KYAT3

kynurenine aminotransferase 3

Basic information

Region (hg38): 1:88935773-88992953

Previous symbols: [ "CCBL2" ]

Links

ENSG00000137944 ∙ NCBI:56267 ∙ OMIM:610656 ∙ HGNC:33238 ∙ Uniprot:Q6YP21 ∙ 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 KYAT3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KYAT3 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			2	1		3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			30			30
Total	0	0	32	1	0

Variants in KYAT3

This is a list of pathogenic ClinVar variants found in the KYAT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-88955210-A-G		not specified	Uncertain significance (Oct 22, 2021)
1-88961245-T-C		not specified	Uncertain significance (Nov 09, 2021)
1-88964947-T-C		not specified	Likely benign (Oct 06, 2021)
1-88982677-C-T		not specified	Uncertain significance (Aug 23, 2021)
1-88982682-T-C		not specified	Uncertain significance (May 04, 2023)
1-88982724-C-T		not specified	Uncertain significance (Oct 22, 2021)
1-88982746-C-T		not specified	Uncertain significance (Apr 01, 2024)
1-88982778-G-C		not specified	Uncertain significance (Sep 27, 2021)
1-88982835-C-T		not specified	Uncertain significance (Oct 26, 2024)
1-88982838-C-T		not specified	Uncertain significance (Aug 30, 2022)
1-88982868-T-C		not specified	Uncertain significance (Oct 27, 2023)
1-88982871-C-G		not specified	Uncertain significance (Nov 08, 2021)
1-88982883-C-A		not specified	Uncertain significance (Aug 02, 2022)
1-88982905-T-G		not specified	Uncertain significance (Jan 04, 2024)
1-88982953-G-A		not specified	Uncertain significance (Sep 08, 2024)
1-88982967-C-T		not specified	Uncertain significance (Nov 21, 2022)
1-88983063-T-C		not specified	Uncertain significance (Oct 11, 2024)
1-88983111-C-A		not specified	Uncertain significance (Aug 02, 2023)
1-88983111-C-T		not specified	Uncertain significance (Apr 10, 2023)
1-88983135-G-A		not specified	Uncertain significance (Dec 03, 2021)
1-88983147-C-T		not specified	Uncertain significance (Nov 17, 2022)
1-88983158-T-G		not specified	Uncertain significance (Nov 09, 2023)
1-88983172-T-C		not specified	Uncertain significance (Jan 10, 2023)
1-88983195-T-C		not specified	Uncertain significance (Jan 29, 2024)
1-88983234-G-A		not specified	Uncertain significance (Nov 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KYAT3	protein_coding	protein_coding	ENST00000260508	13	57181

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.13e-16	0.0159	125594	0	152	125746	0.000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.570	208	232	0.895	0.0000112	2961
Missense in Polyphen		94	106.54	0.8823		1330
Synonymous	1.47	62	78.6	0.789	0.00000372	836
Loss of Function	0.221	24	25.2	0.953	0.00000116	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00186	0.00185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000109
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000675	0.000668
Middle Eastern	0.000113	0.000109
South Asian	0.000603	0.000555
Other	0.000520	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the irreversible transamination of the L- tryptophan metabolite L-kynurenine to form kynurenic acid (KA). May catalyze 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 (By similarity). Has transaminase activity towards L-kynurenine, tryptophan, phenylalanine, serine, cysteine, methionine, histidine, glutamine and asparagine with glyoxylate as an amino group acceptor (in vitro). Has lower activity with 2- oxoglutarate as amino group acceptor (in vitro) (By similarity). {ECO:0000250}.
• 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;Metabolism;L-kynurenine degradation (Consensus)

Recessive Scores

• pRec: 0.153

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.22

Haploinsufficiency Scores

• pHI: 0.0654
• hipred: N
• hipred_score: 0.204
• ghis: 0.503

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Kyat3

Gene ontology

• Biological process: 2-oxoglutarate metabolic process;cellular amino acid metabolic process;biosynthetic process;kynurenine metabolic process;L-kynurenine metabolic process
• Cellular component: cytoplasm;mitochondrion
• Molecular function: RNA binding;kynurenine-oxoglutarate transaminase activity;pyridoxal phosphate binding;protein homodimerization activity;kynurenine-glyoxylate transaminase activity;cysteine-S-conjugate beta-lyase activity