NM_001370658.1(BTD):c.-17+1G>A AND Biotinidase deficiency

Clinical significance:Likely pathogenic (Last evaluated: Sep 2, 2016)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000409752.2

Allele description [Variation Report for NM_001370658.1(BTD):c.-17+1G>A]

NM_001370658.1(BTD):c.-17+1G>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.-17+1G>A
HGVS:
  • NC_000003.12:g.15601895G>A
  • NG_008019.1:g.5148G>A
  • NG_008019.2:g.5544G>A
  • NM_001281723.3:c.-17+125G>A
  • NM_001281724.3:c.-205+1G>A
  • NM_001281726.2:c.-17+1G>A
  • NM_001323582.1:c.-293+1G>A
  • NM_001370658.1:c.-17+1G>AMANE SELECT
  • NM_001370752.1:c.-17+1G>A
  • NM_001370753.1:c.-17+1G>A
  • NC_000003.11:g.15643402G>A
Links:
dbSNP: rs1057516440
NCBI 1000 Genomes Browser:
rs1057516440
Molecular consequence:
  • NM_001281723.3:c.-17+125G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001281724.3:c.-205+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001281726.2:c.-17+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001323582.1:c.-293+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370658.1:c.-17+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370752.1:c.-17+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370753.1:c.-17+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
Observations:
1

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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000485680Counsylcriteria provided, single submitter
Likely pathogenic
(Feb 1, 2016)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

mdi-5618_320494_Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015).pdf,

Citation Link,

SCV000712499Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Likely pathogenic
(Sep 2, 2016)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided21not providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Identification of alternatively spliced human biotinidase mRNAs and putative localization of endogenous biotinidase.

Stanley CM, Hymes J, Wolf B.

Mol Genet Metab. 2004 Apr;81(4):300-12.

PubMed [citation]
PMID:
15059618

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Counsyl, SCV000485680.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000712499.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (1)

Description

The c.44+1G>A variant in BTD has not been previously reported in patients with b iotinidase deficiency and was absent from large population studies. This variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and i s predicted to cause altered splicing leading to an abnormal or absent protein. Biallelic loss of function of BTD has been associated with biotinidase deficienc y. In summary, although additional studies are required to fully establish its c linical significance, the c.44+1G>A variant in BTD is likely pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided2not provided1not provided

Last Updated: Jul 7, 2021

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