SEMA6B

semaphorin 6B, the group of Semaphorins

Basic information

Region (hg38): 19:4542592-4581776

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

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.

• not provided (7 variants)
• Epilepsy, progressive myoclonic, 11 (1 variants)
• See cases (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.

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				25	4	29
missense		3	74	29	1	107
nonsense	2	2	1			5
start loss						0
frameshift	5	2	4			11
inframe indel			1		1	2
splice donor/acceptor (+/-2bp)		1				1
splice region			1			1
non coding					6	6
Total	7	8	80	54	12

Variants in SEMA6B

This is a list of pathogenic ClinVar variants found in the SEMA6B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-4543626-T-C			Uncertain significance (Jun 01, 2023)
19-4543675-C-A		Inborn genetic diseases • SEMA6B-related disorder	Benign/Likely benign (Mar 09, 2022)
19-4543701-G-A		Inborn genetic diseases	Uncertain significance (Dec 14, 2023)
19-4543713-C-T			Uncertain significance (Jan 10, 2023)
19-4543717-T-A		Inborn genetic diseases	Uncertain significance (Jun 01, 2021)
19-4543741-G-A			Likely benign (Mar 01, 2022)
19-4543744-T-G		Inborn genetic diseases	Uncertain significance (Feb 24, 2022)
19-4543752-G-T		Inborn genetic diseases	Uncertain significance (May 18, 2022)
19-4543776-C-A		Inborn genetic diseases	Uncertain significance (Nov 09, 2023)
19-4543791-G-A		SEMA6B-related disorder	Uncertain significance (Apr 18, 2023)
19-4543825-C-T		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
19-4543829-G-C			Likely benign (Jul 06, 2018)
19-4543855-T-C		Inborn genetic diseases	Likely benign (Jul 20, 2021)
19-4543896-G-C		Epilepsy, progressive myoclonic, 11 • Inborn genetic diseases	Conflicting classifications of pathogenicity (Dec 21, 2022)
19-4543904-C-G			Likely benign (Dec 31, 2019)
19-4543910-G-T		Inborn genetic diseases	Uncertain significance (Sep 01, 2021)
19-4543920-G-A			Uncertain significance (Sep 03, 2022)
19-4543926-C-A		Inborn genetic diseases	Benign/Likely benign (Feb 01, 2024)
19-4543951-G-A		not specified	Uncertain significance (Mar 29, 2024)
19-4543953-C-G		Inborn genetic diseases	Likely benign (Apr 07, 2023)
19-4543954-C-T		Inborn genetic diseases	Uncertain significance (Jul 25, 2023)
19-4543956-T-G		Inborn genetic diseases	Uncertain significance (Sep 14, 2021)
19-4543963-T-G		Inborn genetic diseases	Uncertain significance (Sep 14, 2021)
19-4543966-G-A			Uncertain significance (Jan 14, 2022)
19-4543972-C-T			Uncertain significance (Sep 01, 2022)

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
• 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