VCV001802535.1 - ClinVar

NM_001011658.4(TRAPPC2):c.137_138del (p.Leu46fs)

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.137_138del (p.Leu46fs)

Variation ID: 1802535 Accession: VCV001802535.1

Type and length

Microsatellite, 2 bp

Location

Cytogenetic: Xp22.2 X: 13716634-13716635 (GRCh38) [ NCBI UCSC ] X: 13734753-13734754 (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	Dec 11, 2022	Dec 11, 2022	Nov 12, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_001011658.4:c.137_138del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001011658.1:p.Leu46fs	frameshift
NM_001128835.3:c.239_240del	NP_001122307.2:p.Leu80fs	frameshift
NM_014563.6:c.137_138del	NP_055378.1:p.Leu46fs	frameshift
NC_000023.11:g.13716635AG[1]
NC_000023.10:g.13734754AG[1]
NG_008872.2:g.7132AG[1]
NG_011555.1:g.22987TC[1]

... more HGVS ... less HGVS

Protein change

L46fs, L80fs

Other names

p.Leu46ArgfsTer5

Canonical SPDI

NC_000023.11:13716633:GAGAG:GAG

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

protein truncation; Variation Ontology [ VariO:0015]

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	909	1211
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.
Spondyloepiphyseal dysplasia tarda, X-linked	Pathogenic (1)	criteria provided, single submitter	Nov 12, 2022	RCV002465374.2

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 (Nov 12, 2022)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Spondyloepiphyseal dysplasia tarda, X-linked (X-linked recessive inheritance) Affected status: yes Allele origin: germline	Instituto de Genética, Servicios Medicos Yunis Turbay Cia. SAS Accession: SCV002600213.1 First in ClinVar: Dec 11, 2022 Last updated: Dec 11, 2022	Publications: PubMed (1) PubMed: 7192195 Comment: Variant detected in three affected males, detected also in an obligated carrier female. Variant not found in male children of affected individual. Number of individuals with the variant: 3 Clinical Features: SPONDYLOEPIPHYSEAL DYSPLASIA TARDA, X-LINKED; SEDT (present) Age: 50-59 years Sex: male Geographic origin: Colombia Comment on evidence: Variant found in three affected males, in one female obligated carrier, and absent in two male children from one affected individual. Variant segregates with disease. … (more) Variant found in three affected males, in one female obligated carrier, and absent in two male children from one affected individual. Variant segregates with disease. Variant absent in population databases (less) Method: Exome Tru-Sight One

Germline Functional Evidence

Functional Help The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence	Method Help A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter.	Result Help A brief description of the result of this method for 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 functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
protein truncation (VariO:0015)			Instituto de Genética, Servicios Medicos Yunis Turbay Cia. SAS Accession: SCV002600213.1	Publications PubMed (1)

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
X-linked Dyggve-Melchior-Clausen syndrome.	Yunis E	Clinical genetics	1980	PMID: 7192195

Text-mined citations for this variant ...

Record last updated Jun 23, 2024

ClinVar Genomic variation as it relates to human health

NM_001011658.4(TRAPPC2):c.137_138del (p.Leu46fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...