SEMA4C

semaphorin 4C, the group of Immunoglobulin like domain containing|Semaphorins

Basic information

Region (hg38): 2:96859717-96870757

Previous symbols: [ "SEMAI" ]

Links

ENSG00000168758 ∙ NCBI:54910 ∙ OMIM:604462 ∙ HGNC:10731 ∙ Uniprot:Q9C0C4 ∙ 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 SEMA4C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA4C 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			51	2		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	51	2	0

Variants in SEMA4C

This is a list of pathogenic ClinVar variants found in the SEMA4C region.

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

Position	Type	Phenotype	Significance	ClinVar
2-96860696-T-C		not specified	Uncertain significance (Jan 09, 2024)
2-96860730-C-T		not specified	Uncertain significance (Jan 05, 2022)
2-96860784-G-A		not specified	Uncertain significance (Jun 22, 2023)
2-96860840-G-A		not specified	Uncertain significance (Jul 30, 2023)
2-96860876-C-G		not specified	Uncertain significance (Nov 03, 2023)
2-96860876-C-T		not specified	Uncertain significance (Oct 14, 2023)
2-96860903-G-C		not specified	Uncertain significance (Feb 16, 2023)
2-96860925-C-T		not specified	Uncertain significance (Jan 26, 2022)
2-96860976-G-C		not specified	Uncertain significance (Mar 29, 2022)
2-96860976-G-T		not specified	Uncertain significance (Oct 17, 2023)
2-96861030-C-T		not specified	Uncertain significance (Oct 04, 2022)
2-96861056-C-T		not specified	Uncertain significance (Aug 22, 2023)
2-96861062-C-T		not specified	Uncertain significance (Aug 08, 2023)
2-96861248-C-T		not specified	Uncertain significance (Dec 18, 2023)
2-96861320-A-T		not specified	Uncertain significance (Jan 26, 2023)
2-96861321-A-G		not specified	Uncertain significance (Jan 16, 2024)
2-96861350-C-T		not specified	Uncertain significance (Jun 30, 2022)
2-96861368-C-T		not specified	Uncertain significance (Dec 12, 2023)
2-96861369-G-A		not specified	Uncertain significance (Jan 17, 2023)
2-96861401-G-C		not specified	Uncertain significance (Oct 26, 2022)
2-96861449-G-T		not specified	Uncertain significance (Jul 20, 2022)
2-96861608-C-G		not specified	Uncertain significance (Feb 09, 2023)
2-96861765-G-A		not specified	Uncertain significance (Jun 28, 2023)
2-96861791-T-C		not specified	Uncertain significance (Jun 14, 2023)
2-96861837-T-C		not specified	Likely benign (Dec 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEMA4C	protein_coding	protein_coding	ENST00000305476	14	11042

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000452	119147	815	5768	125730	0.0265

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.39	379	534	0.710	0.0000349	5303
Missense in Polyphen		100	207.39	0.48219		2159
Synonymous	0.622	222	234	0.948	0.0000150	1800
Loss of Function	5.63	1	38.9	0.0257	0.00000185	418

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.209	0.208
Ashkenazi Jewish	0.00211	0.00209
East Asian	0.00387	0.00387
Finnish	0.00	0.00
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.00387	0.00387
South Asian	0.0000980	0.0000980
Other	0.0230	0.0224

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell surface receptor for PLXNB2 that plays an important role in cell-cell signaling. PLXNB2 binding promotes downstream activation of RHOA and phosphorylation of ERBB2 at 'Tyr-1248'. Required for normal brain development, axon guidance and cell migration (By similarity). Probable signaling receptor which may play a role in myogenic differentiation through activation of the stress-activated MAPK cascade. {ECO:0000250, ECO:0000269|PubMed:17498836}.
• Pathway: Axon guidance - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.163
• rvis_EVS: -0.78
• rvis_percentile_EVS: 13.05

Haploinsufficiency Scores

• pHI: 0.617
• hipred: Y
• hipred_score: 0.662
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.813

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sema4c
• 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); cellular phenotype

Gene ontology

• Biological process: neural crest cell migration;neural tube closure;cell migration in hindbrain;cerebellum development;positive regulation of cell migration;positive regulation of stress-activated MAPK cascade;muscle cell differentiation;negative regulation of axon extension involved in axon guidance;negative chemotaxis;semaphorin-plexin signaling pathway
• Cellular component: extracellular space;integral component of plasma membrane;postsynaptic density;cell junction;synaptic vesicle membrane;postsynaptic membrane
• Molecular function: protein binding;semaphorin receptor binding;neuropilin binding;chemorepellent activity