VCV000017911.3 - ClinVar

NM_000039.3(APOA1):c.391A>T (p.Lys131Ter)

Germline

Classification

no assertion criteria provided. Learn more about how ClinVar calculates review status.

Pathogenic
Pathogenic (1)

This classification is based on the single submission received

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.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000039.3(APOA1):c.391A>T (p.Lys131Ter)

Variation ID: 17911 Accession: VCV000017911.3

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 11q23.3 11: 116836221 (GRCh38) [ NCBI UCSC ] 11: 116706937 (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	Oct 20, 2016	May 26, 2024	Apr 1, 1986

HGVS

Nucleotide	Protein	Molecular consequence
NM_000039.3:c.391A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000030.1:p.Lys131Ter	nonsense
NM_001318017.2:c.391A>T	NP_001304946.1:p.Lys131Ter	nonsense
NM_001318018.2:c.391A>T	NP_001304947.1:p.Lys131Ter	nonsense
NM_001318021.2:c.64A>T	NP_001304950.1:p.Lys22Ter	nonsense
NR_126362.1:n.105T>A		non-coding transcript variant
NC_000011.10:g.116836221T>A
NC_000011.9:g.116706937T>A
NG_012021.1:g.6402A>T
LRG_767:g.6402A>T
LRG_767t1:c.391A>T	LRG_767p1:p.Lys131Ter

... more HGVS ... less HGVS

Protein change

K131*, K22*

Other names

K107*

Canonical SPDI

NC_000011.10:116836220:T:A

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

ClinGen: CA127543 OMIM: 107680.0002 dbSNP: rs121912716 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.
APOA1		-	-	GRCh38 GRCh37	139	425
APOA1-AS		-	-	GRCh38	-	293

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.
APOLIPOPROTEIN A-I (MARBURG)	Pathogenic (1)	no assertion criteria provided	Apr 1, 1986	RCV000019500.31

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.	Expand all rows Collapse all rows 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 (Apr 01, 1986) C Contributing to aggregate classification	no assertion criteria provided	APOLIPOPROTEIN A-I (MARBURG)	OMIM Accession: SCV000039797.5 First in ClinVar: Apr 04, 2013 Last updated: May 26, 2024	Publications: PubMed (3) PubMed: 3723016‚ 6818131‚ 7082443 Breslow, J. L., Karathanasis, S., (more...) Breslow, J. L., Karathanasis, S., Norum, R., Zannis, V. I. APO A-I deficiency and premature atherosclerosis associated with an insertion in the APO A-I gene. (Abstract) Pediat. Res. 17: 208A-only, 1983. Observation: 1 Collection method: literature only Allele origin: germline Affected status: not provided more Observation 1 Collection method: literature only Allele origin: germline Affected status: not provided Comment on evidence: Utermann et al. (1982) described a variant apolipoprotein, which they named apoA-I(Marburg). Utermann et al. (1982) found a frequency of about 1 per 750 persons … (more) Utermann et al. (1982) described a variant apolipoprotein, which they named apoA-I(Marburg). Utermann et al. (1982) found a frequency of about 1 per 750 persons for apoA-I(Marburg) in West Germany (3 heterozygotes in 2,282 unrelated persons). All 3 heterozygotes had hypertriglyceridemia and subnormal HDL cholesterol (619836). Family data from 2 kindreds were consistent with autosomal codominant inheritance. Rall et al. (1984) demonstrated reduced activation of LCAT (606967) but no reduction in HDL cholesterol or clinical consequences in association with deletion of lysine-107. Breslow (1988) noted that apoA-I(Marburg) described by Utermann et al. (1982) and the lys107del mutation (apoA-I-Munster2A) described by Rall et al. (1984) are likely identical. (less)

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Identification of homozygosity for a human apolipoprotein A-I variant.	Rall SC Jr	Journal of lipid research	1986	PMID: 3723016
Genetic variants of group A apolipoproteins. Rapid methods for screening and characterization without ultracentrifugation.	Utermann G	The Journal of biological chemistry	1982	PMID: 7082443
Apolipoprotein AIMarburg: studies on two kindreds with a mutant of human apolipoprotein AI.	Utermann G	Human genetics	1982	PMID: 6818131
Breslow, J. L., Karathanasis, S., Norum, R., Zannis, V. I. APO A-I deficiency and premature atherosclerosis associated with an insertion in the APO A-I gene. (Abstract) Pediat. Res. 17: 208A-only, 1983.	-	-	-	-

Text-mined citations for rs121912716 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 01, 2024