VCV000014455.2 - ClinVar

NM_000236.3(LIPC):c.[88+16269C>T;88+8149G>A]

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

This haplotype includes the following variants

NM_000236.3(LIPC):c.[88+16269C>T;88+8149G>A]

Other names: LIPC, INTRON 1 HAPLOTYPE, TA
Functional consequence: -
Links: OMIM: 151670.0005

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.
LIPC		-	-	GRCh38 GRCh37	262	285
LIPC-AS1	-	-	-	GRCh38	-	7

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.
High density lipoprotein cholesterol level quantitative trait locus 12	association (1)	no assertion criteria provided	Jan 1, 2008	RCV000015541.4

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 (Jan 01, 2008)	no assertion criteria provided Method: literature only	HIGH DENSITY LIPOPROTEIN CHOLESTEROL LEVEL QUANTITATIVE TRAIT LOCUS 12 Affected status: not provided Allele origin: germline	OMIM Accession: SCV000035806.2 First in ClinVar: Apr 04, 2013 Last updated: Sep 05, 2020	Publications: PubMed (1) PubMed: 18160998 Comment on evidence: Iijima et al. (2008) measured plasma alphalipoprotein (HDL) levels (HDLCQ12; 612797) in 2,970 Japanese individuals and identified a haplotype defined by the T and A … (more) Iijima et al. (2008) measured plasma alphalipoprotein (HDL) levels (HDLCQ12; 612797) in 2,970 Japanese individuals and identified a haplotype defined by the T and A alleles of rs8023503 and rs12594375, 2 SNPs in almost complete linkage disequilibrium in intron 1 of the LIPC gene, that was significantly associated with hyperalphalipoproteinemia (p = 0.00011). The association was replicated in an independent Japanese population consisting of 1,638 individuals (p = 0.0007). (less)

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.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Association of an intronic haplotype of the LIPC gene with hyperalphalipoproteinemia in two independent populations.	Iijima H	Journal of human genetics	2008	PMID: 18160998

Text-mined citations for this variant ...

Record last updated Apr 06, 2024

ClinVar Genomic variation as it relates to human health

NM_000236.3(LIPC):c.[88+16269C>T;88+8149G>A]

Variant Details

NM_000236.3(LIPC):c.[88+16269C>T;88+8149G>A]

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...