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NM_001258392.3(CLPB):c.1159C>T (p.Arg387Ter)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Nov 19, 2021)
Last evaluated:
Jul 15, 2021
Accession:
VCV000187786.3
Variation ID:
187786
Description:
single nucleotide variant
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NM_001258392.3(CLPB):c.1159C>T (p.Arg387Ter)

Allele ID
185684
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11q13.4
Genomic location
11: 72302312 (GRCh38) GRCh38 UCSC
11: 72013356 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.72302312G>A
NC_000011.9:g.72013356G>A
NG_042130.2:g.137373C>T
... more HGVS
Protein change
R417*, R387*, R358*, R372*
Other names
-
Canonical SPDI
NC_000011.10:72302311:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Exome Aggregation Consortium (ExAC) 0.00003
The Genome Aggregation Database (gnomAD), exomes 0.00003
Links
ClinGen: CA198530
OMIM: 616254.0007
dbSNP: rs200203460
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 6 criteria provided, multiple submitters, no conflicts Jul 15, 2021 RCV000167543.9

Clinical features observed in individuals with this variant

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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CLPB - - GRCh38
GRCh37
327 336

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jun 28, 2018)
criteria provided, single submitter
Method: clinical testing
3-methylglutaconic aciduria with cataracts, neurologic involvement, and neutropenia
Allele origin: germline
Invitae
Accession: SCV000821298.1
Submitted: (Aug 29, 2018)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change creates a premature translational stop signal (p.Arg417*) in the CLPB gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Sep 04, 2015)
criteria provided, single submitter
()
Method: research
3-methylglutaconic aciduria with cataracts, neurologic involvement, and neutropenia
Allele origin: maternal
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology
Study: CSER-HudsonAlpha
Accession: SCV000265561.3
Submitted: (May 04, 2017)
Evidence details
Pathogenic
(Jul 15, 2021)
criteria provided, single submitter
Method: clinical testing
3-methylglutaconic aciduria with cataracts, neurologic involvement, and neutropenia
Allele origin: paternal
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
Accession: SCV001762982.1
Submitted: (Jul 31, 2021)
Evidence details
Publications
PubMed (1)
Pathogenic
(Feb 05, 2015)
no assertion criteria provided
Method: literature only
3-@METHYLGLUTACONIC ACIDURIA, TYPE VII
Allele origin: germline
OMIM
Accession: SCV000218401.3
Submitted: (Mar 20, 2015)
Evidence details
Publications
PubMed (2)
Pathogenic
(Sep 14, 2016)
no assertion criteria provided
Method: literature only
3-methylglutaconic aciduria with cataracts, neurologic involvement, and neutropenia
Allele origin: germline
GeneReviews
Accession: SCV000328966.1
Submitted: (Sep 14, 2016)
Evidence details
Publications
PubMed (2)
Other databases
https://www.ncbi.nlm.nih.gov/boo…
Pathogenic
(Sep 12, 2019)
no assertion criteria provided
Method: clinical testing
3-methylglutaconic aciduria with cataracts, neurologic involvement, and neutropenia
Allele origin: germline
PerkinElmer Genomics
Accession: SCV002017385.1
Submitted: (Nov 19, 2021)
Evidence details

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
A scoring system predicting the clinical course of CLPB defect based on the foetal and neonatal presentation of 31 patients. Pronicka E Journal of inherited metabolic disease 2017 PMID: 28687938
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
CLPB Deficiency Wortmann SB - 2016 PMID: 27891836
New perspective in diagnostics of mitochondrial disorders: two years' experience with whole-exome sequencing at a national paediatric centre. Pronicka E Journal of translational medicine 2016 PMID: 27290639
CLPB variants associated with autosomal-recessive mitochondrial disorder with cataract, neutropenia, epilepsy, and methylglutaconic aciduria. Saunders C American journal of human genetics 2015 PMID: 25597511
CLPB mutations cause 3-methylglutaconic aciduria, progressive brain atrophy, intellectual disability, congenital neutropenia, cataracts, movement disorder. Wortmann SB American journal of human genetics 2015 PMID: 25597510
https://www.ncbi.nlm.nih.gov/books/NBK396257/ - - - -

Text-mined citations for rs200203460...

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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 Nov 28, 2021