NM_000039.3(APOA1):c.100C>T (p.Arg34Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 26, 2022
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:: RCV003062460.3

Allele description [Variation Report for NM_000039.3(APOA1):c.100C>T (p.Arg34Ter)]

NM_000039.3(APOA1):c.100C>T (p.Arg34Ter)

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.100C>T (p.Arg34Ter)

HGVS:

NC_000011.10:g.116837101G>A
NG_012021.1:g.5522C>T
NM_000039.3:c.100C>TMANE SELECT
NM_001318017.2:c.100C>T
NM_001318018.2:c.100C>T
NM_001318021.2:c.-228C>T
NP_000030.1:p.Arg34Ter
NP_000030.1:p.Arg34Ter
NP_001304946.1:p.Arg34Ter
NP_001304947.1:p.Arg34Ter
LRG_767t1:c.100C>T
LRG_767:g.5522C>T
LRG_767p1:p.Arg34Ter
NC_000011.9:g.116707817G>A
NM_000039.1:c.100C>T
NM_001318021.1:c.-228C>T

Protein change:

R34*

Molecular consequence:

NM_000039.3:c.100C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001318017.2:c.100C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001318018.2:c.100C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV003440327	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 26, 2022)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 21122686, 26255038, 7583566, 7981179, 8282791, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003440327

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 26, 2022)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

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

Complete Apo AI deficiency in an Iraqi Mandaean family: case studies and review of the literature.

Al-Sarraf A, Al-Ghofaili K, Sullivan DR, Wasan KM, Hegele R, Frohlich J.

J Clin Lipidol. 2010 Sep-Oct;4(5):420-6. doi: 10.1016/j.jacl.2010.05.001. Epub 2010 Jun 1. Review.

PubMed [citation]

PMID:: 21122686

Targeted next-generation sequencing to diagnose disorders of HDL cholesterol.

Sadananda SN, Foo JN, Toh MT, Cermakova L, Trigueros-Motos L, Chan T, Liany H, Collins JA, Gerami S, Singaraja RR, Hayden MR, Francis GA, Frohlich J, Khor CC, Brunham LR.

J Lipid Res. 2015 Oct;56(10):1993-2001. doi: 10.1194/jlr.P058891. Epub 2015 Aug 8.

PubMed [citation]

PMID:: 26255038
PMCID:: PMC4583092

See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003440327.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

For these reasons, this variant has been classified as Pathogenic. This variant is also known as p.R10X. This premature translational stop signal has been observed in individual(s) with APOA1 deficiency (PMID: 21122686, 26255038). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg34*) in the APOA1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in APOA1 are known to be pathogenic (PMID: 7583566, 7981179, 8282791).

#	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

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