NM_001370658.1(BTD):c.-18del AND Biotinidase deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 10, 2018
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:: RCV000794161.3

Allele description [Variation Report for NM_001370658.1(BTD):c.-18del]

NM_001370658.1(BTD):c.-18del

Gene:

BTD:biotinidase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3p25.1

Genomic location:

Preferred name:

NM_001370658.1(BTD):c.-18del

HGVS:

NC_000003.12:g.15601893del
NG_008019.3:g.5543del
NG_098817.1:g.520del
NM_000060.4:c.43delA
NM_001281724.3:c.-206del
NM_001281726.3:c.-18del
NM_001323582.2:c.-294del
NM_001370658.1:c.-18delMANE SELECT
NM_001370752.1:c.-18del
NM_001370753.1:c.-18del
NM_001407365.1:c.-17+246del
NM_001407366.1:c.-583del
NM_001407369.1:c.-569del
NM_001407370.1:c.-569+123del
NM_001407371.1:c.-743+123del
NM_001407372.1:c.-175del
NM_001407373.1:c.-137del
NM_001407374.1:c.-192del
NM_001407378.1:c.-395del
NM_001407380.1:c.-18del
NM_001407384.1:c.-294del
NM_001407390.1:c.-192del
NM_001407394.1:c.-293+123del
NM_001407395.1:c.-133del
NM_001407398.1:c.-18del
NM_001407400.1:c.-18del
NP_000051.1:p.Arg15Aspfs
NC_000003.11:g.15643400del
NG_008019.2:g.5542del
NM_000060.3:c.43del
NR_176358.1:n.149del

Links:

dbSNP: rs2064260290

NCBI 1000 Genomes Browser:

rs2064260290

Molecular consequence:

NM_001281724.3:c.-206del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001281726.3:c.-18del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001323582.2:c.-294del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370658.1:c.-18del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370752.1:c.-18del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001370753.1:c.-18del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407366.1:c.-583del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407369.1:c.-569del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407372.1:c.-175del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407373.1:c.-137del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407374.1:c.-192del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407378.1:c.-395del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407380.1:c.-18del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407384.1:c.-294del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407390.1:c.-192del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407395.1:c.-133del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407398.1:c.-18del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001407400.1:c.-18del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000060.4:c.43delA - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407365.1:c.-17+246del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407370.1:c.-569+123del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407371.1:c.-743+123del - intron variant - [Sequence Ontology: SO:0001627]
NM_001407394.1:c.-293+123del - intron variant - [Sequence Ontology: SO:0001627]
NR_176358.1:n.149del - 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
SCV000933551	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 10, 2018)	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

SCV000933551

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 10, 2018)

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000933551.1

#	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 creates a premature translational stop signal (p.Arg15Aspfs*55) in the BTD gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with BTD-related conditions. Loss-of-function variants in BTD are known to be pathogenic (PMID: 20083419). 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: Sep 29, 2024

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