ATXN10
Basic information
Region (hg38): 22:45671798-45845307
Previous symbols: [ "SCA10" ]
Links
Phenotypes
GenCC
Source:
- spinocerebellar ataxia type 10 (Supportive), mode of inheritance: AD
- spinocerebellar ataxia type 10 (Strong), 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
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.
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 | 4 | |||||
missense | 10 | 11 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 2 | 2 | ||||
non coding | 16 | 16 | ||||
Total | 0 | 0 | 13 | 5 | 16 |
Variants in ATXN10
This is a list of pathogenic ClinVar variants found in the ATXN10 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
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) | ||
22-45689757-A-G | ATXN10-related disorder | Likely benign (Jun 06, 2019) | ||
22-45693008-G-A | not specified • Spinocerebellar ataxia type 10 | Likely benign (Nov 01, 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-A | Spinocerebellar ataxia type 10 | Uncertain significance (Mar 29, 2024) | ||
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) | ||
22-45729527-C-G | ATXN10-related disorder | Likely benign (Apr 08, 2024) | ||
22-45729600-G-T | Likely benign (-) | |||
22-45738744-C-T | Uncertain significance (Jul 22, 2016) |
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