TAT

tyrosine aminotransferase

Basic information

Region (hg38): 16:71565660-71577092

Links

ENSG00000198650 ∙ NCBI:6898 ∙ OMIM:613018 ∙ HGNC:11573 ∙ Uniprot:P17735 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• tyrosinemia type II (Definitive), mode of inheritance: AR
• tyrosinemia type II (Definitive), mode of inheritance: AR
• tyrosinemia type II (Strong), mode of inheritance: AR
• tyrosinemia type II (Strong), mode of inheritance: AR
• tyrosinemia type II (Supportive), mode of inheritance: AR
• tyrosinemia type II (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Tyrosinemia, type II	AR	Biochemical	Dietary measures (controlled intake of phenylalanine and tyrosine) can be effective, including as relates to neurocognitive outcome	Biochemical; Dermatologic; Neurologic; Ophthalmologic	18901242; 33934; 6446465; 1356171; 1357662; 8912606; 12227462; 9544843; 16574453; 16917729; 18945316; 21145993; 21636300

ClinVar

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

• Tyrosinemia type II (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TAT 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				153	3	156
missense		6	47	2	2	57
nonsense	5	7				12
start loss		1				1
frameshift	6	15				21
inframe indel						0
splice donor/acceptor (+/-2bp)	1	16	1			18
splice region		1	5	31		37
non coding			26	86	8	120
Total	12	45	74	241	13

Highest pathogenic variant AF is 0.00000657

Variants in TAT

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

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

Position	Type	Phenotype	Significance	ClinVar
16-71566867-TA-T		Hypertyrosinemia	Uncertain significance (Jun 14, 2016)
16-71566868-A-T		Tyrosinemia type II	Benign (Jan 13, 2018)
16-71567078-C-T		Tyrosinemia type II	Uncertain significance (Jan 12, 2018)
16-71567088-C-G		Tyrosinemia type II	Likely benign (Jan 12, 2018)
16-71567089-T-C		Tyrosinemia type II	Uncertain significance (Jan 12, 2018)
16-71567153-A-G		Tyrosinemia type II	Uncertain significance (Jan 13, 2018)
16-71567161-T-C		Tyrosinemia type II	Uncertain significance (Jan 13, 2018)
16-71567281-C-T		Tyrosinemia type II	Likely benign (Jan 12, 2018)
16-71567292-C-T		Tyrosinemia type II	Uncertain significance (Jan 13, 2018)
16-71567331-C-G		Tyrosinemia type II	Likely benign (Jan 12, 2018)
16-71567370-C-T		Tyrosinemia type II	Uncertain significance (Jan 13, 2018)
16-71567402-C-T		Tyrosinemia type II	Uncertain significance (Jan 13, 2018)
16-71567431-A-C		Tyrosinemia type II	Uncertain significance (Jan 13, 2018)
16-71567462-A-G		Tyrosinemia type II	Likely benign (Jan 12, 2018)
16-71567484-C-G		Tyrosinemia type II	Uncertain significance (Jan 13, 2018)
16-71567563-C-T		Tyrosinemia type II	Uncertain significance (Jan 12, 2018)
16-71567665-A-T		Tyrosinemia type II	Uncertain significance (Jan 13, 2018)
16-71567735-C-T		Tyrosinemia type II	Uncertain significance (Apr 27, 2017)
16-71567741-C-A		Tyrosinemia type II	Uncertain significance (Apr 27, 2017)
16-71567747-T-TAG		Hypertyrosinemia	Likely benign (Jun 14, 2016)
16-71567791-TTTC-T		Hypertyrosinemia	Uncertain significance (Jun 14, 2016)
16-71567891-C-G		Tyrosinemia type II	Uncertain significance (Jan 13, 2018)
16-71567892-G-C		Tyrosinemia type II	Uncertain significance (Jan 12, 2018)
16-71567893-A-T		Tyrosinemia type II	Uncertain significance (Jan 13, 2018)
16-71567925-C-T		Tyrosinemia type II	Uncertain significance (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TAT	protein_coding	protein_coding	ENST00000355962	11	11471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00690	0.992	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.760	220	254	0.866	0.0000147	2969
Missense in Polyphen		57	83.654	0.68138		996
Synonymous	0.384	89	93.7	0.950	0.00000527	884
Loss of Function	2.97	8	23.5	0.340	0.00000139	275

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000880	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transaminase involved in tyrosine breakdown. Converts tyrosine to p-hydroxyphenylpyruvate. Can catalyze the reverse reaction, using glutamic acid, with 2-oxoglutarate as cosubstrate (in vitro). Has much lower affinity and transaminase activity towards phenylalanine. {ECO:0000269|PubMed:16640556, ECO:0000269|PubMed:7999802}.
• Disease: DISEASE: Tyrosinemia 2 (TYRSN2) [MIM:276600]: An inborn error of metabolism characterized by elevations of tyrosine in the blood and urine, and oculocutaneous manifestations. Typical features include palmoplantar keratosis, painful corneal ulcers, and mental retardation. {ECO:0000269|PubMed:1357662}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Ubiquinone and other terpenoid-quinone biosynthesis - Homo sapiens (human);Phenylalanine metabolism - Homo sapiens (human);Phenylalanine, tyrosine and tryptophan biosynthesis - Homo sapiens (human);Cysteine and methionine metabolism - Homo sapiens (human);Tyrosine metabolism - Homo sapiens (human);Tyrosinemia, transient, of the newborn;Dopamine beta-hydroxylase deficiency;Disulfiram Action Pathway;Phenylalanine and Tyrosine Metabolism;Tyrosine Metabolism;Alkaptonuria;Monoamine oxidase-a deficiency (MAO-A);Hawkinsinuria;Tyrosinemia Type I;Phenylketonuria;Tyrosinemia Type 3 (TYRO3);Tyrosinemia Type 2 (or Richner-Hanhart syndrome);Methionine De Novo and Salvage Pathway;Amino Acid metabolism;Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism;Metabolism of amino acids and derivatives;Phenylalanine and tyrosine catabolism;Metabolism;Phenylalanine degradation;tyrosine degradation;4-hydroxybenzoate biosynthesis;Methionine and cysteine metabolism;Tyrosine metabolism;FOXA2 and FOXA3 transcription factor networks (Consensus)

Recessive Scores

• pRec: 0.709

Intolerance Scores

• loftool: 0.244
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.54

Haploinsufficiency Scores

• pHI: 0.376
• hipred: Y
• hipred_score: 0.683
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tat

Gene ontology

• Biological process: 2-oxoglutarate metabolic process;glutamate metabolic process;L-phenylalanine catabolic process;tyrosine catabolic process;response to oxidative stress;biosynthetic process;response to mercury ion;response to glucocorticoid
• Cellular component: cellular_component;mitochondrion;cytosol
• Molecular function: L-tyrosine:2-oxoglutarate aminotransferase activity;protein binding;amino acid binding;pyridoxal phosphate binding