BTD

protein-coding

biotinidase, 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

NM_001370658.1

Inheritance

AR

ClinVar variants

P:310U:191B:192

Top phenotype

Biotinidase deficiency

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr3:15,601,341-15,722,311

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~121.0 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

biotinidase deficiencyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009665

Submitter: G2P

biotinidase deficiencyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009665

Submitter: Ambry Genetics

biotinidase deficiencyDEFINITIVE

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.

biotinidase deficiencySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009665

Submitter: Orphanet

biotinidase deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009665

Submitter: Labcorp Genetics (formerly Invitae)

biotinidase deficiencyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009665

Submitter: Myriad Women's Health

biotinidase deficiencyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009665

Submitter: Natera

Leigh syndromeMODERATE

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).

biotinidase deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009665

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Biotinidase deficiencyAR

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

Refs: 4103667; 917614; 88555; 99258; 7436398; 6790844; 6135889; 6137736; 6848914; 3930842; 3926500; 4000223; 4073853; 196050; 2502673; 2515386; 2109151; 1729884; 8283357; 7550325; 9396567; 9375914; 9654207; 15776412; 7550325; 11313766; 17382128; 21752405; 20301497; 21696988; 21907891; 22378278; 22241090Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BTD variants in ClinVar

12 Conditions Cataloged
Biotinidase deficiencyTotal: 664
not providedTotal: 180
not specifiedTotal: 109
BTD-related disorderTotal: 86
Inborn genetic diseasesTotal: 63
Intellectual disabilityTotal: 4
Fetal anomalies with a likely genetic causeTotal: 2
Global developmental delayTotal: 2

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
2
clinvar
176
clinvar
1
clinvar
180
missense
28
clinvar
132
clinvar
188
clinvar
15
clinvar
363
nonsense
21
clinvar
22
clinvar
43
start loss
1
clinvar
1
frameshift
36
clinvar
53
clinvar
89
splice donor/acceptor (+/-2bp)
4
clinvar
12
clinvar
1
clinvar
17
Total892211911911693

Highest pathogenic variant AF is 0.000952165

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 128 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001370658.1RefSeqNP_001357587.13MANE Select
ENST00000643237.3EnsemblENSP00000495254.23MANE Select
NM_001281723.4RefSeqNP_001268652.23Standard
NM_001281724.3RefSeqNP_001268653.23Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.5253202951.090.00001603608
Missense (PolyPhen)11498.9041.15261193
Synonymous-0.5761241161.070.000006901057
Loss of Function0.6981214.90.8056.53e-7199

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.000120.000087rare
Ashkenazi Jewish00.0absent
East Asian0.000540.00054rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000260.00018rare
South Asian0.00140.00082notable
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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