ClinVar Genomic variation as it relates to human health
NM_012062.5(DNM1L):c.1207C>T (p.Arg403Cys)
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.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_012062.5(DNM1L):c.1207C>T (p.Arg403Cys)
Variation ID: 214313 Accession: VCV000214313.48
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 12p11.21 12: 32884296 (GRCh37) [ NCBI UCSC ] 12: 32731362 (GRCh38) [ 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 Aug 30, 2016 Feb 14, 2024 Aug 30, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_012062.5:c.1207C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_036192.2:p.Arg403Cys missense NM_001278464.2:c.1246C>T MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001265393.1:p.Arg416Cys missense NM_001278463.2:c.1207C>T NP_001265392.1:p.Arg403Cys missense NM_001278465.2:c.1246C>T NP_001265394.1:p.Arg416Cys missense NM_001278466.2:c.598C>T NP_001265395.1:p.Arg200Cys missense NM_001330380.2:c.1246C>T NP_001317309.1:p.Arg416Cys missense NM_005690.4:c.1207C>T NM_005690.5:c.1207C>T NP_005681.2:p.Arg403Cys missense NM_012063.4:c.1207C>T NP_036193.2:p.Arg403Cys missense NC_000012.12:g.32731362C>T NC_000012.11:g.32884296C>T NG_012219.1:g.57160C>T O00429:p.Arg403Cys - Protein change
- R403C, R416C, R200C
- Other names
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p.R403C:CGT>TGT
- Canonical SPDI
- NC_000012.12:32731361: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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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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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. |
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DNM1L | - | - |
GRCh38 GRCh37 |
687 | 760 |
Conditions - Germline
Condition
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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May 10, 2021 | RCV000200196.17 | |
Pathogenic (8) |
criteria provided, multiple submitters, no conflicts
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Aug 30, 2023 | RCV000239677.17 | |
Pathogenic (1) |
criteria provided, single submitter
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Oct 12, 2018 | RCV000850522.1 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 23, 2017 | RCV000622584.2 |
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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Pathogenic
(Sep 26, 2017)
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criteria provided, single submitter
Method: clinical testing
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Encephalopathy, lethal, due to defective mitochondrial peroxisomal fission 1
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
de novo
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Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München
Accession: SCV000680191.1
First in ClinVar: Feb 08, 2018 Last updated: Feb 08, 2018 |
Sex: male
Tissue: blood
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Pathogenic
(Feb 07, 2020)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000251352.11
First in ClinVar: Oct 11, 2015 Last updated: Apr 17, 2019 |
Comment:
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed in large population cohorts (Lek et al., 2016); … (more)
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 27145208, 30711678, 30939602, 29877124, 28969390, 30801875, 30109270, 30767894, 30085106, 31216405) (less)
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Pathogenic
(Mar 16, 2017)
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criteria provided, single submitter
Method: research
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Encephalopathy, lethal, due to defective mitochondrial peroxisomal fission 1
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
de novo
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Cavalleri Lab, Royal College of Surgeons in Ireland
Accession: SCV000864022.1
First in ClinVar: May 15, 2019 Last updated: May 15, 2019 |
Clinical Features:
Multifocal epileptiform discharges (present) , Status epilepticus (present) , Focal seizures (present) , Generalized tonic-clonic seizures with focal onset (present) , Generalized myoclonic seizures (present) … (more)
Multifocal epileptiform discharges (present) , Status epilepticus (present) , Focal seizures (present) , Generalized tonic-clonic seizures with focal onset (present) , Generalized myoclonic seizures (present) , Cerebellar atrophy (present) , Abnormality of the endocrine system (present) , Intellectual disability, profound (present) (less)
Method: Single read FASTQ files were aligned to human reference genome build GRCh37 with samtools and Burrows Wheeler Aligner (BWA). Duplicate reads were checked and removed with Picard tools. Variant calling was performed with Genome Analysis Toolkit Haplotype Caller (GATK v3.0).
Testing laboratory: Edinburgh Genomics
Date variant was reported to submitter: 2015-07-28
Testing laboratory interpretation: not provided
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Pathogenic
(Oct 12, 2018)
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criteria provided, single submitter
Method: clinical testing
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Encephalopathy, lethal, due to defective mitochondrial peroxisomal fission 1
Optic atrophy 5
Affected status: yes
Allele origin:
germline
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Baylor Genetics
Accession: SCV000992728.1
First in ClinVar: Sep 21, 2019 Last updated: Sep 21, 2019 |
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Pathogenic
(May 28, 2019)
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criteria provided, single submitter
Method: clinical testing
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Encephalopathy, lethal, due to defective mitochondrial peroxisomal fission 1
Affected status: unknown
Allele origin:
unknown
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Mendelics
Accession: SCV001138671.1
First in ClinVar: Jan 09, 2020 Last updated: Jan 09, 2020 |
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Pathogenic
(Jan 23, 2017)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: yes
Allele origin:
germline
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Ambry Genetics
Accession: SCV000742216.3
First in ClinVar: Apr 15, 2018 Last updated: Jan 07, 2023 |
Number of individuals with the variant: 1
Clinical Features:
Seizures (present) , Encephalopathy (present) , Choreoathetosis (present) , Developmental regression (present) , Pancreatitis (present) , Brain atrophy (present) , Ventriculomegaly (present) , Multiple joint … (more)
Seizures (present) , Encephalopathy (present) , Choreoathetosis (present) , Developmental regression (present) , Pancreatitis (present) , Brain atrophy (present) , Ventriculomegaly (present) , Multiple joint contractures (present) , Hyperreflexia (present) , Ankle clonus (present) , Cortical visual impairment (present) , Progressive spastic quadriplegia (present) (less)
Sex: female
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Pathogenic
(Apr 01, 2022)
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criteria provided, single submitter
Method: clinical testing
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Encephalopathy, lethal, due to defective mitochondrial peroxisomal fission 1
Affected status: yes
Allele origin:
unknown
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Accession: SCV003921905.1
First in ClinVar: May 06, 2023 Last updated: May 06, 2023 |
Comment:
0103 - Dominant negative and loss of function are known mechanisms of disease in this gene and are associated with encephalopathy due to defective mitochondrial … (more)
0103 - Dominant negative and loss of function are known mechanisms of disease in this gene and are associated with encephalopathy due to defective mitochondrial peroxisomal fission 1 (EMPF1; MIM#614388) and optic atrophy 5 (MIM#610708). Missense variants with a dominant negative mechanism has been mostly reported in individuals with dominant EMPF1, with optic atrophy less common. Loss of functional null and missense variants have been reported in individuals with recessive EMPF1 (OMIM, PMID: 29529134). (I) 0108 - This gene is associated with both recessive and dominant disease (OMIM, PMID: 29529134). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to cysteine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0603 - Missense variant in a region that is highly intolerant to missense variation (high constraint region in DECIPHER). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported many times as pathogenic, and observed in multiple de novo individuals with initially normal development, followed by mitochondrial encephalopathy, refractory status epilepticus and/or global developmental delay (ClinVar, PMID: 30939602). (SP) 1207 - Parental origin of the variant is unresolved. Testing of this individual's mother has proven the variant was not maternally inherited (by duo analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
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Pathogenic
(Aug 30, 2023)
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criteria provided, single submitter
Method: clinical testing
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Encephalopathy, lethal, due to defective mitochondrial peroxisomal fission 1
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV001526301.2
First in ClinVar: Mar 22, 2021 Last updated: Oct 06, 2023 |
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Encephalopathy, lethal, due to defective mitochondrial peroxisomal fission 1
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV004047904.1
First in ClinVar: Oct 28, 2023 Last updated: Oct 28, 2023 |
Comment:
The DNM1L c.1207C>T variant has been previously reported as disease-causing heterozygous de novo variant in multiple patients affected with Encephalopathy, lethal, due to defective mitochondrial … (more)
The DNM1L c.1207C>T variant has been previously reported as disease-causing heterozygous de novo variant in multiple patients affected with Encephalopathy, lethal, due to defective mitochondrial peroxisomal fission 1 (Fahrner et al., 2016; Schmid et. al., 2019; McCormack et. al., 2020). The p.Arg403Cys variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic. The amino acid change p.Arg403Cys in DNM1L is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. In silico analysis supports that this missense variant has a deleterious effect on protein structure/function. The amino acid Arg at position 403 is changed to a Cys changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic (less)
Clinical Features:
Spastic paraparesis (present)
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Pathogenic
(May 10, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001199068.5
First in ClinVar: Apr 15, 2020 Last updated: Feb 14, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. This variant has been reported to affect DNM1L protein function (PMID:¬†27145208, 29877124). This variant has … (more)
For these reasons, this variant has been classified as Pathogenic. This variant has been reported to affect DNM1L protein function (PMID: 27145208, 29877124). This variant has been observed to be de novo in individuals affected with DNM1L-related conditions (PMID: 27145208, 29877124). ClinVar contains an entry for this variant (Variation ID: 214313). This variant is not present in population databases (ExAC no frequency). This sequence change replaces arginine with cysteine at codon 403 of the DNM1L protein (p.Arg403Cys). The arginine residue is highly conserved and there is a large physicochemical difference between arginine and cysteine. (less)
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Pathogenic
(Aug 25, 2016)
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no assertion criteria provided
Method: literature only
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ENCEPHALOPATHY DUE TO DEFECTIVE MITOCHONDRIAL AND PEROXISOMAL FISSION 1
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000298168.1
First in ClinVar: Aug 30, 2016 Last updated: Aug 30, 2016 |
Comment on evidence:
In 2 unrelated boys with encephalopathy due to defective mitochondrial and peroxisomal fission-1 (EMPF1; 614388), Fahrner et al. (2016) identified a de novo heterozygous c.1207C-T … (more)
In 2 unrelated boys with encephalopathy due to defective mitochondrial and peroxisomal fission-1 (EMPF1; 614388), Fahrner et al. (2016) identified a de novo heterozygous c.1207C-T transition in the DNM1L gene, resulting in an arg403-to-cys (R403C) substitution in the middle domain, which is thought to be important for higher-order assembly into oligomeric rings. The mutations were found by whole-exome sequencing. In vitro expression studies in mouse embryonic fibroblasts and yeast showed that the R403C mutation results in impaired self-assembly and higher-order oligomerization, decreased colocalization to the mitochondria, and defective mitochondrial fission activity in a dominant-negative manner. The effects of this mutation were not as severe as those of A395D (603850.0001), which may explain the later onset of symptoms in these children at ages 4 and 5 years, respectively. (less)
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Likely pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001809318.1 First in ClinVar: Aug 25, 2021 Last updated: Aug 25, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001958619.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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Encephalopathy, lethal, due to defective mitochondrial peroxisomal fission 1
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
de novo
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Pediatric Department, Xiangya Hospital, Central South University
Accession: SCV002761199.1
First in ClinVar: Jun 17, 2023 Last updated: Jun 17, 2023 |
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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. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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A novel de novo dominant negative mutation in DNM1L impairs mitochondrial fission and presents as childhood epileptic encephalopathy. | Fahrner JA | American journal of medical genetics. Part A | 2016 | PMID: 27145208 |
DNM1L-related mitochondrial fission defect presenting as refractory epilepsy. | Vanstone JR | European journal of human genetics : EJHG | 2016 | PMID: 26604000 |
A lethal de novo mutation in the middle domain of the dynamin-related GTPase Drp1 impairs higher order assembly and mitochondrial division. | Chang CR | The Journal of biological chemistry | 2010 | PMID: 20696759 |
Text-mined citations for rs863223953 ...
HelpRecord last updated Sep 29, 2024
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.