ClinVar Genomic variation as it relates to human health
NM_001353214.3(DYM):c.610C>T (p.Arg204Ter)
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_001353214.3(DYM):c.610C>T (p.Arg204Ter)
Variation ID: 2503430 Accession: VCV002503430.4
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 18q21.1 18: 49333738 (GRCh38) [ NCBI UCSC ] 18: 46860108 (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 Sep 16, 2023 Apr 6, 2024 Mar 17, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001353214.3:c.610C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001340143.1:p.Arg204Ter nonsense NM_001353210.3:c.610C>T NP_001340139.1:p.Arg204Ter nonsense NM_001353211.3:c.607C>T NP_001340140.1:p.Arg203Ter nonsense NM_001353212.3:c.607C>T NP_001340141.1:p.Arg203Ter nonsense NM_001353213.3:c.610C>T NP_001340142.1:p.Arg204Ter nonsense NM_001353215.3:c.610C>T NP_001340144.1:p.Arg204Ter nonsense NM_001353216.3:c.610C>T NP_001340145.1:p.Arg204Ter nonsense NM_001374428.1:c.610C>T NP_001361357.1:p.Arg204Ter nonsense NM_001374429.1:c.607C>T NP_001361358.1:p.Arg203Ter nonsense NM_001374430.1:c.610C>T NP_001361359.1:p.Arg204Ter nonsense NM_001374431.1:c.610C>T NP_001361360.1:p.Arg204Ter nonsense NM_001374432.1:c.495-1732C>T intron variant NM_001374433.1:c.610C>T NP_001361362.1:p.Arg204Ter nonsense NM_001374434.1:c.610C>T NP_001361363.1:p.Arg204Ter nonsense NM_001374435.1:c.610C>T NP_001361364.1:p.Arg204Ter nonsense NM_001374436.1:c.495-1732C>T intron variant NM_001374437.1:c.610C>T NP_001361366.1:p.Arg204Ter nonsense NM_001374438.1:c.610C>T NP_001361367.1:p.Arg204Ter nonsense NM_001374439.1:c.607C>T NP_001361368.1:p.Arg203Ter nonsense NM_001374440.1:c.382C>T NP_001361369.1:p.Arg128Ter nonsense NM_001374441.1:c.194-47122C>T intron variant NM_001374442.1:c.194-47122C>T intron variant NM_001374443.1:c.194-47125C>T intron variant NM_001374444.1:c.194-47122C>T intron variant NM_017653.6:c.610C>T NP_060123.3:p.Arg204Ter nonsense NC_000018.10:g.49333738G>A NC_000018.9:g.46860108G>A NG_009239.2:g.131996C>T NG_009239.3:g.131907C>T - Protein change
- R128*, R203*, R204*
- Other names
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- Canonical SPDI
- NC_000018.10:49333737:G:A
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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
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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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DYM | - | - |
GRCh38 GRCh37 |
293 | 372 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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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 (2) |
criteria provided, single submitter
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Mar 17, 2024 | RCV003326703.3 | |
Pathogenic (1) |
criteria provided, single submitter
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Dec 9, 2023 | RCV003561251.1 |
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
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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
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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
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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
(Dec 09, 2023)
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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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Invitae
Accession: SCV004297841.1
First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Arg204*) in the DYM gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Arg204*) in the DYM gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DYM are known to be pathogenic (PMID: 12491225, 12554689, 18996921). This variant is present in population databases (rs752868357, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with Dyggve–Melchior–Clausen syndrome (PMID: 12554689, 29620724). ClinVar contains an entry for this variant (Variation ID: 2503430). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects DYM function (PMID: 18996921). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Mar 17, 2024)
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criteria provided, single submitter
Method: research
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Dyggve-Melchior-Clausen syndrome
Affected status: unknown
Allele origin:
germline
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Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
Accession: SCV004804691.2
First in ClinVar: Mar 30, 2024 Last updated: Apr 06, 2024 |
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Pathogenic
(Apr 01, 2023)
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no assertion criteria provided
Method: clinical testing
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Dyggve-Melchior-Clausen syndrome
Affected status: yes
Allele origin:
germline
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Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS)
Accession: SCV003927900.1
First in ClinVar: Sep 16, 2023 Last updated: Sep 16, 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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Expanding the phenome and variome of skeletal dysplasia. | Maddirevula S | Genetics in medicine : official journal of the American College of Medical Genetics | 2018 | PMID: 29620724 |
The gene responsible for Dyggve-Melchior-Clausen syndrome encodes a novel peripheral membrane protein dynamically associated with the Golgi apparatus. | Dimitrov A | Human molecular genetics | 2009 | PMID: 18996921 |
Mutations in a novel gene Dymeclin (FLJ20071) are responsible for Dyggve-Melchior-Clausen syndrome. | El Ghouzzi V | Human molecular genetics | 2003 | PMID: 12554689 |
Mental retardation and abnormal skeletal development (Dyggve-Melchior-Clausen dysplasia) due to mutations in a novel, evolutionarily conserved gene. | Cohn DH | American journal of human genetics | 2003 | PMID: 12491225 |
Text-mined citations for this variant ...
HelpRecord last updated Apr 06, 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.