NM_000039.3(APOA1):c.448C>A (p.Leu150Ile) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 10, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002035576.4

Allele description [Variation Report for NM_000039.3(APOA1):c.448C>A (p.Leu150Ile)]

NM_000039.3(APOA1):c.448C>A (p.Leu150Ile)

Genes:

APOA1-AS:APOA1 antisense RNA [Gene - OMIM - HGNC]
APOA1:apolipoprotein A1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_000039.3(APOA1):c.448C>A (p.Leu150Ile)

HGVS:

NC_000011.10:g.116836164G>T
NG_012021.1:g.6459C>A
NM_000039.3:c.448C>AMANE SELECT
NM_001318017.2:c.448C>A
NM_001318018.2:c.448C>A
NM_001318021.2:c.121C>A
NP_000030.1:p.Leu150Ile
NP_000030.1:p.Leu150Ile
NP_001304946.1:p.Leu150Ile
NP_001304947.1:p.Leu150Ile
NP_001304950.1:p.Leu41Ile
NP_001304950.1:p.Leu41Ile
LRG_767t1:c.448C>A
LRG_767:g.6459C>A
LRG_767p1:p.Leu150Ile
NC_000011.9:g.116706880G>T
NM_000039.1:c.448C>A
NM_001318021.1:c.121C>A
NR_126362.1:n.48G>T

Protein change:

L150I

Links:

dbSNP: rs911528468

NCBI 1000 Genomes Browser:

rs911528468

Molecular consequence:

NM_000039.3:c.448C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318017.2:c.448C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318018.2:c.448C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318021.2:c.121C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_126362.1:n.48G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002286018	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 10, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002286018

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 10, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002286018.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Not Available"). This variant has not been reported in the literature in individuals with APOA1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with isoleucine at codon 150 of the APOA1 protein (p.Leu150Ile). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and isoleucine.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

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