NM_000039.3(APOA1):c.83C>G (p.Pro28Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 22, 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:: RCV001851952.6

Allele description [Variation Report for NM_000039.3(APOA1):c.83C>G (p.Pro28Arg)]

NM_000039.3(APOA1):c.83C>G (p.Pro28Arg)

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.83C>G (p.Pro28Arg)

Other names:

P4R

HGVS:

NC_000011.10:g.116837118G>C
NG_012021.1:g.5505C>G
NM_000039.3:c.83C>GMANE SELECT
NM_001318017.2:c.83C>G
NM_001318018.2:c.83C>G
NM_001318021.2:c.-240-5C>G
NM_001425090.1:c.83C>G
NM_001425091.1:c.-128+227C>G
NM_001425092.1:c.-245C>G
NM_001425093.1:c.83C>G
NP_000030.1:p.Pro28Arg
NP_000030.1:p.Pro28Arg
NP_001304946.1:p.Pro28Arg
NP_001304947.1:p.Pro28Arg
NP_001412019.1:p.Pro28Arg
NP_001412022.1:p.Pro28Arg
LRG_767t1:c.83C>G
LRG_767:g.5505C>G
LRG_767p1:p.Pro28Arg
NC_000011.9:g.116707834G>C
NM_000039.1:c.83C>G
P02647:p.Pro28Arg

Protein change:

P28R; PRO4ARG

Links:

UniProtKB: P02647#VAR_000607; OMIM: 107680.0008; dbSNP: rs121912721

NCBI 1000 Genomes Browser:

rs121912721

Molecular consequence:

NM_001425092.1:c.-245C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001318021.2:c.-240-5C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001425091.1:c.-128+227C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000039.3:c.83C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318017.2:c.83C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318018.2:c.83C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425090.1:c.83C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001425093.1:c.83C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Mus musculus cDNA, clone:Y2G0137E03, strand:plus, reference:ENSEMBL:Mouse-Transc...
Mus musculus cDNA, clone:Y2G0137E03, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000008999, based on BLAT search
gi|56040291|dbj|AK216114.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002222994	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 22, 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

SCV002222994

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 22, 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002222994.3

#	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: "Probably Damaging"; Align-GVGD: "Not Available"). ClinVar contains an entry for this variant (Variation ID: 17915). This variant has not been reported in the literature in individuals affected with APOA1-related conditions. This variant is present in population databases (rs121912721, gnomAD 0.004%). This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 28 of the APOA1 protein (p.Pro28Arg).

#	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: Sep 29, 2024

ClinVar

Relating variation to medicine