NM_001370658.1(BTD):c.-59T>A AND Biotinidase deficiency

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Apr 23, 2022
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:: RCV000667774.10

Allele description [Variation Report for NM_001370658.1(BTD):c.-59T>A]

NM_001370658.1(BTD):c.-59T>A

Gene:

BTD:biotinidase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.1

Genomic location:

Preferred name:

NM_001370658.1(BTD):c.-59T>A

HGVS:

NC_000003.12:g.15601852T>A
NG_008019.2:g.5501T>A
NG_008019.3:g.5502T>A
NG_098817.1:g.479T>A
NM_000060.4:c.2T>A
NM_001281724.3:c.-247T>A
NM_001281726.3:c.-59T>A
NM_001284413.1:c.-389A>T
NM_001284415.1:c.-389A>T
NM_001284416.1:c.-389A>T
NM_001323582.2:c.-335T>A
NM_001370658.1:c.-59T>AMANE SELECT
NM_001370752.1:c.-59T>A
NM_001370753.1:c.-59T>A
NM_001407365.1:c.-17+205T>A
NM_001407366.1:c.-624T>A
NM_001407369.1:c.-610T>A
NM_001407370.1:c.-569+82T>A
NM_001407371.1:c.-743+82T>A
NM_001407372.1:c.-216T>A
NM_001407373.1:c.-178T>A
NM_001407374.1:c.-233T>A
NM_001407378.1:c.-436T>A
NM_001407380.1:c.-59T>A
NM_001407384.1:c.-335T>A
NM_001407390.1:c.-233T>A
NM_001407394.1:c.-293+82T>A
NM_001407395.1:c.-174T>A
NM_001407398.1:c.-59T>A
NM_001407400.1:c.-59T>A
NM_012260.3:c.-389A>T
NP_000051.1:p.Met1Lys
NC_000003.11:g.15643359T>A
NR_104315.1:n.1A>T
NR_176358.1:n.108T>A

Links:

dbSNP: rs768258310

NCBI 1000 Genomes Browser:

rs768258310

Molecular consequence:

NM_001281724.3:c.-247T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001281726.3:c.-59T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001323582.2:c.-335T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370658.1:c.-59T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370752.1:c.-59T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370753.1:c.-59T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407366.1:c.-624T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407369.1:c.-610T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407372.1:c.-216T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407373.1:c.-178T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407374.1:c.-233T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407378.1:c.-436T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407380.1:c.-59T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407384.1:c.-335T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407390.1:c.-233T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407395.1:c.-174T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407398.1:c.-59T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407400.1:c.-59T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407365.1:c.-17+205T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407370.1:c.-569+82T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407371.1:c.-743+82T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407394.1:c.-293+82T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000060.4:c.2T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_176358.1:n.108T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV000792278	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Uncertain significance (Jun 13, 2017)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 11668630, 10655158 Citation Link,
SCV003501596	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 23, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000792278

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Uncertain significance
(Jun 13, 2017)

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV003501596

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 23, 2022)

germline

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	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

Mutations in BTD causing biotinidase deficiency.

Hymes J, Stanley CM, Wolf B.

Hum Mutat. 2001 Nov;18(5):375-81. Review.

PubMed [citation]

PMID:: 11668630

Examination of the signal peptide region of human biotinidase using a baculovirus expression system.

Norrgard KJ, Hymes J, Wolf B.

Mol Genet Metab. 2000 Jan;69(1):56-63.

PubMed [citation]

PMID:: 10655158

See all PubMed Citations (3)

Details of each submission

From Counsyl, SCV000792278.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

#	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

From Invitae, SCV003501596.1

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

Description

This sequence change affects the initiator methionine of the BTD mRNA. The next in-frame methionine is located at codon 21. This variant is present in population databases (rs768258310, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with BTD-related conditions. ClinVar contains an entry for this variant (Variation ID: 552501). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Apr 15, 2024

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