VCV002499527.1 - ClinVar

NM_001160372.4(TRAPPC9):c.2123del (p.His708fs)

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.

not provided

no classification provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001160372.4(TRAPPC9):c.2123del (p.His708fs)

Variation ID: 2499527 Accession: VCV002499527.1

Type and length

Deletion, 1 bp

Location

Cytogenetic: 8q24.3 8: 140275813 (GRCh38) [ NCBI UCSC ] 8: 141285912 (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	Apr 30, 2023	Apr 30, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_001160372.4:c.2123del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001153844.1:p.His708fs	frameshift
NM_001321646.2:c.2096del	NP_001308575.1:p.His699fs	frameshift
NM_001374682.1:c.2144del	NP_001361611.1:p.His715fs	frameshift
NM_001374683.1:c.2123del	NP_001361612.1:p.His708fs	frameshift
NM_001374684.1:c.1979del	NP_001361613.1:p.His660fs	frameshift
NM_031466.8:c.2123del	NP_113654.5:p.His708fs	frameshift
NR_164662.1:n.2212del		non-coding transcript variant
NC_000008.11:g.140275813del
NC_000008.10:g.141285912del
NG_016478.3:g.187767del
LRG_1041:g.187767del
LRG_1041t1:c.2123del	LRG_1041p1:p.His708fs
LRG_1041t2:c.2123del	LRG_1041p2:p.His708fs

... more HGVS ... less HGVS

Protein change

H660fs, H699fs, H708fs, H715fs

Other names

Canonical SPDI

NC_000008.11:140275812:T:

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.
TRAPPC9		-	-	GRCh38 GRCh37	868	949

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.
Intellectual disability, autosomal recessive 13	not provided (1)	no classification provided	-	RCV003223456.2

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.
not provided (-)	no classification provided Method: phenotyping only	Intellectual disability, autosomal recessive 13 Affected status: unknown Allele origin: maternal	GenomeConnect - Brain Gene Registry Accession: SCV003918879.1 First in ClinVar: Apr 30, 2023 Last updated: Apr 30, 2023	Comment: Variant interpreted as Likely pathogenic and reported on 09-08-2020 by lab The Children's Hospital of Philadelphia. Assertions are reported exactly as they appear on the … (more) Variant interpreted as Likely pathogenic and reported on 09-08-2020 by lab The Children's Hospital of Philadelphia. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator John Constantino MD PhD from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. (less) Clinical Features: Global developmental delay (present) , Autistic behavior (present) , Hearing impairment (present) , Hypotonia (present) Indication for testing: Diagnostic Age: 0-9 years Sex: male Method: Exome Sequencing Testing laboratory: Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia Date variant was reported to submitter: 2020-09-08 Testing laboratory interpretation: Likely pathogenic

Comment:

Variant interpreted as Likely pathogenic and reported on 09-08-2020 by lab The Children's Hospital of Philadelphia. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator John Constantino MD PhD from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect.

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

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Jun 23, 2024

ClinVar Genomic variation as it relates to human health

NM_001160372.4(TRAPPC9):c.2123del (p.His708fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...