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NM_001370658.1(BTD):c.683T>C (p.Ile228Thr)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(2);Pathogenic(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Mar 5, 2020
Accession:
VCV000025037.4
Variation ID:
25037
Description:
single nucleotide variant
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NM_001370658.1(BTD):c.683T>C (p.Ile228Thr)

Allele ID
36374
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p25.1
Genomic location
3: 15644599 (GRCh38) GRCh38 UCSC
3: 15686106 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.15686106T>C
NC_000003.12:g.15644599T>C
NG_008019.1:g.47852T>C
... more HGVS
Protein change
I228T
Other names
-
Canonical SPDI
NC_000003.12:15644598:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00002
Exome Aggregation Consortium (ExAC) 0.00002
Links
ClinGen: CA278254
dbSNP: rs397514382
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Oct 31, 2019 RCV001284605.1
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Mar 5, 2020 RCV000021960.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
BTD - - GRCh38
GRCh37
427 464

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Feb 17, 2017)
criteria provided, single submitter
Method: clinical testing
Biotinidase deficiency
(Autosomal recessive inheritance)
Allele origin: germline
Research and Development, ARUP Laboratories
Accession: SCV000042629.2
Submitted: (Mar 10, 2017)
Evidence details
Publications
PubMed (1)
Comment:
Enzyme activity @ < 0.4 U/L with a paired control in the normal range. Seen with c.528G>T,p.K176N.
Uncertain significance
(Nov 14, 2017)
criteria provided, single submitter
Method: clinical testing
Biotinidase deficiency
Allele origin: unknown
Counsyl
Accession: SCV000800591.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (1)
Likely pathogenic
(May 23, 2019)
criteria provided, single submitter
Method: clinical testing
Biotinidase deficiency
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV000602896.2
Submitted: (Aug 05, 2019)
Evidence details
Comment:
The BTD c.743T>C; p.Ile248Thr variant (rs397514382) is reported in the literature in at least one individual affected with biotinidase deficiency who carried a second, pathogenic … (more)
Likely pathogenic
(Oct 31, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: unknown
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV001470475.1
Submitted: (Dec 31, 2020)
Evidence details
Publications
PubMed (2)
Comment:
Found in at least one patient with expected phenotype for this gene. Predicted to have a damaging effect on the protein. In multiple individuals, this … (more)
Pathogenic
(Mar 05, 2020)
criteria provided, single submitter
Method: clinical testing
Biotinidase deficiency
Allele origin: germline
Invitae
Accession: SCV001585143.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces isoleucine with threonine at codon 248 of the BTD protein (p.Ile248Thr). The isoleucine residue is highly conserved and there is a … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Forty-eight novel mutations causing biotinidase deficiency. Procter M Molecular genetics and metabolism 2016 PMID: 26810761
Increased incidence of profound biotinidase deficiency among Hispanic newborns in California. Cowan TM Molecular genetics and metabolism 2012 PMID: 22698809
Procter et al, unpublished - - - -

Text-mined citations for rs397514382...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021