0.00338	0.00338
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.000164	0.000109
South Asian	0.000264	0.000261
Other	0.000326	0.000326

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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