VCV002683847.1 - ClinVar

NM_001904.4(CTNNB1):c.1683+1del

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

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001904.4(CTNNB1):c.1683+1del

Variation ID: 2683847 Accession: VCV002683847.1

Type and length

Deletion, 1 bp

Location

Cytogenetic: 3p22.1 3: 41234297 (GRCh38) [ NCBI UCSC ] 3: 41275788 (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	Jan 26, 2024	Jan 26, 2024	Jun 18, 2021

HGVS

Nucleotide	Protein	Molecular consequence
NM_001904.4:c.1683+1del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice donor
NM_001904.4:c.1683+1delG MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice donor
NM_001098209.2:c.1683+1del		splice donor
NM_001098210.2:c.1683+1del		splice donor
NM_001330729.2:c.1662+1del		splice donor
NC_000003.12:g.41234298del
NC_000003.11:g.41275789del
NG_013302.2:g.39848del
NG_082979.1:g.972del
LRG_1108:g.39848del
LRG_1108t1:c.1683+1del

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000003.12:41234296:GG:G

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.
CTNNB1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	401	779
LOC126806659	-	-	-	GRCh38	-	146

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.
Severe intellectual disability-progressive spastic diplegia syndrome	Pathogenic (1)	no assertion criteria provided	Jun 18, 2021	RCV003484460.2

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 (Jun 18, 2021)	no assertion criteria provided Method: clinical testing	Severe intellectual disability-progressive spastic diplegia syndrome (Autosomal dominant inheritance) Affected status: yes Allele origin: germline	Clinical Genomics Laboratory, Stanford Medicine Accession: SCV004228497.1 First in ClinVar: Jan 26, 2024 Last updated: Jan 26, 2024	Comment: The c.1683+1delG variant in the CTNNB1 gene was identified de novo in this individual, but has not been previously reported in association with disease. Notably, … (more) The c.1683+1delG variant in the CTNNB1 gene was identified de novo in this individual, but has not been previously reported in association with disease. Notably, a different nucleotide change, c.1683+1G>A, disrupting the same canonical splice site has been previously reported in an affected individual (Kuechler et al., 2015). This variant was absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). The c.1683+1delG variant alters the canonical donor splice site in intron 10, which is predicted to result in abnormal gene splicing. Heterozygous loss of function is an established mechanism of disease for the CTNNB1 gene. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the c.1683+1delG variant as pathogenic for autosomal dominant CTNNB1-related neurodevelopmental disorder based on the information above. (less) Comment on evidence: Heterozygous (de novo)

Comment:

The c.1683+1delG variant in the CTNNB1 gene was identified de novo in this individual, but has not been previously reported in association with disease. Notably, a different nucleotide change, c.1683+1G>A, disrupting the same canonical splice site has been previously reported in an affected individual (Kuechler et al., 2015). This variant was absent from large population databases, including the Genome Aggregation Database (http://gnomad.broadinstitute.org/). The c.1683+1delG variant alters the canonical donor splice site in intron 10, which is predicted to result in abnormal gene splicing. Heterozygous loss of function is an established mechanism of disease for the CTNNB1 gene. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the c.1683+1delG variant as pathogenic for autosomal dominant CTNNB1-related neurodevelopmental disorder based on the information above.

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 Jul 07, 2024

ClinVar Genomic variation as it relates to human health

NM_001904.4(CTNNB1):c.1683+1del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...