AANAT

aralkylamine N-acetyltransferase, the group of GCN5 related N-acetyltransferases

Basic information

Region (hg38): 17:76453350-76470117

Links

ENSG00000129673 ∙ NCBI:15 ∙ OMIM:600950 ∙ HGNC:19 ∙ Uniprot:Q16613 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (15 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AANAT 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				2	2	4
missense			14	2	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	4	3

Variants in AANAT

This is a list of pathogenic ClinVar variants found in the AANAT region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-76468754-C-T			Benign (Jul 31, 2018)
17-76468832-G-A			Likely benign (Apr 24, 2018)
17-76468838-C-T		not specified	Uncertain significance (Oct 25, 2022)
17-76468900-G-C		not specified	Uncertain significance (Aug 11, 2022)
17-76469176-T-C		not specified	Uncertain significance (May 26, 2022)
17-76469221-G-A		not specified	Uncertain significance (Jun 22, 2023)
17-76469239-G-A		not specified	Uncertain significance (Dec 14, 2023)
17-76469307-G-C		not specified	Uncertain significance (Dec 19, 2023)
17-76469311-A-G		not specified	Uncertain significance (Dec 22, 2023)
17-76469323-T-A		not specified	Uncertain significance (Dec 19, 2022)
17-76469712-T-C			Likely benign (May 24, 2018)
17-76469729-G-A		not specified	Uncertain significance (Aug 18, 2021)
17-76469730-C-T			Likely benign (Mar 01, 2023)
17-76469731-G-A		Delayed sleep phase syndrome, susceptibility to	Uncertain significance (Apr 01, 2003)
17-76469737-C-T		not specified	Uncertain significance (Apr 09, 2022)
17-76469738-G-A		not specified	Uncertain significance (Jun 22, 2021)
17-76469771-G-A		not specified	Uncertain significance (Nov 15, 2021)
17-76469812-G-C		not specified	Uncertain significance (Oct 26, 2021)
17-76469814-C-T			Benign (Mar 29, 2018)
17-76469827-G-A		not specified	Uncertain significance (Mar 17, 2023)
17-76469830-G-A		not specified	Uncertain significance (Jun 14, 2022)
17-76469860-A-T		not specified	Uncertain significance (Mar 22, 2023)
17-76469889-C-A			Benign (Jul 31, 2018)
17-76469902-C-T		not specified	Uncertain significance (Apr 27, 2022)
17-76469905-A-G		not specified	Likely benign (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AANAT	protein_coding	protein_coding	ENST00000250615	4	16767

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00297	0.825	125730	0	11	125741	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0909	154	157	0.980	0.0000105	1604
Missense in Polyphen		58	55.658	1.0421		590
Synonymous	-0.505	70	64.8	1.08	0.00000435	522
Loss of Function	1.13	5	8.55	0.585	3.65e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000284	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Controls the night/day rhythm of melatonin production in the pineal gland. Catalyzes the N-acetylation of serotonin into N- acetylserotonin, the penultimate step in the synthesis of melatonin. {ECO:0000269|PubMed:11313340, ECO:0000305}.
• Pathway: Tryptophan metabolism - Homo sapiens (human);Tryptophan Metabolism;Melatonin metabolism and effects;Tryptophan metabolism;Biogenic Amine Synthesis;serotonin and melatonin biosynthesis;Metabolism of amino acids and derivatives;Metabolism;Tryptophan degradation;superpathway of tryptophan utilization;Serotonin and melatonin biosynthesis;Amine-derived hormones (Consensus)

Recessive Scores

• pRec: 0.211

Intolerance Scores

• loftool: 0.635
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.54

Haploinsufficiency Scores

• pHI: 0.208
• hipred: N
• hipred_score: 0.461
• ghis: 0.402

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Aanat
• Phenotype: endocrine/exocrine gland 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)

Zebrafish Information Network

• Gene name: aanat2
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: N-terminal protein amino acid acetylation;circadian rhythm;response to light stimulus;photoperiodism;response to zinc ion;melatonin biosynthetic process;response to insulin;response to cytokine;response to prostaglandin E;indolalkylamine biosynthetic process;response to copper ion;response to corticosterone;response to calcium ion;cellular response to cAMP
• Cellular component: cytoplasm;cytosol;perinuclear region of cytoplasm
• Molecular function: aralkylamine N-acetyltransferase activity;arylamine N-acetyltransferase activity;protein binding;14-3-3 protein binding