BTD
protein-codingbiotinidase, the group of Vanin family
Gene summary
The protein encoded by this gene functions to recycle protein-bound biotin by cleaving biocytin (biotin-epsilon-lysine), a normal product of carboxylase degradation, resulting in regeneration of free biotin. The encoded protein has also been shown to have biotinyl transferase activity. Mutations in this gene are associated with biotinidase deficiency. Multiple transcript variants encoding different isoforms have been described. [provided by RefSeq, Aug 2013]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~121.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0009665
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0009665
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0009665
Submitter: ClinGen
BTD and autosomal recessive Biotinidase Deficiency was reported in 1994 by Cole et al. (PMID: 7509806). Profound biotinidase deficiency is defined as less than 10% of mean normal serum enzyme activity; partial biotinidase deficiency is defined as between 10% and 30% of mean normal serumactivity (PMID: 26810761). Patients with Biotinidase deficiency are treated with biotin. At least 200 unique variants (missense, frameshift, nonsense etc.) have been reported in humans. Evidence supporting this gene-disease relationship includes case-level data and experimental data, including an animal model. More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. In summary, BTD is definitively associated with autosomal recessive Biotinidase Deficiency. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the Hearing Loss Gene Curation Expert Panel in collaboration with the ClinGen General Gene Curation Working Group on 9/25/19.
Inheritance Pattern: AR
Disease ID:MONDO:0009665
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009665
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0009665
Submitter: Myriad Women's Health
Inheritance Pattern: AR
Disease ID:MONDO:0009665
Submitter: Natera
Inheritance Pattern: AR
Disease ID:MONDO:0009723
Submitter: ClinGen
The relationship between BTD and Leigh syndrome spectrum was evaluated using the ClinGen Clinical Validity Framework as of October 12, 2020. The BTD gene encodes biotinidase, the enzyme responsible for recycling biotin. Biotin is an essential vitamin and coenzyme for four mitochondrial carboxylases necessary for metabolism in humans: acetyl-CoA carboxylase, propionyl-CoA carboxylase, 3-methylcrotonyl-CoA carboxylase, and pyruvate carboxylase. The BTD gene was first reported in relation to autosomal recessive Leigh syndrome spectrum (LSS) in 2008 (PMID: 18645204). It is important to note, however, that there were many earlier reports of biotinidase deficiency resulting in a phenotype consistent with LSS, however genetic testing was not routinely performed at the time of these early case reports. By the time genetic testing was more widely utilized, biotinidase deficiency had been adopted into many newborn screening programs and was being treated presymptomatically, therefore preventing manifestation of LSS. Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included one variant identified in two cases from two publications (PMIDs: 21907891, 18645204), although as stated above there are many other probands in whom LSS was prevented with biotin treatment. No segregation data were available. Loss of function is implicated as the mechanism of disease. This gene-disease association is also supported by biochemical function, expression, and animal models (PMIDs: 27977873, 25613900, 21051254). In summary, there is currently limited evidence to support this gene-disease relationship. However, the expert panel agreed to increase this gene-disease association to moderate, primarily due to the fact that there would be many more cases to score if this was not a treatable condition that is screened for at birth in many countries. While more evidence is needed to establish this relationship definitively, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the NICHD U24 ClinGen Mitochondrial Disease Gene Curation Expert Panel on October 12, 2020 (SOP Version 7).
Inheritance Pattern: AR
Disease ID:MONDO:0009665
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious; Biochemical; Dermatologic; Neurologic; Ophthalmologic
Intervention: Biochemical
Rationale: Individuals with severe biotinidase deficiency can present with a range of neurologic, visual, and dermatologic anomalies, which are typically not reversible after manifesting, and medical management (with oral biotin) is indicated and can prevent sequelae if instituted early; Raw eggs should be avoided due to resultant decreased biotin bioavailability
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to BTD variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001370658.1. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 2 | 176 | 1 | 180 | |
| missense | 28 | 132 | 188 | 15 | 363 | |
| nonsense | 21 | 22 | 43 | |||
| start loss | 1 | 1 | ||||
| frameshift | 36 | 53 | 89 | |||
| splice donor/acceptor (+/-2bp) | 4 | 12 | 1 | 17 | ||
| Total | 89 | 221 | 191 | 191 | 1 | 693 |
Highest pathogenic variant AF is 0.000952165
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001357587.1 | 3 | MANE Select | |
| Ensembl | ENSP00000495254.2 | 3 | MANE Select | |
| RefSeq | NP_001268652.2 | 3 | Standard | |
| RefSeq | NP_001268653.2 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vitamin digestion and absorption - Homo sapiens (human)
- Biotin metabolism - Homo sapiens (human)
- Biotin Metabolism
- Multiple carboxylase deficiency, neonatal or early onset form
- Biotinidase Deficiency
Biological Process
- biotin metabolic process
- central nervous system development
Molecular Function
- biotinidase activity
Cellular Component
- extracellular region
- extracellular space
- mitochondrial matrix
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000303498
- Coding exons
- 4
- Length
- 44482
- Individuals with no LoFs
- 125687
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 61
- Defined
- 125748
- p
- 0.000243
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.525 | 320 | 295 | 1.09 | 0.0000160 | 3608 |
| Missense (PolyPhen) | 114 | 98.904 | 1.1526 | 1193 | ||
| Synonymous | -0.576 | 124 | 116 | 1.07 | 0.00000690 | 1057 |
| Loss of Function | 0.698 | 12 | 14.9 | 0.805 | 6.53e-7 | 199 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00012 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00054 | 0.00054 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00026 | 0.00018 | rare |
| South Asian | 0.0014 | 0.00082 | notable |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalytic release of biotin from biocytin, the product of biotin-dependent carboxylases degradation.;
- Disease
- DISEASE: Biotinidase deficiency (BTD deficiency) [MIM:253260]: A juvenile form of multiple carboxylase deficiency, an autosomal recessive disorder of biotin metabolism, characterized by ketoacidosis, hyperammonemia, excretion of abnormal organic acid metabolites, and dermatitis. Biotinidase deficiency is characterized by seizures, hypotonia, skin rash, alopecia, ataxia, hearing loss, and optic atrophy. If untreated, symptoms usually become progressively worse, and coma and death may occur. {ECO:0000269|PubMed:10206677, ECO:0000269|PubMed:9099842, ECO:0000269|PubMed:9654207}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.236
Intolerance Scores
- LoFtool
- 0.126
- RVIS EVS
- 0.02
- RVIS percentile EVS
- 55.76
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.879
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |