SPAG6
Basic information
Region (hg38): 10:22345445-22454224
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 SPAG6 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 | |||||
missense | 36 | 37 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 36 | 2 | 1 |
Variants in SPAG6
This is a list of pathogenic ClinVar variants found in the SPAG6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
10-22345802-G-C | not specified | Uncertain significance (Aug 05, 2023) | ||
10-22360822-A-C | SPAG6-related disorder | Likely benign (Sep 29, 2020) | ||
10-22364898-C-G | not specified | Uncertain significance (Feb 16, 2023) | ||
10-22364950-T-A | not specified | Uncertain significance (Nov 15, 2024) | ||
10-22368495-C-T | not specified | Uncertain significance (Aug 10, 2024) | ||
10-22368505-A-G | not specified | Uncertain significance (Aug 19, 2024) | ||
10-22368567-A-G | not specified | Uncertain significance (Oct 19, 2024) | ||
10-22368647-G-C | not specified | Uncertain significance (Jan 18, 2022) | ||
10-22368663-G-A | not specified | Uncertain significance (Aug 05, 2024) | ||
10-22386815-G-A | Benign (Jun 01, 2018) | |||
10-22386838-T-C | not specified | Uncertain significance (Nov 08, 2021) | ||
10-22386849-G-A | not specified | Uncertain significance (Mar 30, 2024) | ||
10-22386862-T-C | not specified | Uncertain significance (May 07, 2024) | ||
10-22386864-G-T | not specified | Likely benign (Mar 30, 2024) | ||
10-22386942-C-A | not specified | Uncertain significance (Nov 09, 2023) | ||
10-22387844-A-T | not specified | Uncertain significance (Oct 07, 2022) | ||
10-22387865-G-A | not specified | Uncertain significance (Jul 22, 2024) | ||
10-22387907-G-C | not specified | Uncertain significance (Sep 21, 2023) | ||
10-22387994-G-A | not specified | Uncertain significance (May 30, 2023) | ||
10-22389220-T-A | not specified | Uncertain significance (Oct 12, 2022) | ||
10-22389235-C-T | not specified | Uncertain significance (Dec 13, 2023) | ||
10-22389236-G-T | not specified | Uncertain significance (Feb 17, 2024) | ||
10-22389265-G-A | not specified | Uncertain significance (Apr 04, 2024) | ||
10-22389289-G-A | not specified | Uncertain significance (Mar 20, 2023) | ||
10-22389305-T-C | not specified | Uncertain significance (Nov 10, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SPAG6 | protein_coding | protein_coding | ENST00000376624 | 11 | 108755 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.30e-13 | 0.0891 | 125678 | 0 | 70 | 125748 | 0.000278 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.743 | 238 | 273 | 0.873 | 0.0000136 | 3274 |
Missense in Polyphen | 60 | 75.33 | 0.7965 | 986 | ||
Synonymous | -0.688 | 114 | 105 | 1.09 | 0.00000582 | 1038 |
Loss of Function | 0.674 | 22 | 25.7 | 0.857 | 0.00000135 | 305 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000272 | 0.000272 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.00105 | 0.00103 |
Finnish | 0.000277 | 0.000277 |
European (Non-Finnish) | 0.000257 | 0.000255 |
Middle Eastern | 0.00105 | 0.00103 |
South Asian | 0.000239 | 0.000229 |
Other | 0.000329 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Important for structural integrity of the central apparatus in the sperm tail and for flagellar motility. {ECO:0000250, ECO:0000269|PubMed:10493827}.;
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- loftool
- 0.770
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.66
Haploinsufficiency Scores
- pHI
- 0.131
- hipred
- N
- hipred_score
- 0.454
- ghis
- 0.457
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.278
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Spag6
- Phenotype
Gene ontology
- Biological process
- spermatid development;cell projection organization
- Cellular component
- nucleus;microtubule;axoneme;microtubule cytoskeleton;motile cilium
- Molecular function