SEMA6A

semaphorin 6A, the group of Semaphorins

Basic information

Region (hg38): 5:116443554-116574823

Previous symbols: [ "SEMAQ" ]

Links

ENSG00000092421 ∙ NCBI:57556 ∙ OMIM:605885 ∙ HGNC:10738 ∙ Uniprot:Q9H2E6 ∙ 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 SEMA6A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA6A 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				2	5	7
missense		1	58	4		63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	1	58	6	5

Variants in SEMA6A

This is a list of pathogenic ClinVar variants found in the SEMA6A region.

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

Position	Type	Phenotype	Significance	ClinVar
5-116446678-C-T		not specified	Uncertain significance (Oct 27, 2021)
5-116446689-A-C		not specified	Uncertain significance (May 23, 2023)
5-116446698-G-A		not specified	Uncertain significance (Nov 15, 2021)
5-116446708-G-C		not specified	Uncertain significance (Aug 08, 2022)
5-116446792-G-A		not specified	Uncertain significance (Aug 12, 2021)
5-116446797-T-G			Benign/Likely benign (Oct 01, 2023)
5-116446912-T-A		not specified	Uncertain significance (Aug 02, 2022)
5-116446915-C-G			Likely benign (Jan 18, 2018)
5-116446915-C-T		not specified	Uncertain significance (Sep 27, 2021)
5-116446933-G-A		not specified	Uncertain significance (Jun 07, 2023)
5-116446955-C-G		not specified	Uncertain significance (Apr 07, 2023)
5-116446999-G-A		not specified	Uncertain significance (Mar 05, 2024)
5-116447028-G-T		not specified	Uncertain significance (Dec 27, 2023)
5-116447034-G-A			Likely benign (Jul 20, 2018)
5-116447034-G-T		not specified	Uncertain significance (Feb 05, 2024)
5-116447097-A-G		not specified	Uncertain significance (Mar 23, 2022)
5-116447128-T-C		not specified	Uncertain significance (Dec 13, 2021)
5-116447142-A-C		not specified	Uncertain significance (Mar 07, 2024)
5-116447178-A-G		not specified	Uncertain significance (Nov 15, 2021)
5-116447205-T-C		not specified	Uncertain significance (Nov 14, 2023)
5-116447217-A-G		not specified	Uncertain significance (Jul 16, 2021)
5-116447244-G-A		not specified	Uncertain significance (Jun 11, 2021)
5-116447251-G-A		not specified	Uncertain significance (Oct 27, 2021)
5-116447283-G-A		not specified	Uncertain significance (Nov 09, 2021)
5-116447284-A-G		not specified	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEMA6A	protein_coding	protein_coding	ENST00000343348	18	131319

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000244	124630	0	15	124645	0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.747	543	594	0.914	0.0000353	6744
Missense in Polyphen		209	278.27	0.75108		3108
Synonymous	-1.23	269	244	1.10	0.0000165	2028
Loss of Function	5.39	4	41.4	0.0965	0.00000196	541

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000945	0.0000935
Ashkenazi Jewish	0.0000994	0.0000994
East Asian	0.000111	0.000111
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.0000725	0.0000708
Middle Eastern	0.000111	0.000111
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell surface receptor for PLXNA2 that plays an important role in cell-cell signaling. Required for normal granule cell migration in the developing cerebellum. Promotes reorganization of the actin cytoskeleton and plays an important role in axon guidance in the developing central nervous system. Can act as repulsive axon guidance cue. Has repulsive action towards migrating granular neurons. May play a role in channeling sympathetic axons into the sympathetic chains and controlling the temporal sequence of sympathetic target innervation (By similarity). {ECO:0000250}.
• Pathway: Axon guidance - Homo sapiens (human);Spinal Cord Injury;Developmental Biology;Other semaphorin interactions;Semaphorin interactions;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.470

Intolerance Scores

• loftool: 0.133
• rvis_EVS: -0.06
• rvis_percentile_EVS: 48.91

Haploinsufficiency Scores

• pHI: 0.565
• hipred: Y
• hipred_score: 0.785
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.878

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sema6a
• 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

Zebrafish Information Network

• Gene name: sema6a
• Affected structure: optic cup
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: neural crest cell migration;apoptotic process;cytoskeleton organization;cell surface receptor signaling pathway;nervous system development;axon guidance;animal organ morphogenesis;negative regulation of angiogenesis;positive regulation of cell migration;cellular response to vascular endothelial growth factor stimulus;negative regulation of axon extension involved in axon guidance;negative chemotaxis;negative regulation of ERK1 and ERK2 cascade;semaphorin-plexin signaling pathway;negative regulation of cell adhesion involved in sprouting angiogenesis;negative regulation of vascular endothelial growth factor signaling pathway;negative regulation of sprouting angiogenesis;positive regulation of neuron migration
• Cellular component: extracellular space;integral component of plasma membrane;integral component of membrane;axon
• Molecular function: protein binding;semaphorin receptor binding;chemorepellent activity