ATAT1
alpha tubulin acetyltransferase 1, the group of Lysine acetyltransferases
Basic information
Region (hg38): 6:30626842-30646823
Previous symbols: [ "C6orf134" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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 ATAT1 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 | 0 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in ATAT1
This is a list of pathogenic ClinVar variants found in the ATAT1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-30640405-T-G | High myopia | Uncertain significance (Dec 17, 2018) | ||
| 6-30640420-A-G | not specified | Uncertain significance (Oct 03, 2023) | ||
| 6-30640559-C-A | not specified | Uncertain significance (Oct 12, 2021) | ||
| 6-30640565-G-A | not specified | Uncertain significance (Dec 28, 2022) | ||
| 6-30642842-C-A | not specified | Uncertain significance (Aug 02, 2023) | ||
| 6-30642848-C-G | not specified | Uncertain significance (Mar 06, 2023) | ||
| 6-30642848-C-T | not specified | Uncertain significance (Aug 16, 2022) | ||
| 6-30642852-C-T | not specified | Uncertain significance (Dec 06, 2023) | ||
| 6-30642891-G-A | not specified | Uncertain significance (Oct 04, 2022) | ||
| 6-30642953-G-A | not specified | Uncertain significance (Dec 06, 2022) | ||
| 6-30642999-G-A | not specified | Uncertain significance (Mar 01, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ATAT1 | protein_coding | protein_coding | ENST00000330083 | 13 | 19982 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.32e-7 | 0.989 | 125701 | 0 | 47 | 125748 | 0.000187 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.38 | 180 | 240 | 0.750 | 0.0000142 | 2596 |
| Missense in Polyphen | 57 | 82.947 | 0.68719 | 868 | ||
| Synonymous | 1.15 | 69 | 82.3 | 0.839 | 0.00000412 | 829 |
| Loss of Function | 2.34 | 16 | 29.8 | 0.537 | 0.00000206 | 268 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00150 | 0.00135 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000110 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000133 | 0.000123 |
| Middle Eastern | 0.000110 | 0.000109 |
| South Asian | 0.000220 | 0.000196 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Specifically acetylates 'Lys-40' in alpha-tubulin on the lumenal side of microtubules. Promotes microtubule destabilization and accelerates microtubule dynamics; this activity may be independent of acetylation activity. Acetylates alpha-tubulin with a slow enzymatic rate, due to a catalytic site that is not optimized for acetyl transfer. Enters the microtubule through each end and diffuses quickly throughout the lumen of microtubules. Acetylates only long/old microtubules because of its slow acetylation rate since it does not have time to act on dynamically unstable microtubules before the enzyme is released. Required for normal sperm flagellar function. Promotes directional cell locomotion and chemotaxis, through AP2A2-dependent acetylation of alpha-tubulin at clathrin-coated pits that are concentrated at the leading edge of migrating cells. May facilitate primary cilium assembly. {ECO:0000255|HAMAP-Rule:MF_03130, ECO:0000269|PubMed:20829795, ECO:0000269|PubMed:21068373, ECO:0000269|PubMed:24097348, ECO:0000269|PubMed:24906155}.;
- Pathway
- miR-targeted genes in lymphocytes - TarBase;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.91
Haploinsufficiency Scores
- pHI
- 0.0776
- hipred
- N
- hipred_score
- 0.471
- ghis
- 0.498
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Atat1
- 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); normal phenotype; reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- atat1
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- spermatogenesis;dentate gyrus development;regulation of fat cell differentiation;neuron development;cilium assembly;regulation of microtubule cytoskeleton organization;alpha-tubulin acetylation;positive regulation of NLRP3 inflammasome complex assembly
- Cellular component
- Golgi apparatus;cytosol;microtubule;clathrin-coated pit;focal adhesion;axon;mitotic spindle;microtubule bundle
- Molecular function
- lysine N-acetyltransferase activity, acting on acetyl phosphate as donor;tubulin N-acetyltransferase activity;coenzyme binding