VCV001809607.1 - ClinVar

GRCh38/hg38 1q32.2-42.13(chr1:228006998-228061271)x2

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.

association

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

GRCh38/hg38 1q32.2-42.13(chr1:228006998-228061271)x2

Variation ID: 1809607 Accession: VCV001809607.1

Type and length

copy number loss, -

Location

Cytogenetic: 1q32.2-42.13 1: 208430918-228938006 (GRCh38) [ 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

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.

loss of heterozygosity; Sequence Ontology [ SO:0001786]

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.
IRF6		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	332	354
WDR26		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	187	232
DISP1		No evidence available	No evidence available	GRCh38 GRCh37	335	369
KCNH1		No evidence available	No evidence available	GRCh38 GRCh37	723	748
ACBD3		-	-	GRCh38 GRCh37	12	68
ACBD3-AS1	-	-	-	GRCh38	-	27
AIDA		-	-	GRCh38 GRCh37	10	42
ANGEL2		-	-	GRCh38 GRCh37	30	56
ARF1		-	-	GRCh38 GRCh37	1	76
ATF3		-	-	GRCh38 GRCh37	18	38

There are 712 more genes affected by this variant. See the full set of genes in Variation Viewer (GRCh38).

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.
Orofacial cleft 2	association (1)	no assertion criteria provided	-	RCV002481175.1

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.
association (-)	no assertion criteria provided Method: research	Orofacial cleft 2 (Sporadic) Affected status: yes Allele origin: unknown	Craniofacial science Laboratory, School of Dental Sciences, universiti sains malaysia Accession: SCV002758751.1 First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022	Publications: pmc: 3661199 pmc: 3661199 Comment: In NSCL/P subjects, loss of peaks at 203 bp indicated loss one allele and are scored as loss of heterozygosity (LOH). Number of individuals with the variant: 5 Age: 7-13 years Sex: mixed Ethnicity/Population group: Malay Geographic origin: Malaysia

Germline Functional Evidence

Functional Help The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence	Method Help A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter.	Result Help A brief description of the result of this method for 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 functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
loss of heterozygosity (SO:0001786)	Method not provided	Result not provided	Craniofacial science Laboratory, School of Dental Sciences, universiti sains malaysia Accession: SCV002758751.1	Publications pmc: 3661199

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Roles of BMP signaling pathway in lip and palate development.	Parada C	Frontiers of oral biology	2012	PMC3661199

Text-mined citations for this variant ...

Record last updated Oct 15, 2023

ClinVar Genomic variation as it relates to human health

GRCh38/hg38 1q32.2-42.13(chr1:228006998-228061271)x2

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...