This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
ClinVar Genomic variation as it relates to human health
NM_001370658.1(BTD):c.1041C>T (p.Gly347=)
Germline
Classification
Help
criteria provided, conflicting classifications. Learn more about how ClinVar calculates review status.
Conflicting classifications of pathogenicity
Uncertain significance(1); Benign(3); Likely benign(2)
Uncertain significance(1); Benign(3); Likely benign(2)
6 out of 7 submissions contributed to this classification
Help
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
7
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001370658.1(BTD):c.1041C>T (p.Gly347=)
Variation ID: 282920 Accession: VCV000282920.23
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 3p25.1 3: 15644957 (GRCh38) [ NCBI UCSC ] 3: 15686464 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Dec 6, 2016 Apr 13, 2025 Feb 2, 2025 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001370658.1:c.1041C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001357587.1:p.Gly347= synonymous NM_000060.4:c.1101C>T NP_000051.1:p.Gly367= synonymous NM_001281723.4:c.1041C>T NP_001268652.2:p.Gly347= synonymous NM_001281724.3:c.1041C>T NP_001268653.2:p.Gly347= synonymous NM_001281725.3:c.1041C>T NP_001268654.1:p.Gly347= synonymous NM_001281726.2:c.*2819C>T NM_001323582.2:c.1041C>T NP_001310511.1:p.Gly347= synonymous NM_001370752.1:c.1015+26C>T intron variant NM_001370753.1:c.399+2900C>T intron variant NM_001407364.1:c.1041C>T NP_001394293.1:p.Gly347= synonymous NM_001407365.1:c.1041C>T NP_001394294.1:p.Gly347= synonymous NM_001407366.1:c.1041C>T NP_001394295.1:p.Gly347= synonymous NM_001407367.1:c.1041C>T NP_001394296.1:p.Gly347= synonymous NM_001407368.1:c.1041C>T NP_001394297.1:p.Gly347= synonymous NM_001407369.1:c.1041C>T NP_001394298.1:p.Gly347= synonymous NM_001407370.1:c.1041C>T NP_001394299.1:p.Gly347= synonymous NM_001407371.1:c.1041C>T NP_001394300.1:p.Gly347= synonymous NM_001407372.1:c.1041C>T NP_001394301.1:p.Gly347= synonymous NM_001407373.1:c.1041C>T NP_001394302.1:p.Gly347= synonymous NM_001407374.1:c.1041C>T NP_001394303.1:p.Gly347= synonymous NM_001407375.1:c.1041C>T NP_001394304.1:p.Gly347= synonymous NM_001407376.1:c.1041C>T NP_001394305.1:p.Gly347= synonymous NM_001407377.1:c.1041C>T NP_001394306.1:p.Gly347= synonymous NM_001407378.1:c.1041C>T NP_001394307.1:p.Gly347= synonymous NM_001407379.1:c.1015+26C>T intron variant NM_001407380.1:c.399+2900C>T intron variant NM_001407398.1:c.399+2900C>T intron variant NM_001407399.1:c.399+2900C>T intron variant NM_001407400.1:c.399+2900C>T intron variant NM_001407401.1:c.399+2900C>T intron variant NC_000003.12:g.15644957C>T NC_000003.11:g.15686464C>T NG_008019.2:g.48606C>T NG_008019.3:g.48607C>T - Protein change
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- Other names
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- Canonical SPDI
- NC_000003.12:15644956:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.00300 (T)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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Trans-Omics for Precision Medicine (TOPMed) 0.00137
1000 Genomes Project 30x 0.00297
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
The Genome Aggregation Database (gnomAD) 0.00086
1000 Genomes Project 0.00300
- Links
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
| BTD | Gene associated with autosomal recessive phenotype | No evidence available |
GRCh38 GRCh37 |
726 | 830 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Benign/Likely benign (3) |
criteria provided, multiple submitters, no conflicts
|
Aug 10, 2020 | RCV000371736.16 | |
| Conflicting classifications of pathogenicity (4) |
criteria provided, conflicting classifications
|
Feb 2, 2025 | RCV000352964.29 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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|---|---|---|---|---|---|
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Uncertain significance
(Jun 14, 2016)
C
Contributing to aggregate classification
|
criteria provided, single submitter
Method: clinical testing
|
Biotinidase Deficiency
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000441828.2
First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016 |
|
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Likely benign
(Aug 10, 2015)
C
Contributing to aggregate classification
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV000518360.4
First in ClinVar: Mar 08, 2017 Last updated: Mar 08, 2017 |
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. (less)
|
|
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Benign
(Aug 10, 2020)
C
Contributing to aggregate classification
|
criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
unknown
|
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV001470279.1
First in ClinVar: Jan 26, 2021 Last updated: Jan 26, 2021 |
|
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Benign
(Feb 02, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
Method: clinical testing
|
Biotinidase deficiency
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000630319.5
First in ClinVar: Dec 26, 2017 Last updated: Feb 25, 2025 |
|
|
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Benign
(Aug 28, 2015)
C
Contributing to aggregate classification
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Eurofins Ntd Llc (ga)
Accession: SCV000334665.5
First in ClinVar: Dec 06, 2016 Last updated: Apr 13, 2025 |
Number of individuals with the variant: 1
Zygosity: Single Heterozygote
Sex: mixed
|
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Likely benign
(May 18, 2021)
C
Contributing to aggregate classification
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criteria provided, single submitter
Method: clinical testing
|
Biotinidase deficiency
Affected status: no
Allele origin:
germline
|
Genome-Nilou Lab
Accession: SCV001653439.2
First in ClinVar: Jun 03, 2021 Last updated: Apr 13, 2025 |
Sex: mixed
|
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Benign
(Oct 21, 2019)
N
Not contributing to aggregate classification
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no assertion criteria provided
Method: clinical testing
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Biotinidase deficiency
Affected status: unknown
Allele origin:
germline
|
Natera, Inc.
Accession: SCV002081568.1
First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022 |
|
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Comment:
Germline Functional Evidence
| 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. |
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=BTD | - | - | - | - |
Text-mined citations for rs142421934 ...
HelpThese 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 Jun 14, 2025
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.