SEMA5B

semaphorin 5B, the group of Semaphorins

Basic information

Region (hg38): 3:122909081-123028605

Previous symbols: [ "SEMAG" ]

Links

ENSG00000082684 ∙ NCBI:54437 ∙ OMIM:609298 ∙ HGNC:10737 ∙ Uniprot:Q9P283 ∙ 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 SEMA5B gene.

• Inborn genetic diseases (52 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA5B 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			49	3	1	53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	49	3	3

Variants in SEMA5B

This is a list of pathogenic ClinVar variants found in the SEMA5B region.

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

Position	Type	Phenotype	Significance	ClinVar
3-122910186-C-T		not specified	Uncertain significance (Jun 01, 2023)
3-122910854-G-C		not specified	Uncertain significance (Aug 31, 2022)
3-122910884-C-T		not specified	Uncertain significance (May 10, 2022)
3-122910904-T-C		not specified	Uncertain significance (May 17, 2023)
3-122910914-C-A		not specified	Uncertain significance (Dec 09, 2023)
3-122911021-G-C		not specified	Uncertain significance (Dec 19, 2022)
3-122911033-A-G		not specified	Uncertain significance (Oct 10, 2023)
3-122911476-T-G			Benign (Sep 12, 2018)
3-122911499-T-C			Benign (Sep 12, 2018)
3-122911515-T-C		not specified	Likely benign (Aug 16, 2021)
3-122911937-G-C		not specified	Uncertain significance (Jul 25, 2023)
3-122911951-C-G		not specified	Uncertain significance (Aug 02, 2021)
3-122912030-T-G		not specified	Uncertain significance (Nov 27, 2023)
3-122912060-G-A		not specified	Uncertain significance (May 31, 2023)
3-122912201-T-C		not specified	Uncertain significance (Dec 03, 2021)
3-122912208-T-A		not specified	Uncertain significance (Sep 14, 2022)
3-122912903-C-T		not specified	Uncertain significance (Feb 10, 2022)
3-122912930-A-C		not specified	Uncertain significance (Jul 05, 2023)
3-122912932-G-A		not specified	Uncertain significance (Aug 09, 2021)
3-122912990-C-G		not specified	Uncertain significance (Dec 18, 2023)
3-122913004-C-A		not specified	Uncertain significance (Oct 26, 2022)
3-122913008-C-A		not specified	Uncertain significance (Feb 28, 2023)
3-122913017-T-C		not specified	Uncertain significance (May 31, 2022)
3-122913022-G-C		not specified	Uncertain significance (Feb 03, 2022)
3-122913200-G-T		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEMA5B	protein_coding	protein_coding	ENST00000451055	23	119412

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.64e-10	1.00	125656	0	92	125748	0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	625	740	0.845	0.0000486	7682
Missense in Polyphen		239	314.17	0.76073		3136
Synonymous	0.0341	314	315	0.998	0.0000218	2444
Loss of Function	4.09	27	61.6	0.438	0.00000325	633

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000608	0.000604
Ashkenazi Jewish	0.000235	0.000198
East Asian	0.000228	0.000217
Finnish	0.000677	0.000554
European (Non-Finnish)	0.000370	0.000343
Middle Eastern	0.000228	0.000217
South Asian	0.000586	0.000523
Other	0.000337	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as positive axonal guidance cues. {ECO:0000250}.
• Pathway: Axon guidance - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.668
• rvis_EVS: -0.45
• rvis_percentile_EVS: 23.73

Haploinsufficiency Scores

• pHI: 0.712
• hipred: Y
• hipred_score: 0.733
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.131

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sema5b
• Phenotype: immune system phenotype; 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); vision/eye phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: neural crest cell migration;positive regulation of cell migration;axon extension;negative regulation of axon extension involved in axon guidance;detection of light stimulus involved in visual perception;negative chemotaxis;semaphorin-plexin signaling pathway;neuron projection guidance
• Cellular component: integral component of membrane
• Molecular function: semaphorin receptor binding;chemorepellent activity