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NM_000483.5(APOC2):c.229A>C (p.Lys77Gln) AND Familial apolipoprotein C-II deficiency

Clinical significance:Benign/Likely benign (Last evaluated: Oct 23, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

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Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000991188.5

Allele description [Variation Report for NM_000483.5(APOC2):c.229A>C (p.Lys77Gln)]

NM_000483.5(APOC2):c.229A>C (p.Lys77Gln)

Genes:
APOC4-APOC2:APOC4-APOC2 readthrough (NMD candidate) [Gene - HGNC]
APOC2:apolipoprotein C2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19q13.32
Genomic location:
Preferred name:
NM_000483.5(APOC2):c.229A>C (p.Lys77Gln)
Other names:
APOC2, LYS55GLN
HGVS:
  • NC_000019.10:g.44949172A>C
  • NG_008837.1:g.8187A>C
  • NM_000483.5:c.229A>CMANE SELECT
  • NP_000474.2:p.Lys77Gln
  • NC_000019.9:g.45452429A>C
  • NM_000483.4:c.229A>C
  • NR_037932.1:n.1436A>C
  • P02655:p.Lys77Gln
Protein change:
K77Q
Links:
UniProtKB: P02655#VAR_000642; OMIM: 608083.0001; dbSNP: rs5126
NCBI 1000 Genomes Browser:
rs5126
Molecular consequence:
  • NM_000483.5:c.229A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_037932.1:n.1436A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Familial apolipoprotein C-II deficiency
Synonyms:
APOC2 DEFICIENCY; C-II ANAPOLIPOPROTEINEMIA; HYPERLIPOPROTEINEMIA, TYPE IB; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008810; MedGen: C1720779; Orphanet: 444490; OMIM: 207750

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001142491Reproductive Health Research and Development,BGI Genomicsno assertion criteria providedBenign
(Jan 6, 2020) 		germlinecuration

SCV001295706Illumina Laboratory Services, Illuminacriteria provided, single submitter
Benign
(Jan 13, 2018) 		germlineclinical testing

Citation Link,

SCV002811419Fulgent Genetics, Fulgent Geneticscriteria provided, single submitter
Likely benign
(Oct 23, 2021) 		unknownclinical testing

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

Summary from all submissions

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EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, curation
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Reproductive Health Research and Development,BGI Genomics, SCV001142491.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

NM_000483.4:c.229A>C in the APOC2 gene has an allele frequency of 0.026 in African subpopulation in the gnomAD database, including 8 homozygous occurrences. Pathogenic computational verdict because pathogenic predictions from DANN, MutationAssessor, MutationTaster and SIFTT. aken together, we interprete this variant as Benign/Likely benign variant. ACMG/AMP criteria applied: BS1, BS2.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV001295706.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV002811419.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 4, 2023