ATAT1

alpha tubulin acetyltransferase 1, the group of Lysine acetyltransferases

Basic information

Region (hg38): 6:30626842-30646823

Previous symbols: [ "C6orf134" ]

Links

ENSG00000137343 ∙ NCBI:79969 ∙ OMIM:615556 ∙ HGNC:21186 ∙ Uniprot:Q5SQI0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 15.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001413067.1	NP_001399996.1	13	yes	-
ENST00000376485.9	ENSP00000365668.4	13	yes	-
NM_024909.5	NP_079185.2	11	-	-
NM_001031722.4	NP_001026892.1	13	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATAT1 gene.

• not_specified (32 variants)
• High_myopia (1 variants)

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. These statistics are base on transcript: NM_001413067.1. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2			2
missense			30	4		34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	34	4	0

GnomAD

Source: gnomAD

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
		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: dbNSFP

• 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

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

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

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