BAAT

bile acid-CoA:amino acid N-acyltransferase

Basic information

Region (hg38): 9:101354181-101385400

Links

ENSG00000136881 ∙ NCBI:570 ∙ OMIM:602938 ∙ HGNC:932 ∙ Uniprot:Q14032 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hypercholanemia, familial 1 (Strong), mode of inheritance: AR
• familial hypercholanemia (Limited), mode of inheritance: Unknown
• familial hypercholanemia (Supportive), mode of inheritance: AR
• bile acid CoA:amino acid N-acyltransferase deficiency (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypercholanemia, familial; Bile acid conjugation defect 1	AR	Gastrointestinal; Hematologic	Individuals with Hypercholanemia may present with manifestations including pruritus, sequelae of fat malabsorption (which can be severe), and elevated serum bile acid concentrations, which typically respond to medical treatment (eg, with ursodeoxycholic acid and fat-soluble vitamins); Individuals with Bile acid conjugation defect , which can include janudice, failure to thrive, rickets, growth deficiency, and coagulopathy, have been reported as responding to medical management (eg, with ursodeoxycholic acid, FFP and vitamin K); Liver transplant has been described	Gastrointestinal; Hematologic	12704386; 22783059; 23415802

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BAAT 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			8	11	1	20
missense			46	5	4	55
nonsense			3			3
start loss			1			1
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			38	7	19	64
Total	0	0	98	23	24

Variants in BAAT

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

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

Position	Type	Phenotype	Significance	ClinVar
9-101360430-A-G		Hypercholanemia, familial 1	Benign (Jan 13, 2018)
9-101360538-G-T		Hypercholanemia, familial 1	Uncertain significance (Jan 13, 2018)
9-101360542-A-G		Hypercholanemia, familial 1	Benign (Jan 13, 2018)
9-101360544-C-T		Hypercholanemia, familial 1	Benign (Jan 13, 2018)
9-101360564-C-A		Hypercholanemia, familial 1	Uncertain significance (Jan 12, 2018)
9-101360600-G-A		Hypercholanemia, familial 1	Uncertain significance (Jan 12, 2018)
9-101360604-G-A		Hypercholanemia, familial 1	Likely benign (Jan 13, 2018)
9-101360716-C-G		Hypercholanemia, familial 1	Uncertain significance (Jan 15, 2018)
9-101360727-C-G		Hypercholanemia, familial 1	Likely benign (Jan 13, 2018)
9-101360811-G-A		Hypercholanemia, familial 1	Likely benign (Jan 13, 2018)
9-101360831-G-T		Hypercholanemia, familial 1	Uncertain significance (Jan 13, 2018)
9-101360853-A-C		Hypercholanemia, familial 1	Uncertain significance (Jan 13, 2018)
9-101360871-G-T		Hypercholanemia, familial 1	Uncertain significance (Jan 12, 2018)
9-101360900-G-T		Hypercholanemia, familial 1	Uncertain significance (Jan 13, 2018)
9-101360953-C-T		Hypercholanemia, familial 1	Benign (Jan 13, 2018)
9-101360970-C-T		Hypercholanemia, familial 1	Benign (Jan 13, 2018)
9-101361006-T-C		Hypercholanemia, familial 1	Uncertain significance (Jan 13, 2018)
9-101361087-T-C		Hypercholanemia, familial 1	Uncertain significance (Jan 12, 2018)
9-101361112-T-G		Hypercholanemia, familial	Uncertain significance (Jun 14, 2016)
9-101361121-A-T		Hypercholanemia, familial 1	Uncertain significance (Jan 13, 2018)
9-101361210-T-C		Hypercholanemia, familial 1	Uncertain significance (Jan 13, 2018)
9-101361222-TG-T		Hypercholanemia, familial	Uncertain significance (Jun 14, 2016)
9-101361251-CTA-C		Hypercholanemia, familial	Likely benign (Jun 14, 2016)
9-101361264-G-A		Hypercholanemia, familial	Uncertain significance (Jun 14, 2016)
9-101361289-A-C		Hypercholanemia, familial 1	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BAAT	protein_coding	protein_coding	ENST00000259407	3	23103

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.87e-8	0.292	125693	0	44	125737	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0134	221	222	0.997	0.0000115	2696
Missense in Polyphen		57	75.642	0.75355		965
Synonymous	-0.546	92	85.6	1.08	0.00000446	868
Loss of Function	0.500	12	14.0	0.856	8.23e-7	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000446	0.000446
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000109	0.000109
South Asian	0.000327	0.000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in bile acid metabolism. In liver hepatocytes catalyzes the second step in the conjugation of C24 bile acids (choloneates) to glycine and taurine before excretion into bile canaliculi. The major components of bile are cholic acid and chenodeoxycholic acid. In a first step the bile acids are converted to an acyl-CoA thioester, either in peroxisomes (primary bile acids deriving from the cholesterol pathway), or cytoplasmic at the endoplasmic reticulum (secondary bile acids). May catalyze the conjugation of primary or secondary bile acids, or both. The conjugation increases the detergent properties of bile acids in the intestine, which facilitates lipid and fat-soluble vitamin absorption. In turn, bile acids are deconjugated by bacteria in the intestine and are recycled back to the liver for reconjugation (secondary bile acids). May also act as an acyl-CoA thioesterase that regulates intracellular levels of free fatty acids. In vitro, catalyzes the hydrolysis of long- and very long-chain saturated acyl-CoAs to the free fatty acid and coenzyme A (CoASH), and conjugates glycine to these acyl-CoAs. {ECO:0000269|PubMed:12810727, ECO:0000269|PubMed:8034703}.
• Pathway: Bile secretion - Homo sapiens (human);Peroxisome - Homo sapiens (human);Biosynthesis of unsaturated fatty acids - Homo sapiens (human);Taurine and hypotaurine metabolism - Homo sapiens (human);Primary bile acid biosynthesis - Homo sapiens (human);27-Hydroxylase Deficiency;Bile Acid Biosynthesis;Congenital Bile Acid Synthesis Defect Type II;Cerebrotendinous Xanthomatosis (CTX);Zellweger Syndrome;Familial Hypercholanemia (FHCA);Congenital Bile Acid Synthesis Defect Type III;Drug Induction of Bile Acid Pathway;Farnesoid X Receptor Pathway;Nuclear Receptors Meta-Pathway;One carbon metabolism and related pathways;Metapathway biotransformation Phase I and II;metabolism of anandamide an endogenous cannabinoid;Metabolism of lipids;Metabolism of proteins;Tyrosine metabolism;Leukotriene metabolism;Saturated fatty acids beta-oxidation;Metabolism;Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol;Methionine Cysteine metabolism;Synthesis of bile acids and bile salts;Recycling of bile acids and salts;Bile acid and bile salt metabolism;Peroxisomal protein import;Metabolism of steroids;Bile acid biosynthesis;De novo fatty acid biosynthesis;Vitamin E metabolism;bile acid biosynthesis, neutral pathway (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.846
• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.63

Haploinsufficiency Scores

• pHI: 0.0447
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.256

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Baat

Gene ontology

• Biological process: liver development;bile acid conjugation;glycine metabolic process;protein targeting to peroxisome;fatty acid metabolic process;acyl-CoA metabolic process;bile acid biosynthetic process;bile acid metabolic process;taurine metabolic process;animal organ regeneration
• Cellular component: peroxisome;peroxisomal matrix;cytosol
• Molecular function: signaling receptor binding;protein binding;palmitoyl-CoA hydrolase activity;N-acyltransferase activity;transferase activity, transferring acyl groups;acyl-CoA hydrolase activity;glycine N-choloyltransferase activity;carboxylic ester hydrolase activity;medium-chain acyl-CoA hydrolase activity;long-chain acyl-CoA hydrolase activity;very long chain acyl-CoA hydrolase activity;myristoyl-CoA hydrolase activity