ClinVar Genomic variation as it relates to human health
NM_001377.3(DYNC2H1):c.9044A>G (p.Asp3015Gly)
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.
Pathogenic(12); Likely pathogenic(4); Uncertain significance(1)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001377.3(DYNC2H1):c.9044A>G (p.Asp3015Gly)
Variation ID: 6503 Accession: VCV000006503.41
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 11q22.3 11: 103220720 (GRCh38) [ NCBI UCSC ] 11: 103091449 (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 Jun 8, 2016 Mar 16, 2024 Jan 29, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001377.3:c.9044A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001368.2:p.Asp3015Gly missense NM_001080463.2:c.9044A>G MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001073932.1:p.Asp3015Gly missense NM_001377.2:c.9044A>G NC_000011.10:g.103220720A>G NC_000011.9:g.103091449A>G NG_016423.2:g.116290A>G Q8NCM8:p.Asp3015Gly - Protein change
- D3015G
- Other names
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- Canonical SPDI
- NC_000011.10:103220719:A:G
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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
Help
The frequency of the allele represented by this VCV record.
The Genome Aggregation Database (gnomAD), exomes 0.00024
Trans-Omics for Precision Medicine (TOPMed) 0.00025
Exome Aggregation Consortium (ExAC) 0.00026
The Genome Aggregation Database (gnomAD) 0.00026
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 | ||
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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
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. |
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DYNC2H1 | - | - |
GRCh38 GRCh37 |
3549 | 3582 |
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. |
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Pathogenic/Likely pathogenic (7) |
criteria provided, multiple submitters, no conflicts
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Oct 9, 2023 | RCV000006876.30 | |
Pathogenic/Likely pathogenic (8) |
criteria provided, multiple submitters, no conflicts
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May 2, 2022 | RCV000224348.24 | |
Uncertain significance (1) |
criteria provided, single submitter
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Jun 14, 2016 | RCV000292391.13 | |
Pathogenic/Likely pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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Jan 29, 2024 | RCV000386710.18 | |
Pathogenic (1) |
criteria provided, single submitter
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Jul 2, 2015 | RCV000415231.10 | |
DYNC2H1-related disorder
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Pathogenic/Likely pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Jan 18, 2024 | RCV003924807.3 |
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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Uncertain significance
(Jun 14, 2016)
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criteria provided, single submitter
Method: clinical testing
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Short Rib Polydactyly Syndrome
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000366772.2
First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016 |
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Pathogenic
(Jul 02, 2015)
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criteria provided, single submitter
Method: clinical testing
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Bowing of the long bones
Fetal growth restriction Narrow chest
Affected status: yes
Allele origin:
unknown
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Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV000492857.1
First in ClinVar: Jan 13, 2017 Last updated: Jan 13, 2017 |
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Likely pathogenic
(May 01, 2018)
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criteria provided, single submitter
Method: research
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Jeune thoracic dystrophy
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
maternal
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Rare Disease Group, Clinical Genetics, Karolinska Institutet
Accession: SCV000788360.1
First in ClinVar: Oct 10, 2018 Last updated: Oct 10, 2018 |
Observation 1:
Number of individuals with the variant: 1
Clinical Features:
Thoracic hypoplasia (present) , Short ribs (present) , Aplasia/Hypoplasia involving the pelvis (present) , Short long bone (present) , Finger symphalangism (present) , Femoral bowing … (more)
Thoracic hypoplasia (present) , Short ribs (present) , Aplasia/Hypoplasia involving the pelvis (present) , Short long bone (present) , Finger symphalangism (present) , Femoral bowing (present) (less)
Observation 2:
Number of individuals with the variant: 1
Clinical Features:
Thoracic hypoplasia (present) , Short ribs (present) , Aplasia/Hypoplasia involving the pelvis (present) , Short long bone (present) , Femoral bowing (present) , Brachydactyly (present)
Observation 3:
Number of individuals with the variant: 1
Clinical Features:
Bell-shaped thorax (present) , Short ribs (present) , Aplasia/Hypoplasia involving the pelvis (present) , Short long bone (present) , Femoral bowing (present) , Coxa vara … (more)
Bell-shaped thorax (present) , Short ribs (present) , Aplasia/Hypoplasia involving the pelvis (present) , Short long bone (present) , Femoral bowing (present) , Coxa vara (present) , Metaphyseal widening (present) (less)
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Pathogenic
(May 07, 2018)
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criteria provided, single submitter
Method: clinical testing
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DYNC2H1-Related Disorders
Affected status: unknown
Allele origin:
germline
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Illumina Laboratory Services, Illumina
Accession: SCV000366771.3
First in ClinVar: Dec 06, 2016 Last updated: May 24, 2019 |
Comment:
The DYNC2H1 c.9044A>G (p.Asp3015Gly) missense variant has been reported in two studies in which it is found in a compound heterozygous state with a null … (more)
The DYNC2H1 c.9044A>G (p.Asp3015Gly) missense variant has been reported in two studies in which it is found in a compound heterozygous state with a null variant in five individuals diagnosed with asphyxiating thoracic dystrophy (ATD), including two from one family. One of the individuals also carried a large deletion in the DYNC2H1 gene (Dagoneau et al. 2009; Schmidts et al. 2013). The p.Asp3015Gly variant was also found in a heterozygous state in three unaffected family members. The variant has not been reported in the literature in association with short-rib polydactyly syndrome which is also associated with variants in the DYNC2H1 gene. The p.Asp3015Gly variant was present at a frequency of < 0.005 in 1210 control chromosomes and is reported at a frequency of 0.000789 in the Ashkenazi Jewish population of the Genome Aggregation Database. Functional studies in patient fibroblasts demonstrated accumulation of transport proteins in the ciliary tips compared to wild type suggesting disrupted retrograde intraflagellar transport in cilia (Schmidts et al. 2013). Based on the collective evidence, the p.Asp3015Gly variant is classified as pathogenic for DYNC2H1-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. (less)
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Likely pathogenic
(May 19, 2020)
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criteria provided, single submitter
Method: clinical testing
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Asphyxiating thoracic dystrophy 3
Affected status: unknown
Allele origin:
germline
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Johns Hopkins Genomics, Johns Hopkins University
Accession: SCV001425373.1
First in ClinVar: Aug 01, 2020 Last updated: Aug 01, 2020 |
Comment:
This DYNC2H1 variant (rs137853027) is rare (<0.1%) in a large population dataset (gnomAD: 73/279976 total alleles; 0.026%; no homozygotes). It has been reported previously in … (more)
This DYNC2H1 variant (rs137853027) is rare (<0.1%) in a large population dataset (gnomAD: 73/279976 total alleles; 0.026%; no homozygotes). It has been reported previously in patients with Short-rib thoracic dysplasia (SRTD) and has an entry in ClinVar. Three bioinformatic tools queried predict that p.Asp3051Gly would be damaging, and the asparatic acid residue at this position is strongly conserved across all species assessed. Bioinformatic analysis predicts that this variant would not affect normal exon 57 splicing, although this has not been confirmed experimentally to our knowledge. In addition, functional studies using patient fibroblasts containing this variant show abnormal accumulation of transport proteins in the tips of cilia, suggesting a disruption of retrograde intraflagellar transport. We consider this variant to be likely pathogenic. (less)
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Pathogenic
(Jun 25, 2015)
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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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Clinical Genetics and Genomics, Karolinska University Hospital
Accession: SCV001449805.1
First in ClinVar: Dec 10, 2020 Last updated: Dec 10, 2020 |
Number of individuals with the variant: 3
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Asphyxiating thoracic dystrophy 3
Affected status: unknown
Allele origin:
de novo
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Genomic Medicine Lab, University of California San Francisco
Study: CSER
Accession: SCV002576358.1 First in ClinVar: Oct 01, 2022 Last updated: Oct 01, 2022 |
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Pathogenic
(Jul 19, 2023)
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criteria provided, single submitter
Method: clinical testing
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Asphyxiating thoracic dystrophy 3
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004040902.1
First in ClinVar: Oct 07, 2023 Last updated: Oct 07, 2023 |
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Pathogenic
(May 26, 2023)
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criteria provided, single submitter
Method: clinical testing
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Asphyxiating thoracic dystrophy 3
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV002021817.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Jan 29, 2024)
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criteria provided, single submitter
Method: clinical testing
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Jeune thoracic dystrophy
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000814721.4
First in ClinVar: Oct 10, 2018 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces aspartic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 3015 of the DYNC2H1 protein … (more)
This sequence change replaces aspartic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 3015 of the DYNC2H1 protein (p.Asp3015Gly). This variant is present in population databases (rs137853027, gnomAD 0.08%). This missense change has been observed in individual(s) with asphyxiating thoracic dystrophy (PMID: 23339108, 23456818, 29068549). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 6503). 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 DYNC2H1 protein function with a positive predictive value of 95%. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Oct 09, 2023)
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criteria provided, single submitter
Method: clinical testing
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Asphyxiating thoracic dystrophy 3
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001156775.4
First in ClinVar: Feb 10, 2020 Last updated: Feb 20, 2024 |
Comment:
The DYNC2H1 c.9044A>G; p.Asp3015Gly variant (rs137853027) has been described in the compound heterozygous state in several individuals affected with asphyxiating thoracic dystrophy (ATD; Baujat 2013, … (more)
The DYNC2H1 c.9044A>G; p.Asp3015Gly variant (rs137853027) has been described in the compound heterozygous state in several individuals affected with asphyxiating thoracic dystrophy (ATD; Baujat 2013, Dagoneau 2009, Schmidts 2013, Zhang 2018). It contains an entry in ClinVar (Variation ID: 6503), and is observed in the general population at an overall frequency of 0.026% (73/279976 alleles) in the Genome Aggregation Database. The aspartic acid at codon 3015 is highly conserved, and computational algorithms (PolyPhen-2, SIFT) predict that this variant is deleterious. Functional studies using fibroblasts from patients who harbor this variant demonstrate abnormal accumulation of anterograde transport proteins in the tips of cilia and disrupted intraflagellar transport (Schmidts 2013). Based on available information, this variant is considered pathogenic. REFERENCES Baujat G et al. Asphyxiating thoracic dysplasia: clinical and molecular review of 39 families. J Med Genet. 2013 Feb;50(2):91-8. Dagoneau N et al. DYNC2H1 mutations cause asphyxiating thoracic dystrophy and short rib-polydactyly syndrome, type III. Am J Hum Genet. 2009 May;84(5):706-11. Schmidts M et al. Exome sequencing identifies DYNC2H1 mutations as a common cause of asphyxiating thoracic dystrophy (Jeune syndrome) without major polydactyly, renal or retinal involvement. J Med Genet. 2013 May;50(5):309-23. Zhang W et al. Expanding the genetic architecture and phenotypic spectrum in the skeletal ciliopathies. Hum Mutat. 2018 Jan;39(1):152-166. (less)
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Likely pathogenic
(Jan 18, 2024)
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criteria provided, single submitter
Method: clinical testing
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DYNC2H1-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004740275.1
First in ClinVar: Mar 16, 2024 Last updated: Mar 16, 2024 |
Comment:
The DYNC2H1 c.9044A>G variant is predicted to result in the amino acid substitution p.Asp3015Gly. This variant has been reported in the compound heterozygous state in … (more)
The DYNC2H1 c.9044A>G variant is predicted to result in the amino acid substitution p.Asp3015Gly. This variant has been reported in the compound heterozygous state in multiple individuals with asphyxiating thoracic dystrophy (Dagoneau et al. 2009. PubMed ID: 19442771; Baujat et al. 2013. PubMed ID: 23339108; Schmidts et al. 2013. PubMed ID: 23456818; Zhang et al. 2017. PubMed ID: 29068549; Marchuk et al. 2018. PubMed ID: 30557390; Čechová et al. 2019. PubMed ID: 31935347; Vora et al. 2020. PubMed ID: 31974414). In vitro functional studies using patient fibroblasts reveal abnormal accumulation of anterograde transport proteins in the tips of cilia, suggesting a disruption of retrograde intraflagellar transport (Schmidts et al. 2013. PubMed ID: 23456818). This variant is interpreted as likely pathogenic. (less)
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Pathogenic
(Mar 13, 2015)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: not provided
Allele origin:
germline
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Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
Accession: SCV000281195.2
First in ClinVar: Jun 08, 2016 Last updated: Jun 08, 2016 |
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Likely pathogenic
(Jun 23, 2017)
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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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Eurofins Ntd Llc (ga)
Accession: SCV000708108.2
First in ClinVar: Feb 13, 2018 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 1
Sex: mixed
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Pathogenic
(Nov 30, 2019)
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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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Blueprint Genetics
Accession: SCV001832427.1
First in ClinVar: Sep 08, 2021 Last updated: Sep 08, 2021
Comment:
Patient analyzed with Skeletal Dysplasias Core Panel
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Pathogenic
(May 02, 2022)
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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: SCV002013003.3
First in ClinVar: Nov 12, 2021 Last updated: Mar 04, 2023 |
Comment:
In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; In silico analysis supports that this missense variant has a deleterious … (more)
In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 19442771, 30557390, 28492532, 31974414, 31935347, 23456818, 29068549, 23339108, 34426522, 33726816) (less)
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Pathogenic
(Sep 02, 2021)
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criteria provided, single submitter
Method: clinical testing
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Asphyxiating thoracic dystrophy 3
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
paternal
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Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
Accession: SCV001985042.2
First in ClinVar: Oct 30, 2021 Last updated: Mar 26, 2023 |
Comment:
This variant was observed in compound heterozygosity with variant c.10109del
Method: Exome sequencing
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Pathogenic
(Jun 01, 2017)
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no assertion criteria provided
Method: research
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Asphyxiating thoracic dystrophy
Affected status: yes
Allele origin:
maternal,
paternal,
unknown
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Dan Cohn Lab, University Of California Los Angeles
Accession: SCV000611921.1
First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016 |
Observation 1: Observation 2: Observation 3: Observation 4: Observation 5: Observation 6: Observation 7: Observation 8: Observation 9: |
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Pathogenic
(May 01, 2009)
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no assertion criteria provided
Method: literature only
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SHORT-RIB THORACIC DYSPLASIA 3 WITHOUT POLYDACTYLY
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000027072.3
First in ClinVar: Apr 04, 2013 Last updated: Feb 13, 2018 |
Comment on evidence:
In a nonconsanguineous French family with 2 fetuses clinically diagnosed with asphyxiating thoracic dystrophy (SRTD3; 613091), Dagoneau et al. (2009) identified an A-to-G transition at … (more)
In a nonconsanguineous French family with 2 fetuses clinically diagnosed with asphyxiating thoracic dystrophy (SRTD3; 613091), Dagoneau et al. (2009) identified an A-to-G transition at nucleotide 9044 in exon 57 of the DYNC2H1 gene resulting in an asp-to-gly substitution at codon 3015 (D3015G). A frameshift mutation was present on the other allele (603297.0003). In affected members of 3 unrelated Dutch families (JATD-1, JATD-2, and JATD-6) with SRTD3, Schmidts et al. (2013) identified the D3015G mutation in compound heterozygous state with other mutations in the DYNC2H1 gene. (less)
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Likely pathogenic
(-)
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no assertion criteria provided
Method: research
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asphyxiating thoracic dystrophy
Affected status: yes
Allele origin:
inherited
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University of Washington Center for Mendelian Genomics, University of Washington
Accession: SCV001479536.1
First in ClinVar: Feb 20, 2021 Last updated: Feb 20, 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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Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001797452.1 First in ClinVar: Aug 21, 2021 Last updated: Aug 21, 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: SCV001953493.1 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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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: SCV001809399.1 First in ClinVar: Aug 25, 2021 Last updated: Aug 25, 2021 |
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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 genetic architecture and phenotypic spectrum in the skeletal ciliopathies. | Zhang W | Human mutation | 2018 | PMID: 29068549 |
Exome sequencing identifies DYNC2H1 mutations as a common cause of asphyxiating thoracic dystrophy (Jeune syndrome) without major polydactyly, renal or retinal involvement. | Schmidts M | Journal of medical genetics | 2013 | PMID: 23456818 |
Asphyxiating thoracic dysplasia: clinical and molecular review of 39 families. | Baujat G | Journal of medical genetics | 2013 | PMID: 23339108 |
DYNC2H1 mutations cause asphyxiating thoracic dystrophy and short rib-polydactyly syndrome, type III. | Dagoneau N | American journal of human genetics | 2009 | PMID: 19442771 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=DYNC2H1 | - | - | - | - |
Text-mined citations for rs137853027 ...
HelpRecord last updated Sep 17, 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.