KYAT1

kynurenine aminotransferase 1

Basic information

Region (hg38): 9:128832942-128882494

Previous symbols: [ "CCBL1" ]

Links

ENSG00000171097 ∙ NCBI:883 ∙ OMIM:600547 ∙ HGNC:1564 ∙ Uniprot:Q16773 ∙ 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 KYAT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KYAT1 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			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	8	1	1

Variants in KYAT1

This is a list of pathogenic ClinVar variants found in the KYAT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-128833769-C-T		not specified	Uncertain significance (Jun 18, 2021)
9-128833795-T-A		not specified	Uncertain significance (Aug 09, 2021)
9-128833811-G-A		not specified	Uncertain significance (Aug 09, 2021)
9-128835400-T-C		not specified	Uncertain significance (Jul 21, 2021)
9-128835574-G-A		not specified	Uncertain significance (Jul 09, 2021)
9-128837701-T-C		not specified	Uncertain significance (Aug 12, 2021)
9-128837737-G-C		not specified	Uncertain significance (Aug 02, 2021)
9-128837747-C-T		not specified	Likely benign (Aug 09, 2021)
9-128838327-C-G		not specified	Uncertain significance (Aug 12, 2021)
9-128847452-G-A			Benign (Mar 06, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KYAT1	protein_coding	protein_coding	ENST00000302586	12	49553

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.87e-12	0.114	124955	0	73	125028	0.000292

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.716	233	266	0.876	0.0000162	2809
Missense in Polyphen		77	85.235	0.90339		912
Synonymous	-0.301	109	105	1.04	0.00000691	786
Loss of Function	0.640	20	23.3	0.857	0.00000108	251

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000484	0.000482
Ashkenazi Jewish	0.0000999	0.0000993
East Asian	0.000334	0.000332
Finnish	0.000373	0.000371
European (Non-Finnish)	0.000354	0.000353
Middle Eastern	0.000334	0.000332
South Asian	0.000131	0.000131
Other	0.000165	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the irreversible transamination of the L- tryptophan metabolite L-kynurenine to form kynurenic acid (KA). Metabolizes the cysteine conjugates of certain halogenated alkenes and alkanes to form reactive metabolites. Catalyzes the beta- elimination of S-conjugates and Se-conjugates of L- (seleno)cysteine, resulting in the cleavage of the C-S or C-Se bond. {ECO:0000269|PubMed:19338303}.
• Pathway: Tryptophan metabolism - Homo sapiens (human);Selenocompound metabolism - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);Tryptophan catabolism;Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism;glutathione-mediated detoxification;Metabolism of amino acids and derivatives;Phenylalanine and tyrosine catabolism;Metabolism;Pyrimidine metabolism;L-kynurenine degradation;Tryptophan metabolism;Amino acid synthesis and interconversion (transamination) (Consensus)

Recessive Scores

• pRec: 0.460

Intolerance Scores

• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.82

Haploinsufficiency Scores

• pHI: 0.152
• hipred: N
• hipred_score: 0.204
• ghis: 0.553

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Kyat1

Gene ontology

• Biological process: L-phenylalanine catabolic process;tryptophan catabolic process;cellular modified amino acid metabolic process;cellular amino acid biosynthetic process;kynurenine metabolic process;L-kynurenine catabolic process
• Cellular component: nucleoplasm;cytoplasm;mitochondrion;cytosol
• Molecular function: protein binding;transaminase activity;kynurenine-oxoglutarate transaminase activity;pyridoxal phosphate binding;protein homodimerization activity;L-phenylalanine:pyruvate aminotransferase activity;glutamine-phenylpyruvate transaminase activity;cysteine-S-conjugate beta-lyase activity;L-glutamine:pyruvate aminotransferase activity