SEPTIN6
Basic information
Region (hg38): X:119615724-119693370
Previous symbols: [ "SEPT6" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (27 variants)
- not_provided (4 variants)
- SEPTIN6-related_disorder (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEPTIN6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000145799.4. 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 | 3 | |||||
| missense | 28 | 30 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 28 | 5 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SEPTIN6 | protein_coding | protein_coding | ENST00000343984 | 10 | 77647 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.932 | 0.0682 | 125619 | 0 | 3 | 125622 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.70 | 112 | 175 | 0.639 | 0.0000144 | 2884 |
| Missense in Polyphen | 50 | 93.69 | 0.53367 | 1537 | ||
| Synonymous | 0.402 | 70 | 74.4 | 0.941 | 0.00000666 | 793 |
| Loss of Function | 3.42 | 2 | 17.4 | 0.115 | 0.00000146 | 266 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000372 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Filament-forming cytoskeletal GTPase. Required for normal organization of the actin cytoskeleton. Involved in cytokinesis. May play a role in HCV RNA replication. Forms a filamentous structure with SEPT12, SEPT6, SEPT2 and probably SEPT4 at the sperm annulus which is required for the structural integrity and motility of the sperm tail during postmeiotic differentiation (PubMed:25588830). {ECO:0000269|PubMed:17229681, ECO:0000269|PubMed:17803907, ECO:0000305|PubMed:25588830}.;
- Pathway
- Bacterial invasion of epithelial cells - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.146
Intolerance Scores
- loftool
- 0.111
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35.42
Haploinsufficiency Scores
- pHI
- 0.461
- hipred
- Y
- hipred_score
- 0.749
- ghis
- 0.652
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.358
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sept6
- Phenotype
- normal phenotype;
Zebrafish Information Network
- Gene name
- sept6
- Affected structure
- pronephric tubule
- Phenotype tag
- abnormal
- Phenotype quality
- dilated
Gene ontology
- Biological process
- mitotic cytokinesis;spermatogenesis;viral process;cell differentiation;cilium assembly;cytoskeleton-dependent cytokinesis
- Cellular component
- condensed chromosome kinetochore;spindle;septin ring;synaptic vesicle;microtubule cytoskeleton;midbody;septin complex;cleavage furrow;septin collar;axon terminus;sperm annulus
- Molecular function
- GTPase activity;protein binding;GTP binding;protein-containing complex scaffold activity