SEMA6A
Basic information
Region (hg38): 5:116443554-116574823
Previous symbols: [ "SEMAQ" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 7 | |||||
missense | 58 | 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) | |||
5-116446834-T-G | not specified | Uncertain significance (May 06, 2024) | ||
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) | ||
5-116447272-T-C | not specified | Uncertain significance (Apr 06, 2024) |
GnomAD
Source:
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:
- 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