VCV001340561.1 - ClinVar

GRCh37/hg19 3q26.2-26.33(chr3:168118411-179867071)x3

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.

Likely pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh37/hg19 3q26.2-26.33(chr3:168118411-179867071)x3

Variation ID: 1340561 Accession: VCV001340561.1

Type and length

copy number gain, -

Location

Cytogenetic: 3q26.2-26.33 3: 168118411-179867071 (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 13, 2022	Feb 13, 2022	May 1, 2021

HGVS

Protein change

Other names

Canonical SPDI

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.
TBL1XR1		Sufficient evidence for dosage pathogenicity	Little evidence for dosage pathogenicity	GRCh38 GRCh37	417	599
NAALADL2		No evidence available	No evidence available	GRCh38 GRCh38 GRCh37	54	99
NLGN1		No evidence available	No evidence available	GRCh38 GRCh37	93	117
PIK3CA		No evidence available	No evidence available	GRCh38 GRCh37	1297	1331
ACTL6A		-	-	GRCh38 GRCh37	35	65
ACTRT3		-	-	GRCh38 GRCh37	23	54
CLDN11		-	-	GRCh38 GRCh37	13	36
ECT2		-	-	GRCh38 GRCh37	35	65
EIF5A2		-	-	GRCh38 GRCh37	7	29
FNDC3B		-	-	GRCh38 GRCh37	68	98

There are 32 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh37) and ClinGen Dosage Sensitivity Map.

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	Likely pathogenic (1)	no assertion criteria provided	May 1, 2021	RCV001827868.1

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.
Likely pathogenic (May 01, 2021)	no assertion criteria provided Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Quest Diagnostics Nichols Institute San Juan Capistrano Accession: SCV002096496.1 First in ClinVar: Feb 13, 2022 Last updated: Feb 13, 2022	Comment: The copy number gain of 3q26.2q26.33 involves numerous protein-coding genes. A smaller 2 Mb duplication at 3q26.2, arising de novo, was reported in a case … (more) The copy number gain of 3q26.2q26.33 involves numerous protein-coding genes. A smaller 2 Mb duplication at 3q26.2, arising de novo, was reported in a case resembling partial trisomy 3q syndrome including intellectual disability, synophrys, a wide nasal bridge, dysmorphic ears, clinodactyly, and cardiac defects (Molck et al., Mol Syndromol. 2018 Jul;9(4):197-204. PMID: 30140197). The authors further analyzed the case-series of partial trisomy 3q syndrome and suggest 3q26.2 could be triplosensitive. However, Faas et al proposed a critical region of 3q26.3, which is adjacent but not overlapping the 3q26.2 segment in this syndrome (Faas et al., Clin Genet. 2002 Oct;62(4):315-20. PMID: 12372060). The current gain interval fully encompasses the 3q26.2 region by Molck et al and overlaps the 3q26.3 region by Faas et al. Furthermore, cases with overlapping duplications of 3q25q26 have been described without typical features of trisomy 3q syndrome and a milder or nearly normal phenotype, or only developmental delay with minor facial dysmorphism (Meins et al., Am J Med Genet A. 2005 Jan 1;132A(1):84-9. PMID: 15551338; Rizzu et al., Am J Med Genet. 1997 Feb 11;68(4):428-32. PMID: 9021016). This large duplication also includes multiple OMIM genes associated with autosomal dominant phenotypes: MECOM (OMIM 616738), TERC (OMIM 127550), GHSR (OMIM 615925), NLGN1 (OMIM 618830), TBL1XR1 (OMIM 616944 and 602342), and GNB4 (OMIM 615185). Thus, based on literature review, duplication size and gene content, this copy number gain is interpreted as likely pathogenic. (less)

Comment:

The copy number gain of 3q26.2q26.33 involves numerous protein-coding genes. A smaller 2 Mb duplication at 3q26.2, arising de novo, was reported in a case resembling partial trisomy 3q syndrome including intellectual disability, synophrys, a wide nasal bridge, dysmorphic ears, clinodactyly, and cardiac defects (Molck et al., Mol Syndromol. 2018 Jul;9(4):197-204. PMID: 30140197). The authors further analyzed the case-series of partial trisomy 3q syndrome and suggest 3q26.2 could be triplosensitive. However, Faas et al proposed a critical region of 3q26.3, which is adjacent but not overlapping the 3q26.2 segment in this syndrome (Faas et al., Clin Genet. 2002 Oct;62(4):315-20. PMID: 12372060). The current gain interval fully encompasses the 3q26.2 region by Molck et al and overlaps the 3q26.3 region by Faas et al. Furthermore, cases with overlapping duplications of 3q25q26 have been described without typical features of trisomy 3q syndrome and a milder or nearly normal phenotype, or only developmental delay with minor facial dysmorphism (Meins et al., Am J Med Genet A. 2005 Jan 1;132A(1):84-9. PMID: 15551338; Rizzu et al., Am J Med Genet. 1997 Feb 11;68(4):428-32. PMID: 9021016). This large duplication also includes multiple OMIM genes associated with autosomal dominant phenotypes: MECOM (OMIM 616738), TERC (OMIM 127550), GHSR (OMIM 615925), NLGN1 (OMIM 618830), TBL1XR1 (OMIM 616944 and 602342), and GNB4 (OMIM 615185). Thus, based on literature review, duplication size and gene content, this copy number gain is interpreted as likely 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

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 Apr 25, 2022

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 3q26.2-26.33(chr3:168118411-179867071)x3

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...