ClinVar Genomic variation as it relates to human health
NM_001853.4(COL9A3):c.308G>A (p.Arg103Gln)
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_001853.4(COL9A3):c.308G>A (p.Arg103Gln)
Variation ID: 197734 Accession: VCV000197734.29
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 20q13.33 20: 62819981 (GRCh38) [ NCBI UCSC ] 20: 61451333 (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 Oct 2, 2016 Aug 4, 2024 Jul 1, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001853.4:c.308G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001844.3:p.Arg103Gln missense NC_000020.11:g.62819981G>A NC_000020.10:g.61451333G>A NG_016353.1:g.7920G>A LRG_1253:g.7920G>A LRG_1253t1:c.308G>A LRG_1253p1:p.Arg103Gln Q14050:p.Arg103Gln - Protein change
- R103Q
- Other names
- -
- Canonical SPDI
- NC_000020.11:62819980: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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0.01458 (A)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
Trans-Omics for Precision Medicine (TOPMed) 0.00826
The Genome Aggregation Database (gnomAD) 0.00847
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00946
The Genome Aggregation Database (gnomAD), exomes 0.01360
1000 Genomes Project 30x 0.01405
1000 Genomes Project 0.01458
Exome Aggregation Consortium (ExAC) 0.01459
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
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. |
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COL9A3 | - | - |
GRCh38 GRCh37 |
1263 | 1471 |
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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Benign (4) |
criteria provided, multiple submitters, no conflicts
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Aug 6, 2020 | RCV000178854.12 | |
Benign (4) |
criteria provided, multiple submitters, no conflicts
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Jul 1, 2024 | RCV001521625.19 | |
Benign (1) |
criteria provided, single submitter
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Mar 5, 2022 | RCV002277413.3 |
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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Benign
(-)
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criteria provided, single submitter
Method: clinical testing
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NOT SPECIFIED
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV000308422.1
First in ClinVar: Oct 02, 2016 Last updated: Oct 02, 2016 |
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Benign
(Aug 06, 2020)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
unknown
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Athena Diagnostics
Accession: SCV001475625.1
First in ClinVar: Jan 26, 2021 Last updated: Jan 26, 2021 |
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Benign
(Oct 31, 2018)
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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: SCV001840608.1
First in ClinVar: Sep 10, 2021 Last updated: Sep 10, 2021 |
Comment:
This variant is associated with the following publications: (PMID: 30467950)
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Benign
(Mar 05, 2022)
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criteria provided, single submitter
Method: clinical testing
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Connective tissue disorder
Affected status: unknown
Allele origin:
germline
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Genome Diagnostics Laboratory, The Hospital for Sick Children
Accession: SCV002566440.1
First in ClinVar: Aug 29, 2022 Last updated: Aug 29, 2022 |
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Benign
(Mar 07, 2015)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000231019.5
First in ClinVar: Jun 28, 2015 Last updated: Oct 02, 2016 |
Number of individuals with the variant: 1
Sex: mixed
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Benign
(Jan 31, 2024)
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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: SCV001730999.4
First in ClinVar: Jun 15, 2021 Last updated: Feb 20, 2024 |
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Benign
(Jul 01, 2024)
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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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CeGaT Center for Human Genetics Tuebingen
Accession: SCV004033896.9
First in ClinVar: Sep 16, 2023 Last updated: Aug 04, 2024 |
Comment:
COL9A3: BS1, BS2
Number of individuals with the variant: 11
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Likely benign
(-)
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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: SCV001798882.1 First in ClinVar: Aug 21, 2021 Last updated: Aug 21, 2021 |
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Benign
(-)
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no assertion criteria provided
Method: clinical testing
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not specified
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001807699.1 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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Sequence variants in muscle tissue-related genes may determine the severity of muscle contractures in cerebral palsy. | Pingel J | American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics | 2019 | PMID: 30467950 |
Clinical and Molecular Heterogeneity of RTEL1 Deficiency. | Speckmann C | Frontiers in immunology | 2017 | PMID: 28507545 |
Mutation analysis of COL9A3, a gene highly expressed in the cochlea, in hearing loss patients. | Asamura K | Auris, nasus, larynx | 2005 | PMID: 15917166 |
A mutation in COL9A1 causes multiple epiphyseal dysplasia: further evidence for locus heterogeneity. | Czarny-Ratajczak M | American journal of human genetics | 2001 | PMID: 11565064 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=COL9A3 | - | - | - | - |
Text-mined citations for rs142639450 ...
HelpRecord last updated Aug 04, 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.