BCAT2
Basic information
Region (hg38): 19:48795061-48811029
Previous symbols: [ "BCT2" ]
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Hypervalinemia and hyperleucine-isoleucinemia | AR | Biochemical | An individual has been described with clinical and radiological neurologic abnormalities, and biochemical management (eg, with pharmacologic doses of B6) have been reported as yielding clinical and biochemical benefits | Biochemical | 25653144 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (2 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 | 17 | 22 | ||||
missense | 47 | 53 | ||||
nonsense | 1 | |||||
start loss | 1 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 3 | 2 | 3 | 8 | ||
non coding | 12 | 17 | ||||
Total | 2 | 1 | 52 | 33 | 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 |
---|---|---|---|---|
19-48795436-A-T | Uncertain significance (Feb 28, 2023) | |||
19-48795458-T-A | Likely benign (Oct 05, 2023) | |||
19-48795458-T-C | Uncertain significance (Oct 13, 2022) | |||
19-48795471-A-C | Uncertain significance (Jul 20, 2022) | |||
19-48796423-C-T | Uncertain significance (Aug 21, 2022) | |||
19-48796442-G-A | Likely benign (Jul 21, 2022) | |||
19-48796448-T-C | BCAT2-related disorder | Likely benign (Dec 19, 2023) | ||
19-48796456-C-T | not specified | Uncertain significance (Jan 23, 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 (Oct 09, 2023) | |||
19-48796570-C-T | Benign (Jan 26, 2024) | |||
19-48796611-G-A | Likely benign (Jul 11, 2023) | |||
19-48796614-C-T | Uncertain significance (Nov 22, 2022) | |||
19-48796622-C-T | 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) | |||
19-48796645-C-T | not specified | Uncertain significance (Dec 11, 2023) | ||
19-48796646-G-A | Likely benign (Jan 13, 2024) | |||
19-48796646-G-C | not specified | Uncertain significance (Jan 30, 2024) | ||
19-48796651-C-G | not specified | Uncertain significance (Sep 20, 2023) | ||
19-48796670-G-A | Uncertain significance (Nov 08, 2022) | |||
19-48796687-G-C | Uncertain significance (Apr 22, 2022) |
GnomAD
Source:
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:
- 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
- essential_gene_gene_trap
- 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