NM_001370658.1(BTD):c.1207del (p.Cys403fs) AND Biotinidase deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 15, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003498107.2

Allele description [Variation Report for NM_001370658.1(BTD):c.1207del (p.Cys403fs)]

NM_001370658.1(BTD):c.1207del (p.Cys403fs)

Gene:

BTD:biotinidase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3p25.1

Genomic location:

Preferred name:

NM_001370658.1(BTD):c.1207del (p.Cys403fs)

HGVS:

NC_000003.12:g.15645123del
NG_008019.2:g.48772del
NG_008019.3:g.48773del
NM_001281723.4:c.1207del
NM_001281724.3:c.1207del
NM_001281725.3:c.1207del
NM_001281726.2:c.*2985delT
NM_001323582.2:c.1207del
NM_001370658.1:c.1207delMANE SELECT
NM_001370752.1:c.1015+192del
NM_001370753.1:c.399+3066del
NM_001407364.1:c.1207del
NM_001407365.1:c.1207del
NM_001407366.1:c.1207del
NM_001407367.1:c.1207del
NM_001407368.1:c.1207del
NM_001407369.1:c.1207del
NM_001407370.1:c.1207del
NM_001407371.1:c.1207del
NM_001407372.1:c.1207del
NM_001407373.1:c.1207del
NM_001407374.1:c.1207del
NM_001407375.1:c.1207del
NM_001407376.1:c.1207del
NM_001407377.1:c.1207del
NM_001407378.1:c.1207del
NM_001407379.1:c.1015+192del
NM_001407380.1:c.399+3066del
NM_001407398.1:c.399+3066del
NM_001407399.1:c.399+3066del
NM_001407400.1:c.399+3066del
NM_001407401.1:c.399+3066del
NP_001268652.2:p.Cys403fs
NP_001268653.2:p.Cys403fs
NP_001268654.1:p.Cys403fs
NP_001310511.1:p.Cys403fs
NP_001357587.1:p.Cys403fs
NP_001394293.1:p.Cys403fs
NP_001394294.1:p.Cys403fs
NP_001394295.1:p.Cys403fs
NP_001394296.1:p.Cys403fs
NP_001394297.1:p.Cys403fs
NP_001394298.1:p.Cys403fs
NP_001394299.1:p.Cys403fs
NP_001394300.1:p.Cys403fs
NP_001394301.1:p.Cys403fs
NP_001394302.1:p.Cys403fs
NP_001394303.1:p.Cys403fs
NP_001394304.1:p.Cys403fs
NP_001394305.1:p.Cys403fs
NP_001394306.1:p.Cys403fs
NP_001394307.1:p.Cys403fs
NC_000003.11:g.15686630del

Protein change:

C403fs

Molecular consequence:

NM_001281723.4:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281724.3:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001281725.3:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001323582.2:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370658.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407364.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407365.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407366.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407367.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407368.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407369.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407370.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407371.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407372.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407373.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407374.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407375.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407376.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407377.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407378.1:c.1207del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370752.1:c.1015+192del - intron variant - [Sequence Ontology: SO:0001627]
NM_001370753.1:c.399+3066del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407379.1:c.1015+192del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407380.1:c.399+3066del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407398.1:c.399+3066del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407399.1:c.399+3066del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407400.1:c.399+3066del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407401.1:c.399+3066del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Biotinidase deficiency
Synonyms:: BTD deficiency; Late-onset biotin-responsive multiple carboxylase deficiency; Biotin deficiency
Identifiers:: MONDO: MONDO:0009665; MedGen: C0220754; Orphanet: 79241; OMIM: 253260

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004248726	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 15, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 25174816, 25967232, 28498829, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004248726

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 15, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Biotinidase deficiency: clinical and genetic studies of 38 Brazilian patients.

Borsatto T, Sperb-Ludwig F, Pinto LL, Luca GR, Carvalho FL, Souza CF, Medeiros PF, Lourenço CM, Lo Filho R, Neto EC, Bernardi P, Leistner-Segal S, Schwartz IV.

BMC Med Genet. 2014 Sep 1;15:96. doi: 10.1186/s12881-014-0096-3.

PubMed [citation]

PMID:: 25174816
PMCID:: PMC4236587

High Incidence of Biotinidase Deficiency from a Pilot Newborn Screening Study in Minas Gerais, Brazil.

Lara MT, Gurgel-Giannetti J, Aguiar MJ, Ladeira RV, Carvalho NO, Del Castillo DM, Viana MB, Januario JN.

JIMD Rep. 2015;24:103-7. doi: 10.1007/8904_2015_447. Epub 2015 May 13.

PubMed [citation]

PMID:: 25967232
PMCID:: PMC4582019

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004248726.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Cys423Alafs*78) in the BTD gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 121 amino acid(s) of the BTD protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with BTD-related conditions. This variant disrupts a region of the BTD protein in which other variant(s) (p.Asp543Glu) have been determined to be pathogenic (PMID: 25174816, 25967232, 28498829). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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