SEMA6B

semaphorin 6B, the group of Semaphorins

Basic information

Region (hg38): 19:4542588-4581776

Previous symbols: [ "SEMAN" ]

Links

ENSG00000167680

∙ NCBI:10501 ∙ OMIM:608873 ∙ HGNC:10739 ∙ Uniprot:Q9H3T3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

epilepsy, progressive myoclonic, 11 (Moderate), mode of inheritance: AD
epilepsy, progressive myoclonic, 11 (Strong), mode of inheritance: AD
epilepsy, progressive myoclonic, 11 (Moderate), mode of inheritance: AD
epilepsy, progressive myoclonic, 11 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Epilepsy, progressive myoclonic, 11	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	32169168
As with other conditions involving seizures, optimal seizure control is beneficial, and awareness of genetic causes may help with medication selection

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEMA6B gene.

Inborn_genetic_diseases (144 variants)
not_provided (113 variants)
Epilepsy,_progressive_myoclonic,_11 (25 variants)
SEMA6B-related_disorder (23 variants)
Retinal_dystrophy (16 variants)
Optic_atrophy (3 variants)
Intellectual_disability (2 variants)
See_cases (2 variants)
not_specified (2 variants)
Isolated_unilateral_hemispheric_cerebellar_hypoplasia (1 variants)
Grade_I_preterm_intraventricular_hemorrhage (1 variants)
Congenital_cerebellar_hypoplasia (1 variants)
Epilepsy_with_myoclonic_atonic_seizures (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA6B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032108.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	29 clinvar	3 clinvar	33
missense		4 clinvar	178 clinvar	39 clinvar	2 clinvar	223
nonsense	4 clinvar	4 clinvar	3 clinvar			11
start loss						0
frameshift	7 clinvar	3 clinvar	8 clinvar			18
splice donor/acceptor (+/-2bp)		2 clinvar				2
Total	11	13	190	68	5

Highest pathogenic variant AF is 0.000008593383

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEMA6B	protein_coding	protein_coding	ENST00000586582	16	17221

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0623	0.938	125727	0	16	125743	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.22	310	441	0.703	0.0000315	5538
Missense in Polyphen		126	201.14	0.62643		2263
Synonymous	-0.385	219	212	1.03	0.0000173	1999
Loss of Function	3.97	9	34.0	0.265	0.00000189	368

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000938	0.0000462
European (Non-Finnish)	0.0000899	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: May play a role in both peripheral and central nervous system development. {ECO:0000250}.;
Pathway: Axon guidance - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

pHI: 0.254
hipred: Y
hipred_score: 0.563
ghis: 0.654

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: N
gene_indispensability_score: 0.245

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Sema6b
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);

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;integral component of plasma membrane
Molecular function: semaphorin receptor binding;chemorepellent activity