rs13073139

chr3-15644367-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3 PP5

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
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:18 U:1 O:2
• 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]

ACMG classification

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: {Pathogenic=16, not_provided=2, Uncertain_significance=1}. Variant chr3-15644367-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTD	NM_001370658.1	c.451G>A	p.Ala151Thr	missense_variant	4/4	ENST00000643237.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTD	ENST00000643237.3	c.451G>A	p.Ala151Thr	missense_variant	4/4		NM_001370658.1	P1

Frequencies

GnomAD3 genomes AF: 0.000348 AC: 53 AN: 152084 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000262

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000603

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000330 AC: 83 AN: 251332 Hom.: 0 AF XY: 0.000346 AC XY: 47 AN XY: 135832

Gnomad AFR exome AF: 0.000185

Gnomad AMR exome AF: 0.000116

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000651

Gnomad OTH exome AF: 0.000326

GnomAD4 exome AF: 0.000546 AC: 798 AN: 1461884 Hom.: 0 Cov.: 31 AF XY: 0.000535 AC XY: 389 AN XY: 727238

Gnomad4 AFR exome AF: 0.000119

Gnomad4 AMR exome AF: 0.000157

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.0000187

Gnomad4 NFE exome AF: 0.000684

Gnomad4 OTH exome AF: 0.000397

GnomAD4 genome AF: 0.000348 AC: 53 AN: 152084 Hom.: 0 Cov.: 31 AF XY: 0.000242 AC XY: 18 AN XY: 74282

Gnomad4 AFR AF: 0.000169

Gnomad4 AMR AF: 0.000262

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000603

Gnomad4 OTH AF: 0.000478

Alfa AF: 0.000616 Hom.: 0

Bravo AF: 0.000404

TwinsUK AF: 0.00108 AC: 4

ALSPAC AF: 0.000778 AC: 3

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000581 AC: 5

ExAC AF: 0.000387 AC: 47

EpiCase AF: 0.000491

EpiControl AF: 0.000593

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:18 Uncertain:1 Other:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Biotinidase deficiency Pathogenic:10 Uncertain:1 Other:2

Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	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. -
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	Revvity Omics, Revvity	Mar 02, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 25, 2022	- -
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	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. -
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	Fulgent Genetics, Fulgent Genetics	May 18, 2017	- -
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	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. -

not provided Pathogenic:7

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jan 07, 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	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -
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	CeGaT Center for Human Genetics Tuebingen	Dec 01, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Aug 13, 2014	- -

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; Mil&aacute;nkovics, 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: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.28
BayesDel_addAF	Pathogenic	0.23	D
BayesDel_noAF	Pathogenic	0.45
Cadd	Pathogenic	29
Dann	Pathogenic	1.0
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	1.0
FATHMM_MKL	Pathogenic	1.0	D
M_CAP	Uncertain	0.16	D
MetaRNN	Pathogenic	0.79	D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	0.84	D
MutationTaster	Benign	1.0	A;A;A;A
PrimateAI	Uncertain	0.68	T
Polyphen		1.0	.;.;D;.;.;.;.;.
Vest4		0.91, 0.90, 0.88
MVP		1.0
MPC		0.42
ClinPred		0.82	D
GERP RS		6.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.92
gMVP		0.90

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs13073139; hg19: chr3-15685874;