VCV001807694.1 - ClinVar

GRCh37/hg19 1q31.1-32.1(chr1:189633885-199854163)x1

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

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh37/hg19 1q31.1-32.1(chr1:189633885-199854163)x1

Variation ID: 1807694 Accession: VCV001807694.1

Type and length

copy number loss, -

Location

Cytogenetic: 1q31.1-32.1 1: 189633885-199854163 (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	Jun 9, 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	1599	1653
ASPM		-	-	GRCh38 GRCh37	1733	1781
ATP6V1G3		-	-	GRCh38 GRCh38 GRCh37	9	31
B3GALT2		-	-	GRCh38 GRCh37	-	51
BRINP3		-	-	GRCh38 GRCh37	53	79
C1orf53	-	-	-	GRCh38 GRCh37	3	25
CFH		-	-	GRCh38 GRCh38 GRCh37	833	862
CFHR1		-	-	GRCh38 GRCh37	90	132
CFHR2		-	-	GRCh38 GRCh38 GRCh37	47	72
CFHR3		-	-	GRCh38 GRCh37	77	116

There are 20 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)	criteria provided, single submitter	Jun 9, 2021	RCV002472500.1

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 (Jun 09, 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: SCV002772368.1 First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022	Comment: The copy number loss of 1q31.1q32.1 involves multiple protein-coding genes, including KCNT2 (OMIM 610044) and CDC73 (OMIM 607393). A similar 9.5 Mb deletion at this … (more) The copy number loss of 1q31.1q32.1 involves multiple protein-coding genes, including KCNT2 (OMIM 610044) and CDC73 (OMIM 607393). A similar 9.5 Mb deletion at this region, arising de novo, was reported in an individual with intellectual disability, obesity, and dysmorphic features (Hyder et al., Clin Dysmorphol. 2019 Jul;28(3):131-136. PMID: 31045593). Milani et al. also reported a larger de novo deletion of 1q31.1q32.1 in an individual with developmental delay, hyperactivity and behavioral disorder, and dysmorphic features including laterally sparse eyebrows, downslanting palpebral fissures, broad nasal root, long philtrum, thin upper lip and thick lower lip (Milani D, et al. Cytogenet Genome Res. 2012;136(3):167-70. PMID: 22398643). Furthermore, heterozygous pathogenic loss-of-function variants of CDC73 have been associated with autosomal dominant hyperparathyroidism-jaw tumor syndrome (aka parathyroid adenoma with cystic changes; OMIM 145001) and familial primary hyperparathyroidism (OMIM 145000). This large deletion also includes a few genes associated with autosomal dominant OMIM phenotypes: KCNT2 (OMIM 610044), CFH (OMIM 134370), CFHR3 (OMIM 605336), CFHR1 (OMIM 134371), CFHR5 (OMIM 608593), and CRB1 (OMIM 604210). There are no full copy number losses of this region in the general populations of the Database of Genomic Variants. Thus, based on literature review and gene content, this copy number loss is interpreted as likely pathogenic. (less)

Comment:

The copy number loss of 1q31.1q32.1 involves multiple protein-coding genes, including KCNT2 (OMIM 610044) and CDC73 (OMIM 607393). A similar 9.5 Mb deletion at this region, arising de novo, was reported in an individual with intellectual disability, obesity, and dysmorphic features (Hyder et al., Clin Dysmorphol. 2019 Jul;28(3):131-136. PMID: 31045593). Milani et al. also reported a larger de novo deletion of 1q31.1q32.1 in an individual with developmental delay, hyperactivity and behavioral disorder, and dysmorphic features including laterally sparse eyebrows, downslanting palpebral fissures, broad nasal root, long philtrum, thin upper lip and thick lower lip (Milani D, et al. Cytogenet Genome Res. 2012;136(3):167-70. PMID: 22398643). Furthermore, heterozygous pathogenic loss-of-function variants of CDC73 have been associated with autosomal dominant hyperparathyroidism-jaw tumor syndrome (aka parathyroid adenoma with cystic changes; OMIM 145001) and familial primary hyperparathyroidism (OMIM 145000). This large deletion also includes a few genes associated with autosomal dominant OMIM phenotypes: KCNT2 (OMIM 610044), CFH (OMIM 134370), CFHR3 (OMIM 605336), CFHR1 (OMIM 134371), CFHR5 (OMIM 608593), and CRB1 (OMIM 604210). There are no full copy number losses of this region in the general populations of the Database of Genomic Variants. Thus, based on literature review and gene content, this copy number loss 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 Mar 26, 2023

ClinVar Genomic variation as it relates to human health

GRCh37/hg19 1q31.1-32.1(chr1:189633885-199854163)x1

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...