NM_000039.3(APOA1):c.158A>G (p.Tyr53Cys) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 29, 2019
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:: RCV001193576.1

Allele description [Variation Report for NM_000039.3(APOA1):c.158A>G (p.Tyr53Cys)]

NM_000039.3(APOA1):c.158A>G (p.Tyr53Cys)

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.158A>G (p.Tyr53Cys)

HGVS:

NC_000011.10:g.116837043T>C
NG_012021.1:g.5580A>G
NM_000039.3:c.158A>GMANE SELECT
NM_001318017.2:c.158A>G
NM_001318018.2:c.158A>G
NM_001318021.2:c.-170A>G
NP_000030.1:p.Tyr53Cys
NP_000030.1:p.Tyr53Cys
NP_001304946.1:p.Tyr53Cys
NP_001304947.1:p.Tyr53Cys
LRG_767t1:c.158A>G
LRG_767:g.5580A>G
LRG_767p1:p.Tyr53Cys
NC_000011.9:g.116707759T>C
NC_000011.9:g.116707759T>C
NM_000039.1:c.158A>G
NM_000039.2:c.158A>G
NM_001318021.1:c.-170A>G

Protein change:

Y53C

Links:

dbSNP: rs750185173

NCBI 1000 Genomes Browser:

rs750185173

Molecular consequence:

NM_000039.3:c.158A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318017.2:c.158A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001318018.2:c.158A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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uncharacterized protein PTSG_01105 [Salpingoeca rosetta]
uncharacterized protein PTSG_01105 [Salpingoeca rosetta]
gi|514699013|ref|XP_004997075.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001362492	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Oct 29, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001362492

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Oct 29, 2019)

germline

clinical testing

Citation Link

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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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001362492.1

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

Description

Variant summary: APOA1 c.158A>G (p.Tyr53Cys) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 2e-05 in 251434 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. The LOVD database has reported a classification of this variant as likely benign without evidence for independent evaluation. To our knowledge, no occurrence of c.158A>G in individuals affected with Cardiomyopathy and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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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