BCAT1

branched chain amino acid transaminase 1

Basic information

Region (hg38): 12:24810024-24949101

Previous symbols: [ "BCT1" ]

Links

ENSG00000060982 ∙ NCBI:586 ∙ OMIM:113520 ∙ HGNC:976 ∙ Uniprot:P54687 ∙ 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 BCAT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCAT1 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	1	3
missense			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	32	2	1

Variants in BCAT1

This is a list of pathogenic ClinVar variants found in the BCAT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-24818019-C-A		not specified	Uncertain significance (Aug 12, 2024)
12-24818032-G-A		BCAT1-related disorder	Benign (Sep 26, 2019)
12-24818047-A-G		BCAT1-related disorder	Likely benign (May 10, 2019)
12-24829852-G-A		not specified	Uncertain significance (May 22, 2023)
12-24829853-G-T		not specified	Uncertain significance (Sep 20, 2023)
12-24829855-T-C		not specified	Uncertain significance (Jan 10, 2025)
12-24829876-C-T		not specified	Uncertain significance (Oct 25, 2022)
12-24832725-C-T		BCAT1-related disorder	Likely benign (Mar 03, 2020)
12-24832735-C-T		BCAT1-related disorder	Likely benign (Apr 08, 2019)
12-24832804-C-T			Likely benign (Jul 07, 2018)
12-24836522-C-T		not specified	Uncertain significance (Dec 01, 2022)
12-24836563-A-T		not specified	Uncertain significance (Feb 06, 2023)
12-24842093-T-A		not specified	Uncertain significance (Nov 10, 2024)
12-24842107-A-T		not specified	Uncertain significance (Feb 24, 2025)
12-24842219-T-C		not specified	Uncertain significance (Oct 13, 2023)
12-24849804-C-G		not specified	Uncertain significance (Dec 10, 2024)
12-24849838-G-A		not specified	Uncertain significance (Nov 13, 2024)
12-24849867-G-T		not specified	Uncertain significance (Nov 20, 2024)
12-24849913-G-A		not specified	Uncertain significance (Jan 11, 2023)
12-24849920-T-A		not specified	Uncertain significance (Mar 20, 2024)
12-24878547-T-C		not specified	Uncertain significance (Aug 22, 2022)
12-24878603-T-G		not specified	Uncertain significance (Jan 03, 2024)
12-24878634-C-T		not specified	Uncertain significance (Jun 18, 2021)
12-24881309-T-C		not specified	Uncertain significance (Sep 13, 2023)
12-24881318-C-G		not specified	Uncertain significance (Sep 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCAT1	protein_coding	protein_coding	ENST00000539282	11	138099

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.80e-8	0.803	124598	0	57	124655	0.000229

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.221	216	207	1.04	0.0000101	2547
Missense in Polyphen		73	80.001	0.91249		1003
Synonymous	-0.288	79	75.8	1.04	0.00000381	781
Loss of Function	1.48	15	22.6	0.664	0.00000109	282

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000391	0.000391
Ashkenazi Jewish	0.000209	0.000199
East Asian	0.000453	0.000445
Finnish	0.00	0.00
European (Non-Finnish)	0.000313	0.000301
Middle Eastern	0.000453	0.000445
South Asian	0.0000327	0.0000327
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the first reaction in the catabolism of the essential branched chain amino acids leucine, isoleucine, and valine.
• 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);3-Methylglutaconic Aciduria Type I;Valine, Leucine and Isoleucine Degradation;2-Methyl-3-Hydroxybutryl CoA Dehydrogenase Deficiency;Isovaleric Aciduria;3-Methylcrotonyl Coa Carboxylase Deficiency Type I;Propionic Acidemia;Maple Syrup Urine Disease;3-Hydroxy-3-Methylglutaryl-CoA Lyase Deficiency;Isobutyryl-coa dehydrogenase deficiency;3-hydroxyisobutyric aciduria;3-hydroxyisobutyric acid dehydrogenase deficiency;Isovaleric acidemia;Methylmalonate Semialdehyde Dehydrogenase Deficiency;Methylmalonic Aciduria;3-Methylglutaconic Aciduria Type IV;3-Methylglutaconic Aciduria Type III;Beta-Ketothiolase Deficiency;Amino Acid metabolism;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;Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

• pRec: 0.178

Intolerance Scores

• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.672
• hipred: N
• hipred_score: 0.251
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.953

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bcat1
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;cell population proliferation;branched-chain amino acid biosynthetic process;branched-chain amino acid catabolic process;leucine biosynthetic process;valine biosynthetic process
• Cellular component: mitochondrion;cytosol
• Molecular function: branched-chain-amino-acid transaminase activity;identical protein binding;L-leucine transaminase activity;L-valine transaminase activity;L-isoleucine transaminase activity