SEMA4B

semaphorin 4B, the group of Semaphorins

Basic information

Region (hg38): 15:90160604-90229679

Previous symbols: [ "SEMAC" ]

Links

ENSG00000185033 ∙ NCBI:10509 ∙ OMIM:617029 ∙ HGNC:10730 ∙ Uniprot:Q9NPR2 ∙ 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 SEMA4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA4B 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				1		1
missense			65	4		69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	65	5	0

Variants in SEMA4B

This is a list of pathogenic ClinVar variants found in the SEMA4B region.

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

Position	Type	Phenotype	Significance	ClinVar
15-90201604-G-A		not specified	Uncertain significance (Nov 03, 2022)
15-90201649-C-T		not specified	Uncertain significance (Nov 09, 2021)
15-90201663-C-A		not specified	Uncertain significance (Jul 19, 2023)
15-90201672-C-G		not specified	Uncertain significance (Jun 17, 2024)
15-90201675-C-T		not specified	Uncertain significance (Apr 15, 2024)
15-90201679-T-A		not specified	Uncertain significance (Jun 01, 2023)
15-90217463-G-C		not specified	Uncertain significance (Jul 20, 2021)
15-90217468-G-C		not specified	Uncertain significance (Feb 05, 2024)
15-90217508-G-A		not specified	Uncertain significance (May 31, 2023)
15-90217828-A-G		not specified	Uncertain significance (Oct 18, 2021)
15-90219793-C-T		not specified	Uncertain significance (Dec 28, 2022)
15-90219820-C-A		not specified	Uncertain significance (Jan 17, 2024)
15-90219834-C-T			Likely benign (Nov 01, 2022)
15-90219854-G-A		not specified	Uncertain significance (Jan 31, 2024)
15-90220982-A-G		not specified	Uncertain significance (Dec 13, 2023)
15-90220986-T-C		not specified	Uncertain significance (Oct 13, 2023)
15-90221017-G-C			Likely benign (Nov 01, 2022)
15-90221024-G-A		not specified	Likely benign (Jul 15, 2021)
15-90221048-C-T		not specified	Uncertain significance (Feb 16, 2023)
15-90221387-A-G		not specified	Uncertain significance (Oct 04, 2022)
15-90221424-C-G		not specified	Uncertain significance (Mar 30, 2024)
15-90221441-C-T		not specified	Uncertain significance (Apr 19, 2024)
15-90221444-C-T		not specified	Uncertain significance (Oct 26, 2022)
15-90223562-G-A		not specified	Uncertain significance (Jan 30, 2024)
15-90223592-C-T		not specified	Uncertain significance (May 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEMA4B	protein_coding	protein_coding	ENST00000411539	14	69076

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000541	0.999	124611	0	44	124655	0.000177

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.956	430	490	0.878	0.0000310	5329
Missense in Polyphen		152	207.3	0.73323		2245
Synonymous	-1.28	236	212	1.11	0.0000142	1695
Loss of Function	3.83	13	38.8	0.335	0.00000216	394

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000349	0.000346
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000223
Finnish	0.000558	0.000557
European (Non-Finnish)	0.000164	0.000159
Middle Eastern	0.000223	0.000223
South Asian	0.0000671	0.0000654
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons. {ECO:0000250}.
• Pathway: Axon guidance - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.841
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.54

Haploinsufficiency Scores

• pHI: 0.135
• hipred: Y
• hipred_score: 0.706
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.809

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sema4b
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype; renal/urinary system phenotype; immune system phenotype

Gene ontology

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