ATXN10
ataxin 10, the group of Armadillo like helical domain containing|MicroRNA protein coding host genes
Basic information
Region (hg38): 22:45671797-45845307
Previous symbols: [ "SCA10" ]
Links
Phenotypes
GenCC
Source:
- spinocerebellar ataxia type 10 (Supportive), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Spinocerebellar ataxia 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 | Neurologic | 11017075; 11506407; 15127363; 16717236; 17420323; 20301354; 20818609; 21236683; 21531163 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (24 variants)
- Inborn genetic diseases (9 variants)
- Spinocerebellar ataxia type 10 (7 variants)
- not specified (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATXN10 gene is commonly pathogenic or not.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 4 | 4 | ||||
missense | 11 | 11 | ||||
nonsense | 1 | 1 | ||||
start loss | 0 | |||||
frameshift | 1 | 1 | ||||
inframe indel | 0 | |||||
splice variant | 2 | 2 | ||||
non coding | 1 | 1 | 16 | 18 | ||
Total | 1 | 0 | 15 | 5 | 16 |
Variants in ATXN10
This is a list of pathogenic ClinVar variants found in the ATXN10 region.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
22-45671813-C-T | Benign (Jun 20, 2021) | |||
22-45672074-C-G | Inborn genetic diseases | Uncertain significance (Jan 03, 2022) | ||
22-45672076-A-G | Spinocerebellar ataxia type 10 | Uncertain significance (Oct 26, 2018) | ||
22-45672094-C-A | Inborn genetic diseases | Uncertain significance (Aug 09, 2021) | ||
22-45672139-C-T | Likely benign (-) | |||
22-45672142-C-T | Inborn genetic diseases | Uncertain significance (Sep 27, 2021) | ||
22-45672183-A-T | Spinocerebellar ataxia type 10 | Uncertain significance (Mar 01, 2019) | ||
22-45672264-G-A | Benign (Nov 10, 2018) | |||
22-45689733-C-G | Inborn genetic diseases | Uncertain significance (Nov 12, 2021) | ||
22-45693008-G-A | not specified • Spinocerebellar ataxia type 10 | Likely benign (Apr 25, 2022) | ||
22-45693025-A-G | Inborn genetic diseases | Uncertain significance (Oct 11, 2021) | ||
22-45700063-T-C | Benign (Jun 19, 2021) | |||
22-45700117-A-G | Benign (Jun 18, 2021) | |||
22-45700294-G-T | Spinocerebellar ataxia type 10 | Uncertain significance (Jul 22, 2021) | ||
22-45702735-A-G | Inborn genetic diseases | Uncertain significance (Apr 01, 2022) | ||
22-45702848-G-GT | Inborn genetic diseases | Uncertain significance (Sep 02, 2021) | ||
22-45718267-C-T | Benign (Nov 10, 2018) | |||
22-45718364-C-T | Benign (Jun 18, 2021) | |||
22-45718518-G-T | Benign (Nov 10, 2018) | |||
22-45729448-T-C | Inborn genetic diseases | Uncertain significance (Jan 03, 2022) | ||
22-45729600-G-T | Likely benign (-) | |||
22-45738744-C-T | Uncertain significance (Jul 22, 2016) | |||
22-45738783-A-AT | Uncertain significance (Oct 10, 2016) | |||
22-45738814-C-T | Likely benign (Jan 01, 2021) | |||
22-45739053-G-A | Benign (Nov 10, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ATXN10 | protein_coding | protein_coding | ENST00000252934 | 11 | 173510 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000345 | 0.998 | 125715 | 0 | 33 | 125748 | 0.000131 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.325 | 270 | 255 | 1.06 | 0.0000135 | 3127 |
Missense in Polyphen | 79 | 75.702 | 1.0436 | 986 | ||
Synonymous | 0.0366 | 100 | 100 | 0.995 | 0.00000537 | 929 |
Loss of Function | 2.69 | 10 | 24.3 | 0.411 | 0.00000130 | 278 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000427 | 0.000427 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000163 | 0.000163 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.000132 | 0.000132 |
Middle Eastern | 0.000163 | 0.000163 |
South Asian | 0.000163 | 0.000163 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Necessary for the survival of cerebellar neurons. Induces neuritogenesis by activating the Ras-MAP kinase pathway. May play a role in the maintenance of a critical intracellular glycosylation level and homeostasis. {ECO:0000250}.;
- Disease
- DISEASE: Note=Defects in ATXN1 may be a cause of nephronophthisis a chronic tubulo-interstitial nephropathy that leads to anemia, polyuria, polydipsia, isosthenuria and death in uremia. {ECO:0000269|PubMed:21565611}.;
Recessive Scores
- pRec
- 0.162
Intolerance Scores
- loftool
- 0.248
- rvis_EVS
- -1.02
- rvis_percentile_EVS
- 7.94
Haploinsufficiency Scores
- pHI
- 0.162
- hipred
- N
- hipred_score
- 0.474
- ghis
- 0.651
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.629
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atxn10
- Phenotype
- skeleton phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- nervous system development;neuron projection development;cilium assembly;protein homotrimerization
- Cellular component
- extracellular space;cytoplasm;cytosol;plasma membrane;membrane;dendrite;neuronal cell body;perinuclear region of cytoplasm
- Molecular function
- protein binding;enzyme binding;identical protein binding