ATXN7
ataxin 7, the group of SAGA complex
Basic information
Region (hg38): 3:63863155-64003462
Previous symbols: [ "SCA7" ]
Links
Phenotypes
GenCC
Source:
- spinocerebellar ataxia type 7 (Moderate), mode of inheritance: AD
- spinocerebellar ataxia type 7 (Supportive), mode of inheritance: AD
- spinocerebellar ataxia 7 (Definitive), mode of inheritance: AD
- spinocerebellar ataxia 7 (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Spinocerebellar ataxia 7 | 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; Ophthalmologic | 7477379; 8908515; 9288099; 9536097; 9736784; 10330346; 10453742; 11030806; 15349877; 15750685; 15747371; 20301433; 23368522 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (154 variants)
- not_provided (22 variants)
- ATXN7-related_disorder (8 variants)
- Spinocerebellar_ataxia_7 (7 variants)
- not_specified (6 variants)
- Retinal_dystrophy (4 variants)
- Abnormality_of_neuronal_migration (2 variants)
- Tip-toe_gait (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATXN7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001377405.1. 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 | 6 | |||||
| missense | 157 | 13 | 172 | |||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 2 | 161 | 15 | 3 |
Highest pathogenic variant AF is 0.0000047883545
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATXN7 | protein_coding | protein_coding | ENST00000398590 | 12 | 138906 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.960 | 0.0405 | 124790 | 0 | 4 | 124794 | 0.0000160 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.623 | 544 | 505 | 1.08 | 0.0000276 | 6099 |
| Missense in Polyphen | 160 | 193.1 | 0.82859 | 2347 | ||
| Synonymous | -0.838 | 221 | 206 | 1.07 | 0.0000126 | 1974 |
| Loss of Function | 4.43 | 5 | 32.1 | 0.156 | 0.00000163 | 435 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000556 | 0.0000556 |
| Finnish | 0.0000464 | 0.0000464 |
| European (Non-Finnish) | 0.00000900 | 0.00000883 |
| Middle Eastern | 0.0000556 | 0.0000556 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000165 | 0.000165 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as component of the STAGA transcription coactivator-HAT complex. Mediates the interaction of STAGA complex with the CRX and is involved in CRX-dependent gene activation. Necessary for microtubule cytoskeleton stabilization. {ECO:0000269|PubMed:22100762}.;
- Disease
- DISEASE: Spinocerebellar ataxia 7 (SCA7) [MIM:164500]: Spinocerebellar ataxia is a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA7 belongs to the autosomal dominant cerebellar ataxias type II (ADCA II) which are characterized by cerebellar ataxia with retinal degeneration and pigmentary macular dystrophy. {ECO:0000269|PubMed:9288099}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Post-translational protein modification;Metabolism of proteins;Chromatin modifying enzymes;HATs acetylate histones;Ub-specific processing proteases;Deubiquitination;Chromatin organization
(Consensus)
Recessive Scores
- pRec
- 0.440
Intolerance Scores
- loftool
- 0.381
- rvis_EVS
- 0.21
- rvis_percentile_EVS
- 67.5
Haploinsufficiency Scores
- pHI
- 0.401
- hipred
- Y
- hipred_score
- 0.518
- ghis
- 0.522
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.671
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | High | Medium | High |
Mouse Genome Informatics
- Gene name
- Atxn7
- Phenotype
- muscle phenotype; growth/size/body region phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system 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);
Zebrafish Information Network
- Gene name
- atxn7
- Affected structure
- photoreceptor cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- microtubule cytoskeleton organization;nucleus organization;visual perception;histone deubiquitination;protein deubiquitination
- Cellular component
- nucleus;nucleoplasm;nucleolus;cytosol;microtubule cytoskeleton;nuclear matrix
- Molecular function
- protein binding;thiol-dependent ubiquitinyl hydrolase activity