ClinVar Genomic variation as it relates to human health
NM_001376.5(DYNC1H1):c.1792C>T (p.Arg598Cys)
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
-
NM_001376.5(DYNC1H1):c.1792C>T (p.Arg598Cys)
Variation ID: 139652 Accession: VCV000139652.46
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 14q32.31 14: 101986017 (GRCh38) [ NCBI UCSC ] 14: 102452354 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
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 Oct 1, 2014 Sep 16, 2024 Feb 23, 2024 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_001376.5:c.1792C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001367.2:p.Arg598Cys missense NC_000014.9:g.101986017C>T NC_000014.8:g.102452354C>T NG_008777.1:g.26490C>T Q14204:p.Arg598Cys - Protein change
- R598C
- Other names
- -
- Canonical SPDI
- NC_000014.9:101986016:C:T
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
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.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
- -
- 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. |
|||
DYNC1H1 | No evidence available | No evidence available |
GRCh38 GRCh37 |
4477 | 4714 |
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. |
---|---|---|---|---|
Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
|
May 6, 2021 | RCV000144249.8 | |
Pathogenic (1) |
criteria provided, single submitter
|
Nov 20, 2013 | RCV000149555.3 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
|
Feb 23, 2024 | RCV000255067.10 | |
Pathogenic (1) |
criteria provided, single submitter
|
Oct 31, 2018 | RCV000762919.4 | |
Pathogenic (1) |
criteria provided, single submitter
|
Oct 28, 2015 | RCV000624400.5 | |
Pathogenic/Likely pathogenic (4) |
criteria provided, multiple submitters, no conflicts
|
Jul 14, 2022 | RCV000755714.12 |
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. |
|
---|---|---|---|---|---|
Pathogenic
(Nov 20, 2013)
|
criteria provided, single submitter
Method: research
|
Hereditary motor and sensory neuropathy
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
|
Molecular Neurogenomics lab, VIB Department of Molecular Genetics; University of Antwerp
Accession: SCV000191985.2
First in ClinVar: Jan 06, 2015 Last updated: Jan 06, 2015 |
Comment:
segregates with the phenotype; absent in 179 ethnically matched controls
Number of individuals with the variant: 5
Family history: yes
Geographic origin: Australia
Method: Sanger sequencing; coIP
|
|
Pathogenic
(May 01, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Eurofins Ntd Llc (ga)
Accession: SCV000708036.2
First in ClinVar: Oct 01, 2014 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 1
Sex: mixed
|
|
Likely pathogenic
(Oct 15, 2018)
|
criteria provided, single submitter
Method: curation
|
Charcot-Marie-Tooth disease axonal type 2O
Affected status: unknown
Allele origin:
germline
|
SIB Swiss Institute of Bioinformatics
Accession: SCV000883188.1
First in ClinVar: Feb 18, 2019 Last updated: Feb 18, 2019 |
Comment:
This variant is interpreted as Likely Pathogenic, for Charcot-Marie-Tooth disease axonal type 20, autosomal dominant. The following ACMG Tag(s) were applied: PM2 => Absent from … (more)
This variant is interpreted as Likely Pathogenic, for Charcot-Marie-Tooth disease axonal type 20, autosomal dominant. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PP1 => Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease. PS3-Moderate => PS3 downgraded in strength to Moderate (https://www.ncbi.nlm.nih.gov/pubmed/25512093). PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. (less)
|
|
Pathogenic
(Aug 02, 2019)
|
criteria provided, single submitter
Method: research
|
Autosomal dominant childhood-onset proximal spinal muscular atrophy without contractures
Affected status: yes
Allele origin:
unknown
|
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology
Study: PGEN
Accession: SCV001190314.1 First in ClinVar: Dec 15, 2018 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 1
Clinical Features:
Intellectual disability, mild (present) , Short stature (present) , Muscle weakness (present) , Unsteady gait (present) , Spasticity (present) , Pes cavus (present)
|
|
Pathogenic
(Oct 28, 2015)
|
criteria provided, single submitter
Method: clinical testing
|
Inborn genetic diseases
Affected status: yes
Allele origin:
germline
|
Ambry Genetics
Accession: SCV000741139.3
First in ClinVar: Apr 15, 2018 Last updated: Jan 07, 2023 |
Number of individuals with the variant: 1
Clinical Features:
Muscle weakness (present) , Muscular hypotonia (present) , Short stature (present) , Growth delay (present) , Small for gestational age (present) , Attention deficit hyperactivity … (more)
Muscle weakness (present) , Muscular hypotonia (present) , Short stature (present) , Growth delay (present) , Small for gestational age (present) , Attention deficit hyperactivity disorder (present) , Specific learning disability (present) , Abnormality of temperature regulation (present) , Motor delay (present) , Decreased muscle mass (present) , Cachexia (present) , Pes cavus (present) , Elbow flexion contracture (present) , Hyperlordosis (present) , Scapular winging (present) , EMG abnormality (present) , Marked delay in bone age (present) (less)
Sex: male
Ethnicity/Population group: Caucasian
|
|
Pathogenic
(Oct 31, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Autosomal dominant childhood-onset proximal spinal muscular atrophy without contractures
Charcot-Marie-Tooth disease axonal type 2O Intellectual disability, autosomal dominant 13
Affected status: unknown
Allele origin:
unknown
|
Fulgent Genetics, Fulgent Genetics
Accession: SCV000893334.1
First in ClinVar: Mar 31, 2019 Last updated: Mar 31, 2019 |
|
|
Pathogenic
(May 06, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Autosomal dominant childhood-onset proximal spinal muscular atrophy without contractures
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
|
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002767314.1
First in ClinVar: Dec 24, 2022 Last updated: Dec 24, 2022 |
Comment:
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and gain of function … (more)
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and gain of function are known mechanisms of disease in this gene and are associated with spinal muscular atrophy, lower extremity-predominant 1 (MIM#158600), intellectual disability (MIM#614563) and Charcot-Marie-Tooth disease, axonal, type 20 (MIM#614228). While there is no clear genotype-phenotype correlation, there is some association between the severity of the variant on protein function and the phenotype that is manifested (PMID: 25512093, PMID: 28196890). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0115 - Variants in this gene are known to have variable expressivity (PMID: 25512093). (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 multiple times as pathogenic. It has been shown to segregate within families, and arise de novo, in individuals with spinal muscular atrophy or spinal muscular atrophy with lower extremity predominant (ClinVar, PMID: 25512093, PMID: 28554554). (SP) 1001 - This variant has strong functional evidence supporting abnormal protein function. Functional analysis of patient lymphoblasts indicated an increased binding in adaptor protein BICD2 (PMID: 25512093). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
|
|
Pathogenic
(Jul 14, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Charcot-Marie-Tooth disease axonal type 2O
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001201024.5
First in ClinVar: Apr 15, 2020 Last updated: Feb 20, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, … (more)
For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt DYNC1H1 protein function. ClinVar contains an entry for this variant (Variation ID: 139652). This missense change has been observed in individual(s) with lower extremity-predominant spinal muscular atrophy (SMALED) (PMID: 25484024, 25497877, 25512093, 27549087, 28554554). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 598 of the DYNC1H1 protein (p.Arg598Cys). (less)
|
|
Pathogenic
(Feb 23, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV000321571.9
First in ClinVar: Oct 09, 2016 Last updated: Sep 16, 2024 |
Comment:
Published functional studies demonstrate a damaging effect (results in a protein that shows increased binding to the BICD2 adaptor as compared to wild type) (PMID: … (more)
Published functional studies demonstrate a damaging effect (results in a protein that shows increased binding to the BICD2 adaptor as compared to wild type) (PMID: 25512093); Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 28554554, 25484024, 25512093, 26100331, 27549087, 36720598, 37337091, 35899263, 34535505, 35468861, 25497877, 37470033, 31618753, 31130284, 33060286, 34758253, 25609763) (less)
|
|
Likely pathogenic
(Jun 10, 2014)
|
no assertion criteria provided
Method: research
|
Spinal muscular atrophy, lower extremity predominant 1, autosomal dominant
Affected status: yes
Allele origin:
de novo
|
Center for Genetic Medicine Research, Children's National Medical Center
Accession: SCV000154972.1
First in ClinVar: Oct 01, 2014 Last updated: Oct 01, 2014
Comment:
This variant was found by exome sequencing of affected proband and unaffected parents. DYNC1H1 variant was confirmed via Sanger sequencing.
|
Number of individuals with the variant: 1
Clinical Features:
SMALED with vertebral abnormality (present)
Sex: female
Geographic origin: Argentina
|
|
Likely pathogenic
(-)
|
no assertion criteria provided
Method: clinical testing
|
Charcot-Marie-Tooth disease axonal type 2O
Affected status: yes
Allele origin:
germline
|
Genomics England Pilot Project, Genomics England
Accession: SCV001760325.1
First in ClinVar: Jul 27, 2021 Last updated: Jul 27, 2021 |
|
|
Likely pathogenic
(Feb 24, 2023)
|
no assertion criteria provided
Method: clinical testing
|
Autosomal dominant childhood-onset proximal spinal muscular atrophy without contractures
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
maternal
|
Département de Neurologie, Hospices Civils de Lyon
Accession: SCV003836495.1
First in ClinVar: Sep 09, 2023 Last updated: Sep 09, 2023 |
|
|
Uncertain significance
(Jan 06, 2016)
|
no assertion criteria provided
Method: literature only
|
Charcot-Marie-Tooth disease axonal type 2O
Affected status: yes
Allele origin:
germline
|
Inherited Neuropathy Consortium Ii, University Of Miami
Accession: SCV004174346.1
First in ClinVar: Dec 09, 2023 Last updated: Dec 09, 2023 |
|
|
click to load more click to collapse |
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 |
---|---|---|---|---|
Expanding the phenotypic spectrum associated with mutations of DYNC1H1. | Beecroft SJ | Neuromuscular disorders : NMD | 2017 | PMID: 28554554 |
DYNC1H1 mutations associated with neurological diseases compromise processivity of dynein-dynactin-cargo adaptor complexes. | Hoang HT | Proceedings of the National Academy of Sciences of the United States of America | 2017 | PMID: 28196890 |
Improving diagnosis of inherited peripheral neuropathies through gene panel analysis. | Laššuthová P | Orphanet journal of rare diseases | 2016 | PMID: 27549087 |
Mutation screen reveals novel variants and expands the phenotypes associated with DYNC1H1. | Strickland AV | Journal of neurology | 2015 | PMID: 26100331 |
Novel mutations in the DYNC1H1 tail domain refine the genetic and clinical spectrum of dyneinopathies. | Peeters K | Human mutation | 2015 | PMID: 25512093 |
Phenotypic and molecular insights into spinal muscular atrophy due to mutations in BICD2. | Rossor AM | Brain : a journal of neurology | 2015 | PMID: 25497877 |
Exome Sequencing Identifies DYNC1H1 Variant Associated With Vertebral Abnormality and Spinal Muscular Atrophy With Lower Extremity Predominance. | Punetha J | Pediatric neurology | 2015 | PMID: 25484024 |
Molecular defects in the motor adaptor BICD2 cause proximal spinal muscular atrophy with autosomal-dominant inheritance. | Peeters K | American journal of human genetics | 2013 | PMID: 23664119 |
AAA domains and organization of the dynein motor unit. | King SM | Journal of cell science | 2000 | PMID: 10862709 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=DYNC1H1 | - | - | - | - |
Text-mined citations for rs587780564 ...
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.