VCV002578195.2 - ClinVar

NM_001369268.1(ACAN):c.17G>A (p.Trp6Ter)

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.

(2)

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.

Conflicting classifications of pathogenicity
Pathogenic(1); Uncertain significance(1)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001369268.1(ACAN):c.17G>A (p.Trp6Ter)

Variation ID: 2578195 Accession: VCV002578195.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 15q26.1 15: 88836223 (GRCh38) [ NCBI UCSC ] 15: 89379454 (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	Sep 9, 2023	Feb 14, 2024	Jan 6, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001369268.1:c.17G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001356197.1:p.Trp6Ter	nonsense
NM_001135.4:c.17G>A	NP_001126.3:p.Trp6Ter	nonsense
NM_001411096.1:c.17G>A	NP_001398025.1:p.Trp6Ter	nonsense
NM_001411097.1:c.17G>A	NP_001398026.1:p.Trp6Ter	nonsense
NM_013227.4:c.17G>A	NP_037359.3:p.Trp6Ter	nonsense
NC_000015.10:g.88836223G>A
NC_000015.9:g.89379454G>A
NG_012794.1:g.37781G>A

... more HGVS ... less HGVS

Protein change

W6*

Other names

Canonical SPDI

NC_000015.10:88836222:G:A

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

Global minor allele frequency (GMAF) Help 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.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

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.
ACAN		-	-	GRCh38 GRCh37	1142	1176

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 provided	Conflicting interpretations of pathogenicity (2)	criteria provided, conflicting classifications	Jan 6, 2024	RCV003325794.3

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.
Uncertain significance (Feb 28, 2023)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV004031729.1 First in ClinVar: Sep 09, 2023 Last updated: Sep 09, 2023	Comment: Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene or region of a gene for which loss of function … (more) Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene or region of a gene for which loss of function is not a well-established mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge (less)
Pathogenic (Jan 06, 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: SCV004261278.1 First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024	Publications: PubMed (2) PubMed: 16080123‚ 24762113 Comment: This sequence change creates a premature translational stop signal (p.Trp6) in the ACAN gene. It is expected to result in an absent or disrupted protein … (more) This sequence change creates a premature translational stop signal (p.Trp6) in the ACAN gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ACAN are known to be pathogenic (PMID: 16080123, 24762113). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ACAN-related conditions. ClinVar contains an entry for this variant (Variation ID: 2578195). For these reasons, this variant has been classified as Pathogenic. (less)

Comment:

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene or region of a gene for which loss of function is not a well-established mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge

Comment:

This sequence change creates a premature translational stop signal (p.Trp6*) in the ACAN gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ACAN are known to be pathogenic (PMID: 16080123, 24762113). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ACAN-related conditions. ClinVar contains an entry for this variant (Variation ID: 2578195). For these reasons, this variant has been classified as Pathogenic.

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.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Short stature, accelerated bone maturation, and early growth cessation due to heterozygous aggrecan mutations.	Nilsson O	The Journal of clinical endocrinology and metabolism	2014	PMID: 24762113
A mutation in the variable repeat region of the aggrecan gene (AGC1) causes a form of spondyloepiphyseal dysplasia associated with severe, premature osteoarthritis.	Gleghorn L	American journal of human genetics	2005	PMID: 16080123

Text-mined citations for this variant ...

Record last updated Sep 30, 2024

ClinVar Genomic variation as it relates to human health

NM_001369268.1(ACAN):c.17G>A (p.Trp6Ter)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...