SEMA3C

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

Basic information

Region (hg38): 7:80742537-80922359

Previous symbols: [ "SEMAE" ]

Links

ENSG00000075223 ∙ NCBI:10512 ∙ OMIM:602645 ∙ HGNC:10725 ∙ Uniprot:Q99985 ∙ 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 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	2	10
missense			42	2	3	47
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region				3	1	4
non coding					2	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 disorder	Likely benign (Apr 19, 2022)
7-80744914-T-C		SEMA3C-related disorder • not specified	Uncertain significance (Nov 29, 2023)
7-80744934-C-T		SEMA3C-related disorder	Uncertain significance (Sep 27, 2022)
7-80744940-T-C		SEMA3C-related disorder	Uncertain significance (Oct 20, 2023)
7-80744964-T-C		not specified	Uncertain significance (Dec 26, 2023)
7-80745012-C-T		SEMA3C-related disorder	Uncertain significance (Jan 27, 2023)
7-80745026-A-G		SEMA3C-related disorder	Benign (Jul 19, 2022)
7-80745029-T-C		SEMA3C-related disorder	Likely benign (May 21, 2021)
7-80745064-C-T		not specified	Uncertain significance (Feb 28, 2023)
7-80745085-G-T		SEMA3C-related disorder • not specified	Uncertain significance (Feb 15, 2024)
7-80745122-T-C		SEMA3C-related disorder	Benign (Jul 19, 2022)
7-80745135-T-C		SEMA3C-related disorder • not specified	Conflicting classifications of pathogenicity (Oct 14, 2023)
7-80745137-C-T		SEMA3C-related disorder	Likely benign (Jun 16, 2023)
7-80745212-T-C		SEMA3C-related disorder	Likely benign (Aug 19, 2021)
7-80745216-G-C			Benign (Dec 31, 2019)
7-80745220-T-C		SEMA3C-related disorder	Uncertain significance (Oct 02, 2023)
7-80745255-G-A		SEMA3C-related disorder	Uncertain significance (May 22, 2023)
7-80745265-G-C		SEMA3C-related disorder	Uncertain significance (Feb 22, 2024)
7-80748901-T-C		SEMA3C-related disorder	Likely benign (Apr 13, 2022)
7-80748909-T-C		not specified	Uncertain significance (May 27, 2022)
7-80748934-C-T		SEMA3C-related disorder	Likely benign (May 11, 2023)
7-80748939-T-C			Benign (Dec 31, 2019)
7-80748945-C-A		SEMA3C-related disorder	Uncertain significance (Sep 28, 2022)
7-80748949-C-T		SEMA3C-related disorder	Benign/Likely benign (May 19, 2021)
7-80748978-T-C		SEMA3C-related disorder • not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

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: 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

	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