VCV002737081.1 - ClinVar

NM_001011658.4(TRAPPC2):c.320dup (p.Phe109fs)

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.

(1)

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

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001011658.4(TRAPPC2):c.320dup (p.Phe109fs)

Variation ID: 2737081 Accession: VCV002737081.1

Type and length

Duplication, 1 bp

Location

Cytogenetic: Xp22.2 X: 13716007-13716008 (GRCh38) [ NCBI UCSC ] X: 13734126-13734127 (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	Feb 14, 2024	Feb 14, 2024	Aug 30, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001011658.4:c.320dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001011658.1:p.Phe109fs	frameshift
NM_001128835.3:c.422dup	NP_001122307.2:p.Phe143fs	frameshift
NM_014563.6:c.320dup	NP_055378.1:p.Phe109fs	frameshift
NC_000023.11:g.13716008dup
NC_000023.10:g.13734127dup
NG_008872.2:g.6505dup
NG_011555.1:g.23616dup

... more HGVS ... less HGVS

Protein change

F109fs, F143fs

Other names

Canonical SPDI

NC_000023.11:13716007:A:AA

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.
OFD1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	905	1207
TRAPPC2		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	76	325

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	Pathogenic (1)	criteria provided, single submitter	Aug 30, 2023	RCV003560193.2

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.
Pathogenic (Aug 30, 2023)	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: SCV004300098.1 First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024	Publications: PubMed (2) PubMed: 11443194‚ 11349230 Comment: For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the TRAPPC2 protein in which other variant(s) (p.Ser124Lysfs4) have … (more) For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the TRAPPC2 protein in which other variant(s) (p.Ser124Lysfs4) have been determined to be pathogenic (PMID: 11443194). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. This premature translational stop signal has been observed in individual(s) with spondyloepiphyseal dysplasia tarda (PMID: 11349230). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Phe109Valfs*8) in the TRAPPC2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 32 amino acid(s) of the TRAPPC2 protein. (less)

Comment:

For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the TRAPPC2 protein in which other variant(s) (p.Ser124Lysfs*4) have been determined to be pathogenic (PMID: 11443194). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. This premature translational stop signal has been observed in individual(s) with spondyloepiphyseal dysplasia tarda (PMID: 11349230). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Phe109Valfs*8) in the TRAPPC2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 32 amino acid(s) of the TRAPPC2 protein.

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
Mutational analysis in X-linked spondyloepiphyseal dysplasia tarda.	Christie PT	The Journal of clinical endocrinology and metabolism	2001	PMID: 11443194
The molecular basis of X-linked spondyloepiphyseal dysplasia tarda.	Gedeon AK	American journal of human genetics	2001	PMID: 11349230

Text-mined citations for this variant ...

Record last updated Sep 30, 2024

ClinVar Genomic variation as it relates to human health

NM_001011658.4(TRAPPC2):c.320dup (p.Phe109fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...