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NM_000384.3(APOB):c.10580G>A (p.Arg3527Gln) AND not provided

Germline classification:
Pathogenic (15 submissions)
Last evaluated:
Aug 1, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000254882.56

Allele description [Variation Report for NM_000384.3(APOB):c.10580G>A (p.Arg3527Gln)]

NM_000384.3(APOB):c.10580G>A (p.Arg3527Gln)

Gene:
APOB:apolipoprotein B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p24.1
Genomic location:
Preferred name:
NM_000384.3(APOB):c.10580G>A (p.Arg3527Gln)
Other names:
R3500Q; 9775G>A
HGVS:
  • NC_000002.12:g.21006288C>T
  • NG_011793.1:g.42786G>A
  • NM_000384.3:c.10580G>AMANE SELECT
  • NP_000375.2:p.Arg3527Gln
  • NP_000375.3:p.Arg3527Gln
  • NC_000002.11:g.21229160C>T
  • NM_000384.2:c.10580G>A
  • NM_000384.3(APOB):c.10580G>AMANE SELECT
  • NP_000375.2:p.R3527Q
  • p.ARG3527GLN
Protein change:
R3527Q; Arg3500Gln
Links:
OMIM: 107730.0009
Molecular consequence:
  • NM_000384.3:c.10580G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
40

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000322134GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Pathogenic
(Jul 10, 2020)
germlineclinical testing

Citation Link,

SCV000612386Athena Diagnostics
criteria provided, single submitter

(Athena Diagnostics Criteria)
Pathogenic
(Apr 18, 2016)
germlineclinical testing

PubMed (27)
[See all records that cite these PMIDs]

SCV000887561Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics criteria)
Pathogenic
(Aug 8, 2022)
unknownclinical testing

PubMed (29)
[See all records that cite these PMIDs]

SCV000924752Stanford Center for Inherited Cardiovascular Disease, Stanford University
no assertion criteria provided
Pathogenic
(May 16, 2017)
germlineprovider interpretation

SCV001447186Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 23, 2020)
germlineclinical testing

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

SCV001713959Mayo Clinic Laboratories, Mayo Clinic
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Nov 23, 2022)
germlineclinical testing

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

Citation Link,

SCV001743505Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus
no assertion criteria provided
Pathogenicgermlineclinical testing

SCV001746348CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Pathogenic
(Aug 1, 2024)
germlineclinical testing

Citation Link,

SCV001808570Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus
no assertion criteria provided
Pathogenicgermlineclinical testing

SCV001922500Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Pathogenicgermlineclinical testing

SCV002018216Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Aug 24, 2023)
germlineclinical testing

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

SCV002048236ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)
Pathogenic
(Jan 26, 2023)
germlineclinical testing

Citation Link,

SCV002502502AiLife Diagnostics, AiLife Diagnostics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Nov 18, 2021)
germlineclinical testing

PubMed (34)
[See all records that cite these PMIDs]

SCV004026259Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 18, 2023)
germlineclinical testing

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

SCV005199565Clinical Genetics Laboratory, Skane University Hospital Lund
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 12, 2023)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown13not providednot providednot providednot providedclinical testing, provider interpretation
not providedgermlineyes27not providednot provided1not providedclinical testing

Citations

PubMed

Familial ligand-defective apolipoprotein B-100: simultaneous detection of the ARG3500-->GLN and ARG3531-->CYS mutations in a French population.

Rabès JP, Varret M, Saint-Jore B, Erlich D, Jondeau G, Krempf M, Giraudet P, Junien C, Boileau C.

Hum Mutat. 1997;10(2):160-3.

PubMed [citation]
PMID:
9259199

Molecular basis of autosomal dominant hypercholesterolemia: assessment in a large cohort of hypercholesterolemic children.

van der Graaf A, Avis HJ, Kusters DM, Vissers MN, Hutten BA, Defesche JC, Huijgen R, Fouchier SW, Wijburg FA, Kastelein JJ, Wiegman A.

Circulation. 2011 Mar 22;123(11):1167-73. doi: 10.1161/CIRCULATIONAHA.110.979450. Epub 2011 Mar 7.

PubMed [citation]
PMID:
21382890
See all PubMed Citations (46)

Details of each submission

From GeneDx, SCV000322134.9

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

Description

Also denoted as R3500Q due to the use of alternate nomenclature; Functional studies indicate that the R3527Q variant causes decreased binding of the APOB protein to the LDL receptor (Fisher et al., 1999); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26643808, 26036859, 26415676, 22859806, 31028937, 24106285, 24507774, 20736250, 18325181, 21868016, 9105560, 18222178, 21919778, 15797858, 2563166, 24956927, 8318993, 10388479, 23375686, 26636822, 27497240, 27872105, 27831900, 27824480, 28502510, 27765764, 28104544, 9259199, 21382890, 30030251, 29555771, 28965616, 27784735, 28428224, 9603795, 30122538, 30592178, 30270359, 31106297, 29284604, 30291343, 32591292, 31447099, 31980526, 34040191, 34570182, 11238294, 21059979, 34037665, 33303402, 32719484, 32522009, 33740630, 33111339, 33418990, 33269076, 1892487, 2067318, 32770674, 33069457)

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

From Athena Diagnostics, SCV000612386.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (27)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000887561.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (29)

Description

The APOB c.10580G>A (p.Arg3527Gln) variant has been reported in the published literature in several individuals and families affected with hypercholesterolemia (PMIDs: 2563166 (1989), 9603795 (1998), 10388479 (1999), 23375686 (2013), 24404629 (2016), 31345425 (2019)). It has been reported to be strongly associated with disease in families affected with hypercholesterolemia (PMIDs: 2563166 (1989), 21868016 (2011)) and has been reported as a founder mutation in the Amish community (PMID: 21059979 (2010)). Published functional studies demonstrate that this variant is damaging to LDL receptor binding (PMIDs: 10388479 (1999), 11115503 (2001)). Based on the available information, this variant is classified as pathogenic.

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

From Stanford Center for Inherited Cardiovascular Disease, Stanford University, SCV000924752.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedprovider interpretationnot provided

Description

p.Arg3527Gln (c.10580G>A) in the APOB gene (NM_000384.2) Given the overwhelming case data and that this is a founder variant, we consider this variant pathogenic and we do feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). This variant is frequently reported in the literature as p.Arg3500Gln. Per the test report, this variant has been reported to be responsible for 2-6% of Western European FH cases and has been reported as an Amish founder mutation (Heath KE et al. Atherosclerosis. 1999;143(1):41-54; Lombardi et al. Clin Genet. 2000;57(2):116-24; Chmara M et al. J Appl Genet. 2010;51(1):95-106; Shen H et al. Arch Intern Med. 2010;170(20):1850-5). 1 in 500 to 1 in 700 Caucasian individuals have this specific variant per a 1992 report by Rauh and colleagues. Tybjaerg-Hansen et al. (1998) found that the R3500Q mutation in the APOB gene is present in approximately 1 in 1,000 persons in Denmark and causes severe hypercholesterolemia and increases the risk of ischemic heart disease. Bednarska-Makaruk et al. (2001) found the arg3500-to-gln mutation in 2.5% (13/525) of unrelated patients with hypercholesterolemia in Poland. All the patients belonged to the type IIA hyperlipoproteinemia group. In 65 patients with the clinical characteristics of familial hypercholesterolemia, the frequency of the arg3500-to-gln mutation was 10.8% (7/65). The same haplotype at the APOB locus in the carriers of this mutation in Poland as in other populations from western Europe suggested its common origin. Horvath et al. (2001) studied 130 unrelated individuals with hypercholesterolemia in Bulgaria. Four of these individuals were found to be carriers of this mutation. Horvath et al. (2001) concluded that this mutation accounts for 0.99 to 8.17% (95% CI) of cases of hypercholesterolemia in Bulgaria and therefore represents the most common single mutation associated with this condition in Bulgaria. Segregation data is strong: Soria et al. (1989) demonstrated that this variant was found in 6 other, unrelated subjects and in 8 affected relatives in 2 of these families. A partial haplotype of this mutant apoB100 allele was constructed by sequence analysis and restriction enzyme digestion at positions where variations in the apoB100 are known to occur. This haplotype was found to be the same in 3 probands and 4 affected members of 1 family and lacks a polymorphic XbaI site whose presence has been correlated with high cholesterol levels. Tybjaerg-Hansen and Humphries (1992) gave a review suggesting that the risk of premature coronary artery disease in the carriers of the mutation is increased to levels as high as those seen in patients with familial hypercholesterolemia; at age 50, about 40% of males and 20% of females heterozygous for the mutation have developed coronary artery disease. Boren et al. (2001) concluded that normal receptor binding of LDL involves an interaction between arginine-3500 and tryptophan-4369 in the carboxyl tail of apoB100. Trp4369 to tyr (W4369Y) LDL and arg3500 to gln (R3500Q) LDL isolated from transgenic mice had identically defective LDL binding. Marz et al 1993 found that he arg3500-to-gln substitution profoundly alters the conformation of the apoB receptor binding domain when apolipoprotein B resides on particles at the lower and upper limits of the LDL density range. Marz et al in 1992 found that higher levels of apoE may be a compensatory mechanism whereby an increase in apoE leads to a decrease in LDL. The arginine at codon 3527 is completely conserved across species. Two alterations at the same codon, p.R3527L and p.R3527W (reported as p.R3500L and p.R3500W), have also been associated with FH (Gaffney D et al. Arterioscler. Thromb. Vasc. Biol. 1995;15:1025-9; Fouchier SW et al. Hum. Mutat. 2005;26:550-6). The variant was reported online in 63 of 122,754 individuals in the Genome Aggregation Consortium Dataset (gnomAD; http://gnomad.broadinstitute.org/), which currently includes variant calls on >140,000 unrelated individuals of African, Asian, European, Ashkenazi, Latino descent. Specifically, the variant was observed in 58 of 55,525 individuals of European descent (MAF=0.05%), 1 of 11,148 individuals of Finnish descent, 1 of 16,779 individuals of Latino descent and 1 of 2,738 individuals of other descent. The phenotype of those individuals is not publicly available. The dataset is comprised of multiple cohorts, some of which were recruited from the general population, others were enriched for common cardiovascular disease. There is a cohort of patients with coronary artery disease in gnomAD. Note that other variants with strong evidence for pathogenicity have been seen at similar frequencies in datasets like this so this does not necessarily rule out pathogenicity (Pan et al 2012).

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

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001447186.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot providednot providednot providednot providednot provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV001713959.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided13not providednot providedclinical testing PubMed (1)

Description

PS3, PS4

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided13not providednot providednot provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001743505.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV001746348.18

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided24not providednot providedclinical testingnot provided

Description

APOB: PP1:Strong, PM1, PM2, PM5, PS4:Moderate, PS3:Supporting

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided24not providednot providednot provided

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV001808570.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001922500.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Revvity Omics, Revvity, SCV002018216.3

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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002048236.2

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

Description

The APOB c.10580G>A; p.Arg3527Gln variant (rs5742904), also reported as Arg3500Gln, is described in the literature in many affected individuals, reported to segregate with disease in affected families, and is one of the most common variants associated with familial hypercholesterolemia in individuals of European ancestry (Braenne 2016, Horvath 2001, Peloso 2014, Tybjaerg-Hansen 1998, Youngblom 2016). The variant is reported as pathogenic by many sources in the ClinVar database (Variation ID: 17890) and is found in the non-Finnish European population with an allele frequency of 0.06% (76/128,568 alleles including 1 homozygote) in the Genome Aggregation Database. The arginine at codon 3527 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL:0.735). In support of this prediction, functional studies show that the variant results in defective LDL binding (Boren 2001). Based on available information, this variant is considered to be pathogenic. References: Boren J et al. The molecular mechanism for the genetic disorder familial defective apolipoprotein B100. J Biol Chem. 2001 Mar 23;276(12):9214-8. PMID: 11115503. Braenne I et al. Systematic analysis of variants related to familial hypercholesterolemia in families with premature myocardial infarction. Eur J Hum Genet. 2016 Feb;24(2):191-7PMID: 26036859. Horvath A et al. High frequency of the ApoB-100 R3500Q mutation in Bulgarian hypercholesterolaemic subjects. J Med Genet. 2001 Aug;38(8):536-40. PMID: 11494965. Peloso GM et al. Association of low-frequency and rare coding-sequence variants with blood lipids and coronary heart disease in 56,000 whites and blacks. Am J Hum Genet. 2014 Feb 6;94(2):223-32. PMID: 24507774. Tybjaerg-Hansen A et al. Association of mutations in the apolipoprotein B gene with hypercholesterolemia and the risk of ischemic heart disease. N Engl J Med. 1998 May 28;338(22):1577-84. PMID: 9603795. Youngblom E et al. Familial Hypercholesterolemia. 2014 Jan 2 (updated 2016 Dec 8). In: Adam MP et al, editors. GeneReviews (Internet). Seattle (WA): University of Washington, Seattle; 1993-2021. PMID: 24404629.

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

From AiLife Diagnostics, AiLife Diagnostics, SCV002502502.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testing PubMed (34)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided3not providednot providednot provided

From Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden, SCV004026259.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

PP1_STR, PP3, PM5, PS3

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

From Clinical Genetics Laboratory, Skane University Hospital Lund, SCV005199565.1

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

Last Updated: Oct 8, 2024