3-15645468-C-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_001370658.1(BTD):c.1552C>T(p.Arg518Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00016 in 1,608,712 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 Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R518L) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.000099 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00017 (0 hom.)
• Consequence: BTD NM_001370658.1 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:16 O:1
• Conservation: PhyloP100: 2.06

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 Pathogenic. Variant got 18 ACMG points.

• PM1: In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 2 uncertain in NM_001370658.1
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr3-15645469-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 25099.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.978
• PP5: Variant 3-15645468-C-T is Pathogenic according to our data. Variant chr3-15645468-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 1898.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-15645468-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTD	NM_001370658.1	c.1552C>T	p.Arg518Cys	missense_variant	4/4	ENST00000643237.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BTD	ENST00000643237.3	c.1552C>T	p.Arg518Cys	missense_variant	4/4		NM_001370658.1	P1

Frequencies

GnomAD3 genomes AF: 0.0000986 AC: 15 AN: 152124 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

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: 0.000176

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000747 AC: 18 AN: 240906 Hom.: 0 AF XY: 0.0000456 AC XY: 6 AN XY: 131570

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000290

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000983

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000119

Gnomad OTH exome AF: 0.000168

GnomAD4 exome AF: 0.000167 AC: 243 AN: 1456588 Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 117 AN XY: 724720

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000580

Gnomad4 FIN exome AF: 0.0000622

Gnomad4 NFE exome AF: 0.000199

Gnomad4 OTH exome AF: 0.000199

GnomAD4 genome AF: 0.0000986 AC: 15 AN: 152124 Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5 AN XY: 74326

Gnomad4 AFR AF: 0.0000724

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000176

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000143 Hom.: 0

Bravo AF: 0.0000907

ExAC AF: 0.0000661 AC: 8

EpiCase AF: 0.000436

EpiControl AF: 0.00

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:16 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Biotinidase deficiency Pathogenic:10 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jul 23, 2021	The BTD c.1612C>T; p.Arg538Cys variant (rs80338686) is the second most common pathogenic variant in the BTD gene and has been reported in both the homozygous and compound heterozygous states in multiple individuals with profound BTD deficiency (Murry 2018, Pomponio 1997). This variant is reported in ClinVar (Variation ID: 1898). It is found in the general population with an overall allele frequency of 0.007% (20/272304 alleles) in the Genome Aggregation Database. The arginine at codon 538 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Based on available information, this variant is considered to be severely pathogenic. REFERENCES Murry JB et al. Reconciling newborn screening and a novel splice variant in BTD associated with partial biotinidase deficiency: a BabySeq Project case report. Cold Spring Harb Mol Case Stud. 2018 Aug 1;4(4). Pomponio RJ et al. Arg538 to Cys mutation in a CpG dinucleotide of the human biotinidase gene is the second most common cause of profound biotinidase deficiency in symptomatic children. Hum Genet. 1997 Apr;99(4):506-12. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Apr 01, 1997	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	May 17, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 30, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jun 20, 2022	Variant summary: BTD c.1552C>T (p.Arg518Cys) results in a non-conservative amino acid change in 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 7.5e-05 in 240906 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in BTD causing Biotinidase Deficiency (7.5e-05 vs 0.0046), allowing no conclusion about variant significance. c.1552C>T has been reported in the literature in multiple individuals affected with Biotinidase Deficiency. These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity. Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Feb 09, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Dec 19, 2019	NM_000060.2(BTD):c.1612C>T(R538C) is classified as pathogenic in the context of biotinidase deficiency. Sources cited for classification include the following: PMID 9099842 and 17185019. Classification of NM_000060.2(BTD):c.1612C>T(R538C) 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	Invitae	Jan 22, 2024	This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 538 of the BTD protein (p.Arg538Cys). This variant is present in population databases (rs80338686, gnomAD 0.01%). This missense change has been observed in individual(s) with biotinidase deficiency (PMID: 9099842, 27207447, 27657684). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 1898). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt BTD protein function with a positive predictive value of 95%. This variant disrupts the p.Arg538 amino acid residue in BTD. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 22698809; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Sep 02, 2016	The p.Arg538Cys variant in BTD has been previously identified in at least 5 comp ound heterozygous and 2 homozygous individuals with severe biotinidase deficienc y and it is the second most common mutation in the biotinidase gene that causes profound biotinidase deficiency in symptomatic children. All these patients had no biotinyl transferase activity in their serum and <10% of mean normal biotiny l-hydrolase activity (Pomponio 1997). This variant has also been identified in 8 /114,620 of chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.b roadinstitute.org; dbSNP rs80338686); however, this frequency is low enough to b e consistent with a recessive carrier frequency. In summary, this variant meets criteria to be classified as pathogenic for biotinidase deficiency in an autoso mal recessive manner based upon case and allelic observations and functional evi dence. -

not provided Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Oct 24, 2013	- -
Pathogenic, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	Jun 21, 2022	DNA sequence analysis of the BTD gene demonstrated a sequence change, c.1552C>T, in exon 4 that results in an amino acid change, p.Arg518Cys. This sequence change has previously been reported in the homozygous or compound heterozygous state in multiple individuals with biotinidase deficiency and has been found to co-segregate with disease in families (PMID: 9099842, 27207447). Homozygous individuals have been found to have no enzyme activity. This sequence change has been described in the gnomAD database with a frequency of 0.007% in the overall population (dbSNP rs80338686). The p.Arg518Cys change affects a highly conserved amino acid residue located in a domain of the BTD protein that is not known to be functional. The p.Arg518Cys amino acid change occurs in a region of the BTD gene where other missense sequence changes have been described in individuals with BTD-related disorders. -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Aug 10, 2020	The c.1612C>T (p.Arg538Cys) variant (also known as R538C) is a common cause of profound biotinidase deficiency reported in the published literature (PMID: 29728376 (2018), 27657684 (2017), 27207447 (2017), 26810761 (2016), 26361991 (2015), 9158148 (1997), and 9099842 (1997)). Variant is found in at a symptomatic patient. It is predicted to have a damaging effect on the protein. It occurs in multiple cases with a lone recessive pathogenic/likely pathogenic variant in the same gene, and have a phenotype known to be consistent with disease. It is also damaging to protein function relevant to disease mechanism. -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	May 01, 2023	BTD: PM3:Strong, PM1, PM2, PM5, PP4:Moderate, PS3:Moderate, PP1 -

BTD-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 28, 2023

The BTD c.1612C>T variant is predicted to result in the amino acid substitution p.Arg538Cys. This variant has been reported in the homozygous state or with a second BTD variant in individuals with biotinidase deficiency (Pomponio et al. 1997. PubMed ID: 9099842; Milánkovics et al. 2007. PubMed ID: 17185019; Cowan et al. 2012. PubMed ID: 22698809; Wolf et al. 2017. PubMed ID: 27657684). It has been reported to be one of the most common variants associated with profound biotinidase deficiency (Pomponio et al. 1997. PubMed ID: 9099842; Wolf. 2012. PubMed ID: 22241090). Alternate substitutions impacting the same amino acid (p.Arg538His, p.Arg538Leu) have been reported in individuals with biotinidase deficiency, although both were reported as likely partial deficiency variants (Liu et al. 2018. PubMed ID: 29359854; Manguolo et al. 2021. PubMed ID: 34136440). The c.1612C>T (p.Arg538Cys) variant is reported in 0.011% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/3-15686975-C-T). Taken together, this variant is interpreted as pathogenic. -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

May 30, 2023

The c.1612C>T (p.R538C) alteration is located in exon 4 (coding exon 4) of the BTD gene. This alteration results from a C to T substitution at nucleotide position 1612, causing the arginine (R) at amino acid position 538 to be replaced by a cysteine (C). Based on data from gnomAD, the T allele has an overall frequency of 0.007% (20/272304) total alleles studied. The highest observed frequency was 0.014% (1/7044) of Other alleles. This alteration has been identified in the homozygous and compound heterozygous state in multiple unrelated patients with biotinidase deficiency (Pomponio, 1997; Milánkovics, 2007; Borsatto, 2014; Girard, 2017; Murry, 2018; Wolf, 2019; Maguolo, 2021; Forny, 2022). Additionally, other alterations at the same codon, c.1612C>A (p.R538S) and c.1613G>A (p.R538H), have been reported previously in the homozygous and compound heterozygous state in individuals with biotinidase deficiency (Sarafoglou, 2009; Cowan, 2012; Procter, 2016; Liu, 2018). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.83
BayesDel_addAF	Pathogenic	0.35	D
BayesDel_noAF	Pathogenic	0.49
Cadd	Pathogenic	29
Dann	Pathogenic	1.0
Eigen	Uncertain	0.62
Eigen_PC	Uncertain	0.56
FATHMM_MKL	Uncertain	0.87	D
M_CAP	Pathogenic	0.46	D
MetaRNN	Pathogenic	0.98	D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationTaster	Benign	1.0	A;A;A;A
PrimateAI	Uncertain	0.59	T
Polyphen		1.0	.;.;D;.;.;.;.
Vest4		0.98, 0.98, 0.98
MVP		0.95
MPC		0.49
ClinPred		0.97	D
GERP RS		4.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.85
gMVP		0.96

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: rs80338686; hg19: chr3-15686975; COSMIC: COSV57728520; COSMIC: COSV57728520;