NM_001370658.1(BTD):c.124G>A (p.Val42Met) AND Biotinidase deficiency

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic/Likely pathogenic (5 submissions)
Last evaluated:: Feb 24, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000021895.27

Allele description

NM_001370658.1(BTD):c.124G>A (p.Val42Met)

Gene:

BTD:biotinidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.1

Genomic location:

Preferred name:

NM_001370658.1(BTD):c.124G>A (p.Val42Met)

Other names:

V62M

HGVS:

NC_000003.12:g.15635563G>A
NG_008019.2:g.39212G>A
NM_000060.4:c.184G>A
NM_001281723.4:c.124G>A
NM_001281724.3:c.124G>A
NM_001281725.3:c.124G>A
NM_001281726.3:c.124G>A
NM_001323582.2:c.124G>A
NM_001370658.1:c.124G>AMANE SELECT
NM_001370752.1:c.124G>A
NM_001370753.1:c.124G>A
NM_001407364.1:c.124G>A
NM_001407365.1:c.124G>A
NM_001407366.1:c.124G>A
NM_001407367.1:c.124G>A
NM_001407368.1:c.124G>A
NM_001407369.1:c.124G>A
NM_001407370.1:c.124G>A
NM_001407371.1:c.124G>A
NM_001407372.1:c.124G>A
NM_001407373.1:c.124G>A
NM_001407374.1:c.124G>A
NM_001407375.1:c.124G>A
NM_001407376.1:c.124G>A
NM_001407377.1:c.124G>A
NM_001407378.1:c.124G>A
NM_001407379.1:c.124G>A
NM_001407380.1:c.124G>A
NM_001407381.1:c.124G>A
NM_001407382.1:c.124G>A
NM_001407383.1:c.124G>A
NM_001407384.1:c.124G>A
NM_001407386.1:c.124G>A
NM_001407388.1:c.124G>A
NM_001407390.1:c.124G>A
NM_001407392.1:c.124G>A
NM_001407394.1:c.124G>A
NM_001407395.1:c.124G>A
NM_001407396.1:c.124G>A
NM_001407397.1:c.124G>A
NM_001407398.1:c.124G>A
NM_001407399.1:c.124G>A
NM_001407400.1:c.124G>A
NM_001407401.1:c.124G>A
NP_000051.1:p.Val62Met
NP_000051.1:p.Val62Met
NP_001268652.2:p.Val42Met
NP_001268652.2:p.Val42Met
NP_001268653.2:p.Val42Met
NP_001268654.1:p.Val42Met
NP_001268654.1:p.Val42Met
NP_001268655.2:p.Val42Met
NP_001268655.2:p.Val42Met
NP_001310511.1:p.Val42Met
NP_001310511.1:p.Val42Met
NP_001357587.1:p.Val42Met
NP_001357681.1:p.Val42Met
NP_001357682.1:p.Val42Met
NP_001394293.1:p.Val42Met
NP_001394294.1:p.Val42Met
NP_001394295.1:p.Val42Met
NP_001394296.1:p.Val42Met
NP_001394297.1:p.Val42Met
NP_001394298.1:p.Val42Met
NP_001394299.1:p.Val42Met
NP_001394300.1:p.Val42Met
NP_001394301.1:p.Val42Met
NP_001394302.1:p.Val42Met
NP_001394303.1:p.Val42Met
NP_001394304.1:p.Val42Met
NP_001394305.1:p.Val42Met
NP_001394306.1:p.Val42Met
NP_001394307.1:p.Val42Met
NP_001394308.1:p.Val42Met
NP_001394309.1:p.Val42Met
NP_001394310.1:p.Val42Met
NP_001394311.1:p.Val42Met
NP_001394312.1:p.Val42Met
NP_001394313.1:p.Val42Met
NP_001394315.1:p.Val42Met
NP_001394317.1:p.Val42Met
NP_001394319.1:p.Val42Met
NP_001394321.1:p.Val42Met
NP_001394323.1:p.Val42Met
NP_001394324.1:p.Val42Met
NP_001394325.1:p.Val42Met
NP_001394326.1:p.Val42Met
NP_001394327.1:p.Val42Met
NP_001394328.1:p.Val42Met
NP_001394329.1:p.Val42Met
NP_001394330.1:p.Val42Met
NC_000003.11:g.15677070G>A
NG_008019.1:g.38816G>A
NM_001281723.3:c.124G>A
NM_001281725.2:c.124G>A
NM_001281726.2:c.124G>A
NM_001323582.1:c.124G>A

Protein change:

V42M

Links:

dbSNP: rs397507170

NCBI 1000 Genomes Browser:

rs397507170

Molecular consequence:

NM_000060.4:c.184G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001281723.4:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001281724.3:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001281725.3:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001281726.3:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001323582.2:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370658.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370752.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370753.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407364.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407365.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407366.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407367.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407368.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407369.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407370.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407371.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407372.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407373.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407374.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407375.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407376.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407377.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407378.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407379.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407380.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407381.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407382.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407383.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407384.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407386.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407388.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407390.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407392.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407394.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407395.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407396.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407397.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407398.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407399.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407400.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407401.1:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV001150030	Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München	criteria provided, single submitter (Classification criteria August 2017)	Pathogenic (Jul 16, 2018)	maternal	clinical testing	Citation Link,
SCV001227192	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 11, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 11313766, 15060693, 17185019, 22698809, 28492532
SCV001460176	Natera, Inc.	no assertion criteria provided	Pathogenic (Sep 16, 2020)	germline	clinical testing
SCV002022099	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 15, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004211397	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 24, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	maternal	yes	1	not provided	not provided	1	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Molecular characterisation of 34 patients with biotinidase deficiency ascertained by newborn screening and family investigation.

Mühl A, Möslinger D, Item CB, Stöckler-Ipsiroglu S.

Eur J Hum Genet. 2001 Apr;9(4):237-43.

PubMed [citation]

PMID:: 11313766

Newborn screening for biotinidase deficiency in Brazil: biochemical and molecular characterizations.

Neto EC, Schulte J, Rubim R, Lewis E, DeMari J, Castilhos C, Brites A, Giugliani R, Jensen KP, Wolf B.

Braz J Med Biol Res. 2004 Mar;37(3):295-9. Epub 2004 Mar 3.

PubMed [citation]

PMID:: 15060693

See all PubMed Citations (6)

Details of each submission

From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV001150030.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

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

From Invitae, SCV001227192.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 62 of the BTD protein (p.Val62Met). This variant is present in population databases (rs397507170, gnomAD 0.006%). This missense change has been observed in individual(s) with biotinidase deficiency (PMID: 11313766, 15060693, 17185019, 22698809). ClinVar contains an entry for this variant (Variation ID: 38487). 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. 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

From Natera, Inc., SCV001460176.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	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

From Revvity Omics, Revvity, SCV002022099.3

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

#	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

From Baylor Genetics, SCV004211397.2

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

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

Last Updated: Sep 16, 2024

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