BTD
Basic information
Region (hg38): 3:15601341-15722311
Links
Phenotypes
GenCC
Source:
- biotinidase deficiency (Definitive), mode of inheritance: AR
- biotinidase deficiency (Definitive), mode of inheritance: AR
- biotinidase deficiency (Strong), mode of inheritance: AR
- biotinidase deficiency (Definitive), mode of inheritance: AR
- biotinidase deficiency (Supportive), mode of inheritance: AR
- Leigh syndrome (Moderate), mode of inheritance: AR
- biotinidase deficiency (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Biotinidase deficiency | AR | Biochemical | 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 | Allergy/Immunology/Infectious; Biochemical; Dermatologic; Neurologic; Ophthalmologic | 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; 22241090 |
ClinVar
This is a list of variants' phenotypes submitted to
- Biotinidase_deficiency (626 variants)
- not_provided (155 variants)
- not_specified (69 variants)
- Inborn_genetic_diseases (60 variants)
- BTD-related_disorder (26 variants)
- Intellectual_disability (4 variants)
- Global_developmental_delay (2 variants)
- Generalized_hypotonia (1 variants)
- Cryptorchidism (1 variants)
- Possible_mitochondrial_disorder_-_nuclear_genes (1 variants)
- Macrocephaly (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BTD gene is commonly pathogenic or not. These statistics are base on transcript: NM_001370658.1. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 163 | 167 | ||||
missense | 30 | 123 | 173 | 11 | 337 | |
nonsense | 20 | 19 | 40 | |||
start loss | 1 | 1 | ||||
frameshift | 33 | 47 | 80 | |||
splice donor/acceptor (+/-2bp) | 11 | 15 | ||||
Total | 86 | 202 | 177 | 174 | 1 |
Highest pathogenic variant AF is 0.000952165
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
BTD | protein_coding | protein_coding | ENST00000303498 | 4 | 44482 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.50e-7 | 0.398 | 125687 | 0 | 61 | 125748 | 0.000243 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.525 | 320 | 295 | 1.09 | 0.0000160 | 3608 |
Missense in 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 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000177 | 0.000177 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000544 | 0.000544 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.000264 | 0.000185 |
Middle Eastern | 0.000544 | 0.000544 |
South Asian | 0.00137 | 0.000817 |
Other | 0.00 | 0.00 |
dbNSFP
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.;
- Pathway
- Vitamin digestion and absorption - Homo sapiens (human);Biotin metabolism - Homo sapiens (human);Biotin Metabolism;Multiple carboxylase deficiency, neonatal or early onset form;Biotinidase Deficiency;Biotin transport and metabolism;Metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;Vitamin H (biotin) metabolism
(Consensus)
Recessive Scores
- pRec
- 0.236
Intolerance Scores
- loftool
- 0.126
- rvis_EVS
- 0.02
- rvis_percentile_EVS
- 55.76
Haploinsufficiency Scores
- pHI
- 0.0625
- hipred
- N
- hipred_score
- 0.199
- ghis
- 0.469
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.879
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Btd
- Phenotype
- 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); muscle phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); pigmentation phenotype; vision/eye phenotype; renal/urinary system phenotype; skeleton phenotype;
Gene ontology
- Biological process
- biotin metabolic process;central nervous system development
- Cellular component
- extracellular region;extracellular space;mitochondrial matrix;extracellular exosome
- Molecular function
- biotinidase activity