SEPTIN12
septin 12, the group of Septins
Basic information
Region (hg38): 16:4777606-4788398
Previous symbols: [ "SEPT12" ]
Links
Phenotypes
GenCC
Source:
- non-syndromic male infertility due to sperm motility disorder (Supportive), mode of inheritance: AR
- spermatogenic failure 10 (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Spermatogenic failure 10 | 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 | Genitourinary | 22275165; 22479503 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (79 variants)
- Spermatogenic_failure_10 (6 variants)
- not_provided (4 variants)
- SEPTIN12-related_disorder (3 variants)
- Non-syndromic_male_infertility_due_to_sperm_motility_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEPTIN12 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000144605.5. 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 | 82 | 87 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 84 | 8 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SEPTIN12 | protein_coding | protein_coding | ENST00000268231 | 9 | 10853 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 3.35e-19 | 0.000175 | 125559 | 0 | 189 | 125748 | 0.000752 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.54 | 292 | 227 | 1.29 | 0.0000145 | 2339 |
| Missense in Polyphen | 131 | 109.81 | 1.193 | 1091 | ||
| Synonymous | -4.65 | 155 | 96.8 | 1.60 | 0.00000661 | 701 |
| Loss of Function | -1.64 | 24 | 16.8 | 1.43 | 8.02e-7 | 179 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000992 | 0.000911 |
| Ashkenazi Jewish | 0.00726 | 0.00727 |
| East Asian | 0.000602 | 0.000598 |
| Finnish | 0.0000929 | 0.0000924 |
| European (Non-Finnish) | 0.000309 | 0.000308 |
| Middle Eastern | 0.000602 | 0.000598 |
| South Asian | 0.00144 | 0.00144 |
| Other | 0.000824 | 0.000815 |
dbNSFP
Source:
- Function
- FUNCTION: Filament-forming cytoskeletal GTPase (By similarity). Involved in spermatogenesis. Involved in the morphogenesis of sperm heads and the elongation of sperm tails probably implicating the association with alpha- and beta-tubulins (PubMed:24213608). Forms a filamentous structure with SEPT7, 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). May play a role in cytokinesis (Potential). {ECO:0000250, ECO:0000269|PubMed:24213608, ECO:0000269|PubMed:25588830, ECO:0000305}.;
- Disease
- DISEASE: Spermatogenic failure 10 (SPGF10) [MIM:614822]: An infertility disorder caused by spermatogenesis defects. It results in decreased sperm motility, concentration, and multiple sperm structural defects. The most prominent feature is a defective sperm annulus, a ring structure that demarcates the midpiece and the principal piece of the sperm tail. {ECO:0000269|PubMed:22275165, ECO:0000269|PubMed:25588830, ECO:0000269|PubMed:25775403}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Bacterial invasion of epithelial cells - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- loftool
- 0.805
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 28.01
Haploinsufficiency Scores
- pHI
- 0.221
- hipred
- N
- hipred_score
- 0.219
- ghis
- 0.450
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.160
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sept12
- Phenotype
- cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype;
Gene ontology
- Biological process
- spermatogenesis;cell differentiation;flagellated sperm motility;cytoskeleton-dependent cytokinesis
- Cellular component
- stress fiber;nucleus;spindle;septin ring;microtubule cytoskeleton;midbody;septin complex;cleavage furrow;perinuclear region of cytoplasm;sperm annulus
- Molecular function
- GTPase activity;protein binding;GTP binding;GDP binding;protein-containing complex scaffold activity;phosphatidylinositol binding;identical protein binding;protein homodimerization activity