VCV001809264.1 - ClinVar

GRCh37/hg19 1q25.3-32.3(chr1:181453460-213107248)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.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh37/hg19 1q25.3-32.3(chr1:181453460-213107248)x3

Variation ID: 1809264 Accession: VCV001809264.1

Type and length

copy number gain, -

Location

Cytogenetic: 1q25.3-32.3 1: 181453460-213107248 (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 31, 2022	Dec 31, 2022	Sep 29, 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.
CDC73		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	1646	1704
IRF6		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	337	359
KDM5B		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	328	363
CACNA1S		No evidence available	No evidence available	GRCh38 GRCh37	2851	2879
KCNH1		No evidence available	No evidence available	GRCh38 GRCh37	726	751
TNNT2		No evidence available	No evidence available	GRCh38 GRCh37	978	997
ADIPOR1		-	-	GRCh38 GRCh37	164	181
ADORA1		-	-	GRCh38 GRCh37	27	44
APOBEC4		-	-	GRCh38 GRCh37	-	48
ARL8A		-	-	GRCh38 GRCh37	4	21

There are 203 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	Pathogenic (1)	criteria provided, single submitter	Sep 29, 2021	RCV002475637.1

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.
Pathogenic (Sep 29, 2021)	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019) Method: clinical testing	not provided Affected status: unknown Allele origin: unknown	Quest Diagnostics Nichols Institute San Juan Capistrano Accession: SCV002772865.1 First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022	Comment: The large copy number gain of 1q25.3q32.3 involves multiple genes, including 26 genes associated with autosomal dominant disorders. Distal duplications of 1q have been associated … (more) The large copy number gain of 1q25.3q32.3 involves multiple genes, including 26 genes associated with autosomal dominant disorders. Distal duplications of 1q have been associated with partial 1q trisomy syndrome, a rare disorder characterized primarily by intellectual disability, short stature, craniofacial dysmorphism, and multiple other congenital anomalies. While pure distal 1q duplications have been reported, most cases are commonly associated with unbalanced chromosomal translocations, which makes it difficult to dissect genetic contributions and establish genotype-phenotype correlations (Sihombing 2019, Watanabe 2016, Morris 2016, Sifakis 2014, Utine 2007). In particular, duplications of the 1q25 to 1q31-32 have been associated with phenotypes ranging from mild intellectual disability and psychomotor delay to severely affected resulting in early demise (Pettenati 2001, Bartsch 2001, DuPont 1994). References: Bartsch et al., Fetal Diagn Ther. Sep-Oct 2001;16(5):265-73. PMID: 11509847. DuPont et al., Am J Med Genet. 1994 Mar 1;50(1):21-7. PMID: 8160748. Morris et al., Mol Syndromol. 2016 Feb;6(6):297-303. PMID: 27022331. Pettenati et al., Prenat Diagn. 2001 Jun;21(6):435-40. PMID: 11438944. Sifakis et al., Birth Defects Res A Clin Mol Teratol. 2014 Apr;100(4):284-93. PMID: 24677675. Sihombing et al., BMJ Case Rep. 2019 Aug 30;12(8):e230941. PMID: 31473642. Utine et al., Prenat Diagn. 2007 Sep;27(9):865-71. PMID: 17605151. Watanabe et al., Am J Med Genet A. 2016 Apr;170A(4):908-17. PMID: 26782913. (less)

Comment:

The large copy number gain of 1q25.3q32.3 involves multiple genes, including 26 genes associated with autosomal dominant disorders. Distal duplications of 1q have been associated with partial 1q trisomy syndrome, a rare disorder characterized primarily by intellectual disability, short stature, craniofacial dysmorphism, and multiple other congenital anomalies. While pure distal 1q duplications have been reported, most cases are commonly associated with unbalanced chromosomal translocations, which makes it difficult to dissect genetic contributions and establish genotype-phenotype correlations (Sihombing 2019, Watanabe 2016, Morris 2016, Sifakis 2014, Utine 2007). In particular, duplications of the 1q25 to 1q31-32 have been associated with phenotypes ranging from mild intellectual disability and psychomotor delay to severely affected resulting in early demise (Pettenati 2001, Bartsch 2001, DuPont 1994). References: Bartsch et al., Fetal Diagn Ther. Sep-Oct 2001;16(5):265-73. PMID: 11509847. DuPont et al., Am J Med Genet. 1994 Mar 1;50(1):21-7. PMID: 8160748. Morris et al., Mol Syndromol. 2016 Feb;6(6):297-303. PMID: 27022331. Pettenati et al., Prenat Diagn. 2001 Jun;21(6):435-40. PMID: 11438944. Sifakis et al., Birth Defects Res A Clin Mol Teratol. 2014 Apr;100(4):284-93. PMID: 24677675. Sihombing et al., BMJ Case Rep. 2019 Aug 30;12(8):e230941. PMID: 31473642. Utine et al., Prenat Diagn. 2007 Sep;27(9):865-71. PMID: 17605151. Watanabe et al., Am J Med Genet A. 2016 Apr;170A(4):908-17. PMID: 26782913.

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 Sep 01, 2024

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 1q25.3-32.3(chr1:181453460-213107248)x3

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...