BCAT2

branched chain amino acid transaminase 2, the group of Minor histocompatibility antigens

Basic information

Region (hg38): 19:48795062-48811029

Previous symbols: [ "BCT2" ]

Links

ENSG00000105552 ∙ NCBI:587 ∙ OMIM:113530 ∙ HGNC:977 ∙ Uniprot:O15382 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hypervalinemia and hyperleucine-isoleucinemia (Limited), mode of inheritance: AR
• hypervalinemia and hyperleucine-isoleucinemia (Strong), mode of inheritance: AR
• hypervalinemia and hyperleucine-isoleucinemia (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypervalinemia and hyperleucine-isoleucinemia	AR	Biochemical	The condition can involve biochemical dysfunction leading to neurologic and other manifestations, and dietary and medical management (eg, with pharmacologic doses of B6 or branched-chain amino acid restricted diet ) have been reported as yielding clinical and biochemical benefits	Biochemical; Neurologic	25653144; 31177572

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BCAT2 gene.

• not provided (2 variants)
• Hypervalinemia and hyperleucine-isoleucinemia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCAT2 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	18	3	23
missense			58	4	2	64
nonsense	1					1
start loss			1			1
frameshift	1		1			2
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region			3	2	3	8
non coding			2	13	3	18
Total	2	1	64	35	8

Highest pathogenic variant AF is 0.0000263

Variants in BCAT2

This is a list of pathogenic ClinVar variants found in the BCAT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48795433-G-A		not specified	Uncertain significance (Sep 26, 2024)
19-48795436-A-T			Uncertain significance (Feb 28, 2023)
19-48795458-T-A			Likely benign (Oct 08, 2024)
19-48795458-T-C			Uncertain significance (Oct 28, 2024)
19-48795470-G-C			Uncertain significance (Nov 21, 2024)
19-48795471-A-C			Uncertain significance (Oct 21, 2024)
19-48796423-C-T			Uncertain significance (Aug 21, 2022)
19-48796442-G-A			Likely benign (Jul 21, 2022)
19-48796442-G-T		not specified	Uncertain significance (Jul 14, 2024)
19-48796448-T-C		BCAT2-related disorder	Likely benign (Jan 19, 2025)
19-48796456-C-T		not specified	Uncertain significance (Oct 15, 2024)
19-48796502-T-C			Uncertain significance (Sep 06, 2024)
19-48796507-G-T			Benign (Oct 03, 2023)
19-48796515-G-T			Likely benign (Jul 16, 2023)
19-48796518-C-T			Likely benign (Jul 12, 2021)
19-48796519-G-A			Likely benign (Dec 19, 2024)
19-48796570-C-T			Benign (Feb 01, 2025)
19-48796571-G-A			Likely benign (Sep 20, 2024)
19-48796611-G-A			Likely benign (Jul 11, 2023)
19-48796614-C-T			Uncertain significance (Nov 22, 2022)
19-48796622-C-T		Hypervalinemia and hyperleucine-isoleucinemia	Uncertain significance (Aug 16, 2022)
19-48796629-C-T			Likely benign (Apr 25, 2023)
19-48796633-C-G			Uncertain significance (Apr 13, 2022)
19-48796634-C-T			Uncertain significance (Feb 24, 2023)
19-48796639-A-G			Likely benign (Jun 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCAT2	protein_coding	protein_coding	ENST00000316273	11	15968

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.83e-12	0.144	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.982	203	246	0.824	0.0000156	2503
Missense in Polyphen		74	94.003	0.78721		930
Synonymous	0.0928	104	105	0.988	0.00000692	798
Loss of Function	0.726	20	23.8	0.840	0.00000129	235

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000845	0.000844
Ashkenazi Jewish	0.00	0.00
East Asian	0.000332	0.000326
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000239	0.000237
Middle Eastern	0.000332	0.000326
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the first reaction in the catabolism of the essential branched chain amino acids leucine, isoleucine, and valine. May also function as a transporter of branched chain alpha-keto acids.
• Pathway: Pantothenate and CoA biosynthesis - Homo sapiens (human);Cysteine and methionine metabolism - Homo sapiens (human);Valine, leucine and isoleucine biosynthesis - Homo sapiens (human);Valine, leucine and isoleucine degradation - Homo sapiens (human);One carbon metabolism and related pathways;Branched-chain amino acid catabolism;Metabolism of amino acids and derivatives;leucine degradation;Metabolism;valine degradation;Valine, leucine and isoleucine degradation;isoleucine degradation;Valine Leucine Isoleucine degradation (Consensus)

Recessive Scores

• pRec: 0.180

Intolerance Scores

• loftool: 0.926
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.208
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bcat2
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype

Gene ontology

• Biological process: isoleucine catabolic process;branched-chain amino acid biosynthetic process;branched-chain amino acid catabolic process;leucine biosynthetic process;valine biosynthetic process;regulation of hormone levels;cellular response to leukemia inhibitory factor
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: branched-chain-amino-acid transaminase activity;L-leucine transaminase activity;L-valine transaminase activity;L-isoleucine transaminase activity