rs13073139
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3PP5
The NM_001370658.1(BTD):c.451G>A(p.Ala151Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000527 in 1,613,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00035 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00055 ( 0 hom. )
Consequence
BTD
NM_001370658.1 missense
NM_001370658.1 missense
Scores
10
7
2
Clinical Significance
Conservation
PhyloP100: 10.0
Genes affected
BTD (HGNC:1122): (biotinidase) 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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.793
PP5
Variant 3-15644367-G-A is Pathogenic according to our data. Variant chr3-15644367-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 38298.We mark this variant Likely_pathogenic, oryginal submissions are: {not_provided=2, Uncertain_significance=1, Pathogenic=17}. Variant chr3-15644367-G-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| BTD | NM_001370658.1 | c.451G>A | p.Ala151Thr | missense_variant | 4/4 | ENST00000643237.3 | NP_001357587.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| BTD | ENST00000643237.3 | c.451G>A | p.Ala151Thr | missense_variant | 4/4 | NM_001370658.1 | ENSP00000495254 | P1 |
Frequencies
GnomAD3 genomes 0.000348 AC: 53AN: 152084Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000330 AC: 83AN: 251332Hom.: 0 AF XY: 0.000346 AC XY: 47AN XY: 135832
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GnomAD4 exome AF: 0.000546 AC: 798AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.000535 AC XY: 389AN XY: 727238
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GnomAD4 genome 0.000348 AC: 53AN: 152084Hom.: 0 Cov.: 31 AF XY: 0.000242 AC XY: 18AN XY: 74282
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:19Uncertain:1Other:2
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Biotinidase deficiency Pathogenic:11Uncertain:1Other:2
| Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 05, 2018 | This sequence change replaces alanine with threonine at codon 171 of the BTD protein (p.Ala171Thr). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and threonine. This variant is present in population databases (rs13073139, ExAC 0.07%). This variant has been reported in the literature in multiple individuals affected with biotinidase (BTD) deficiency co-occurring on the same chromosome with the common pathogenic p.Asp444His BTD variant (PMID: 10206677, 21752405, 9654207, 20556795, 12227467, 25174816, 20549359, 27329734, 9375914). ClinVar contains an entry for this variant (Variation ID: 25016, 38298). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, this variant is a rare missense change with uncertain impact on protein function. Therefore, it has been classified as a Variant of Uncertain Significance. - |
| not provided, no classification provided | literature only | GeneReviews | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 18, 2017 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Knight Diagnostic Laboratories, Oregon Health and Sciences University | Sep 13, 2018 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 30, 2018 | Across a selection of the available literature, the BTD c.511G>A (p.Ala171Thr) variant has been found as part of a complex allele [p.Ala171Thr;p.Asp444His] in a majority of cases including 25 individuals, a majority of whom were newborns, with the variant in a compound heterozygous state, 20 with profound biotinidase deficiency, four with partial biotinidase deficiency, and one individual who did not have information on biotinidase activity (Norrgard et al. 1998; Norrgard et al. 1999; Borsatto et al. 2014; Borsatto et al. 2017). The second variant identified in the compound heterozygous individuals was most often a missense variant. The complex allele has also been reported in a homozygous state in three individuals with profound biotinidase deficiency including a father-daughter pair from a consanguineous family where one parent and two grandparents were all heterozygous carriers of the variant and were unaffected (Wolf et al. 1997). A study by Lindau-Shepart et al. (2012) also identified the p.Ala171Thr variant in at least ten patients without the p.Asp444His variant, including five with a different second variant, but in whom zygosity was not specified. In addition, since a limited number of variants were evaluated in this study, the authors suggest that a less common variant may also be present with the p.Ala171Thr variant in the five individuals with a single variant detected. The p.Ala171Thr variant was absent from 376 normal blood spots and is reported at a frequency of 0.00066 in the European (non-Finnish) population of the Exome Aggregation Consortium. Based on the collective evidence, the p.Ala171Thr variant is classified as pathogenic for biotinidase deficiency. - |
| Pathogenic, criteria provided, single submitter | clinical testing | DASA | Feb 14, 2022 | The c.451G>A;p.(Ala151Thr) missense variant has been observed in affected individual(s) (PMID: 29995633; 28971021; 28498829; 27329734; 25174816) - PS4. The variant is located in a mutational hot spot and/or critical and well-established functional domain (CN_hydrolase) - PM1. The variant is present at low allele frequencies population databases (rs13073139 - gnomAD 0.003485%; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2_supporting. The p.(Ala151Thr) was detected in trans with a pathogenic variant (PMID: 29995633; 28971021; 28498829; 27329734; 25174816) - PM3_very strong. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. The variant was observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern - BP2. In summary, the currently available evidence indicates that the variant is pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 29, 2022 | Variant summary: BTD c.451G>A (p.Ala151Thr) results in a non-conservative amino acid change located in the Carbon-nitrogen hydrolase (IPR003010) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00033 in 251332 control chromosomes (gnomAD), predominantly at a frequency of 0.00065 within the Non-Finnish European subpopulation in the gnomAD database. This frequency is not significantly higher than expected for a pathogenic variant in BTD causing Biotinidase Deficiency (0.00033 vs 0.0046), allowing no conclusion about variant significance. c.451G>A (often reported as c.511G>A) frequently occurs in cis with c.1270G>C [p.Asp424His] (often reported as c.1330G>C, p.Asp444His) as a complex allele. This allele has been reported in the literature in multiple individuals affected with Biotinidase Deficiency (e.g.Pomponio_2000, Borsatto_2019, Sarafoglou_2009, Tangeraas_2020). These data indicate that the variant is very likely to be associated with disease. Although the variant has not been examined in vitro in isolation, the complex allele is expected to have 0-10% enzymatic activity based on plasma biotinidase activity levels from patients whose other allele has a quantified variant (Borsatto_2019). Twelve ClinVar submitters have assessed the variant since 2014: eleven have classified the variant as pathogenic and one as uncertain significance. Based on the evidence outlined above, the variant was classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Mar 02, 2023 | - - |
| not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | Variant interpretted as Pathogenic and reported on 12-12-2018 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Dec 26, 2019 | NM_000060.2(BTD):c.511G>A(A171T) is classified as pathogenic in the context of biotinidase deficiency. Please note that this variant is frequently observed in combination with D444H in the literature, which suggests they are likely to be on the same chromosome. When A171T and D444H are present on the same chromosome, this combination of variants is associated with profound biotinidase deficiency. Sources cited for classification include the following: PMID 27625817, 29995633, 28971021, 21752405 and 18845537. Classification of NM_000060.2(BTD):c.511G>A(A171T) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 28, 2024 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 31, 2017 | The p.Ala171Thr (NM_000060.2 c.511G>A) variant in BTD has previously been reported in several compound heterozygous individuals with biotinidase deficiency (Norrgard 1998 and Borsatto 2014). These reports identify the variant in cis with p.Asp444His (c.1330G>C), a partial deficiency allele on its own. The p.Ala171Thr variant has been identified in 0.04% (47/120,592) of chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs13073139), which is assumed to represent the combined p.[Ala171Thr;Asp444His] allele. In summary, the p.Ala171Thr variant, when found as p.[Ala171Thr;Asp444His], meets our criteria to be classified as pathogenic for biotinidase deficiency in an autosomal recessive manner primarily based upon its occurrence in trans with other pathogenic variants in affected individuals. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | Jul 16, 2023 | Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with biotinidase deficiency (MIM#253260). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0115 - Variants in this gene are known to have variable expressivity. The condition associated with this gene is known to range from partial, with milder symptoms and later onset, to profound, with more severe symptoms and earlier onset. Also, individuals with the same genotype have been observed to have different clinical and biochemical phenotypes (PMIDs: 20301497, 28498829). (I) 0200 - Variant is predicted to result in a missense amino acid change from alanine to threonine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 87 heterozygotes, 0 homozygotes). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogenic by clinical laboratories in ClinVar and observed in multiple individuals with biotinidase deficiency. The variant is often identified in cis with the p.(Asp424His) variant forming a complex pathogenic allele (PMIDs: 28971021, 28498829, 27329734). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign - |
not provided Pathogenic:7
| Pathogenic, criteria provided, single submitter | clinical testing | Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden | Nov 03, 2021 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Sep 13, 2018 | The A171T variant has only been reported on the same allele as D444H comprising what has been described as a double mutation allele, denoted A171T;D444H. A171T;D444H has been observed in approximately 17% of alleles in children with profound biotinidase deficiency ascertained by newborn screening in the United States (Norrgard et al., 1999). The A171T variant was seen with the D444H variant at GeneDx. - |
| Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 13, 2014 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2024 | BTD: PM3:Very Strong, PM2 - |
| Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Jan 07, 2021 | - - |
Inborn genetic diseases Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2021 | The c.511G>A (p.A171T) alteration is located in exon 4 (coding exon 4) of the BTD gene. This alteration results from a G to A substitution at nucleotide position 511, causing the alanine (A) at amino acid position 171 to be replaced by a threonine (T). Manual RD edits for complex allele_x000D_ _x000D_ _x000D_ The c.1330G>C (p.D444H) alteration is located in exon 4 (coding exon 4) of the BTD gene. This alteration results from a G to C substitution at nucleotide position 1330, causing the aspartic acid (D) at amino acid position 444 to be replaced by a histidine (H). The c.511G>A (p.A171T) alteration is located in exon 4 (coding exon 4) of the BTD gene. This alteration results from a G to A substitution at nucleotide position 511, causing the alanine (A) at amino acid position 171 to be replaced by a threonine (T)._x000D_ _x000D_ The [c.1330G>C (p.D444H); c.511G>A (p.A171T)] complex allele results in a profound deficiency allele with <10% of residual enzyme activity. This complex allele has been reported in patients with profound biotinidase deficiency when in trans with another profound allele or in the homozygous state (Swango, 1998; Norrgard, 1998; Milánkovics, 2010; Cowan, 2010)._x000D_ _x000D_ Based on the available evidence, the BTD [c.1330G>C (p.D444H); c.511G>A (p.A171T)] complex allele is classified as pathogenic. Based on the available evidence, this alteration is classified as pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Uncertain
.;.;D;.;.;.;T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
.;D;D;.;.;D;D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
.;.;H;.;.;.;.;.
MutationTaster
Benign
A;A;A;A
PrimateAI
Uncertain
T
PROVEAN
Uncertain
.;D;.;.;.;D;D;D
REVEL
Pathogenic
Sift
Uncertain
.;D;.;.;.;D;D;D
Sift4G
Uncertain
.;D;.;.;.;D;D;D
Polyphen
1.0
.;.;D;.;.;.;.;.
Vest4
0.91, 0.90, 0.88
MVP
1.0
MPC
0.42
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at