VCV000197734.31 - ClinVar

NM_001853.4(COL9A3):c.308G>A (p.Arg103Gln)

Germline

Classification

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.

(10)

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.

Benign

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001853.4(COL9A3):c.308G>A (p.Arg103Gln)

Variation ID: 197734 Accession: VCV000197734.31

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 20q13.33 20: 62819981 (GRCh38) [ NCBI UCSC ] 20: 61451333 (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 2, 2016	Oct 8, 2024	Aug 1, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_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

... more HGVS ... less HGVS

Protein change

R103Q

Other names

Canonical SPDI

NC_000020.11:62819980:G:A

Functional
consequence

The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele
frequency (GMAF)

The 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.

0.01458 (A)

Allele frequency

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

Links

ClinGen: CA203049

UniProtKB: Q14050#VAR_026467

dbSNP: rs142639450

VarSome

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
Gene	OMIM	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.
COL9A3		-	-	GRCh38 GRCh37	1266	1474

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.
not specified	Benign (4)	criteria provided, multiple submitters, no conflicts	Aug 6, 2020	RCV000178854.12
not provided	Benign (5)	criteria provided, multiple submitters, no conflicts	Aug 1, 2024	RCV001521625.21
Connective tissue disorder	Benign (1)	criteria provided, single submitter	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.
Benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	NOT SPECIFIED Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV000308422.1 First in ClinVar: Oct 02, 2016 Last updated: Oct 02, 2016
Benign (Mar 07, 2015)	criteria provided, single submitter (EGL Classification Definitions 2015) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Eurofins Ntd Llc (ga) Accession: SCV000231019.5 First in ClinVar: Jun 28, 2015 Last updated: Oct 02, 2016	Publications: PubMed (2) PubMed: 11565064‚ 15917166 Other databases http://www.egl-eurofins.com/emvc… http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=COL9A3 Number of individuals with the variant: 1 Sex: mixed
Benign (Aug 06, 2020)	criteria provided, single submitter (Athena Diagnostics Criteria) Method: clinical testing	not specified Affected status: unknown Allele origin: unknown	Athena Diagnostics Accession: SCV001475625.1 First in ClinVar: Jan 26, 2021 Last updated: Jan 26, 2021	Publications: PubMed (4) PubMed: 15917166‚ 11565064‚ 30467950‚ 28507545
Benign (Mar 05, 2022)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Connective tissue disorder Affected status: unknown Allele origin: germline	Genome Diagnostics Laboratory, The Hospital for Sick Children Accession: SCV002566440.1 First in ClinVar: Aug 29, 2022 Last updated: Aug 29, 2022
Benign (Jan 31, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001730999.4 First in ClinVar: Jun 15, 2021 Last updated: Feb 20, 2024
Benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: not provided	not provided (Autosomal recessive inheritance) Affected status: yes Allele origin: germline	Breakthrough Genomics, Breakthrough Genomics Accession: SCV005311126.1 First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024
Benign (Oct 31, 2018)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	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)
Benign (Aug 01, 2024)	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2) Method: clinical testing	not provided Affected status: yes Allele origin: germline	CeGaT Center for Human Genetics Tuebingen Accession: SCV004033896.10 First in ClinVar: Sep 16, 2023 Last updated: Oct 08, 2024	Comment: COL9A3: BS1, BS2 Number of individuals with the variant: 12
Likely benign (-)	no assertion criteria provided Method: clinical testing	not provided Affected status: yes Allele origin: germline	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
Benign (-)	no assertion criteria provided Method: clinical testing	not specified Affected status: yes Allele origin: germline	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

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

Title	Author	Journal	Year	Link
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 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2024

ClinVar Genomic variation as it relates to human health

NM_001853.4(COL9A3):c.308G>A (p.Arg103Gln)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs142639450 ...