The APOB NM_000384.3:c.10580G>A (NP_000375.3:p.(Arg3527Gln)) missense variant has not previously been reported in somatic cancers (COSMIC). Experimental evidence: Patient-derived LDL with exact Arg3500Gln showed defective LDL-receptor binding and cosegregated with hypercholesterolemia, but causality was described as circumstantial. Based on available guidelines, this variant is considered to be a Variant of Uncertain Significance (VUS).
Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
Uncertain.The recorded classification is uncertain significance.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.APOB encodes apolipoprotein B, the main protein component of chylomicrons and low-density lipoprotein (LDL) particles and a ligand for the LDL receptor. It is produced as two forms: apoB-48 in the intestine and apoB-100 in the liver. Changes affecting APOB can cause disorders of blood cholesterol and apolipoprotein B levels, including hypobetalipoproteinemia and hypercholesterolemia; APOB has no established cancer-associated role.
The recorded framework is Generic ACMG/AMP 2015 with ClinGen SVI recommendations. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
Met at supporting: patient-derived LDL with exact Arg3500Gln showed defective LDL-receptor binding and cosegregated with hypercholesterolemia, but causality was described as circumstantial.
Met: exact-variant case-control associations were OR 7.0 (95% CI 2.2–22) and OR 78 (95% CI 16–388), both above 5.0 with intervals excluding 1.
Met at supporting strength: REVEL 0.735 meets the supplied PP3 threshold of >= 0.644 for this missense variant.
Met: Amish allele frequency is 6.79825% (62/912), exceeding the generic BA1 stand-alone threshold of 5%.
VUS: PS4 strong plus PS3 and PP3 supporting meet a pathogenic rule, while BA1 independently meets the stand-alone benign rule, creating conflicting evidence.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 679 / 1,613,860 alleles. Recorded AF 0.00042073. Recorded homozygote count 1.
This variant is present in gnomAD v2.1 (AF= 0.000294157; MAF= 0.02942%, 83/282162 alleles, homozygotes = 1) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000591127; MAF= 0.05911%, 76/128568 alleles, homozygotes = 1); grpmax FAF= 0.00049843.
This variant is present in gnomAD-Canada v1.0 (AF= 0.00016290182450043442, 3/18416 alleles, homozygotes = 0).
Recorded REVEL score: 0.735. Refer to the recorded PP3/BP4 rationale for interpretation.
53 Pathogenic · 4 Likely pathogenic · 1 pathogenic. ClinVar API review status: criteria provided, multiple submitters, no conflicts.
No standalone functional evidence summary is recorded in evidence_summary.functional.
This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under Generic ACMG/AMP 2015 with ClinGen SVI recommendations, with the data and sources behind each one.
28 criteria with recorded statuses: 4 met · 6 not met · 13 not assessed · 5 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
PS4 is met from a verified exact-variant case-control study with ORs 7.0 and 78, both exceeding the governing >5.0 threshold and with confidence intervals excluding 1.0.
PP4 and BP5 are not assessed because patient-specific phenotype/family-history and alternate-molecular-basis information are not documented.
PP5 and BP6 are not met because the required exact-variant ClinVar expert-panel assertion is absent; the case audit reports zero expert-panel submissions.
No criteria match.
PS3 is met at supporting strength. Soria et al. studied the exact historical Arg3500Gln substitution, corresponding to current APOB p.Arg3527Gln (NM_000384.3:c.10580G>A), in affected families. Patient-derived LDL carrying the variant showed defective binding to the apoB,E(LDL) receptor on normal human fibroblasts, and the variant cosegregated with defective LDL binding and moderate hypercholesterolemia. The assay used normal human fibroblasts and included allele-specific molecular confirmation and family comparisons, providing biologically relevant functional evidence. However, this was an older patient-derived assay rather than a validated clinical-laboratory assay or a controlled full-length expression experiment, and the authors explicitly described the causal link between the substitution and defective binding as circumstantial; therefore PS3 is not calibrated above supporting strength.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
Met. ACMG/AMP PS4 requires a significantly increased prevalence in affected individuals, with an odds ratio >5.0 and a confidence interval excluding 1. The verified abstract of Tybjaerg-Hansen et al. (PMID:9603795) reports the exact APOB Arg3500Gln variant, corresponding to NM_000384.3:c.10580G>A (p.Arg3527Gln), in 9,255 general-population participants, 948 patients with ischemic heart disease, and 36 patients with familial hypercholesterolemia. It reports OR 7.0 (95% CI 2.2–22) for ischemic heart disease and OR 78 (95% CI 16–388) for familial hypercholesterolemia versus the general population. I verified the paper's case-control comparison from the abstract; the paper directly reports the ORs, so no count-derived OR was needed. The governing comparison is >5.0: 7.0 > 5.0? yes, and 78 > 5.0? yes; both confidence intervals exclude 1.0.
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0.
The variant is a missense variant, NP_000375.3:p.(Arg3527Gln), so the governing generic rule selects the REVEL path only; SpliceAI is not used for PP3/BP4 in this situation. The REVEL score is 0.735, which meets the supplied ClinGen SVI supporting PP3 threshold of >= 0.644 (Pejaver et al. 2022, PMID:36413997). BayesDel is not used because no generic ACMG-strength calibration is established. Therefore PP3 is met at supporting strength.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only. ... PP3 (supporting): >= 0.644 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
BA1 is met because the variant has an observed Amish allele frequency of 0.0679824561 (62/912 alleles; 6.79825%), exceeding the generic stand-alone threshold of 0.05. The elevated frequency is ancestry-specific and the overall gnomAD v4.1 frequency is 0.0004207304, but BA1 is assessed from the observed population frequency and the Amish subgroup exceeds 5%. This is an SNV, so the indel calling caveat does not apply.
BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868)
The variant is NP_000375.3:p.(Arg3527Gln). The selectively reviewed comparator literature reports pathogenic APOB Arg3500Gln, not an established pathogenic alternate nucleotide change producing Arg3527Gln. The exact variant's ClinVar classification and papers listed only as classification assertions cannot substitute for an independently established same-amino-acid comparator under PS1.
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.
PM2 is not met because the variant is present in every population dataset available for this assessment. The default all-comers gnomAD v4.1 frequency is 0.0004207304, above the generic PM2 supporting threshold of 0.0001; the specified non-cancer subsets also contain the variant at 0.0002497037 in v2.1 exomes and 0.0006763154 in v3.1 genomes. The variant is therefore neither absent nor at or below the supplied extremely-low-frequency threshold.
PM2: <= 0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868)
Not met. The governing rule is that a reputable source recently reports the variant as pathogenic when the evidence is unavailable for independent evaluation. Under the specified generic rule for this interpretation, PP5 is restricted to an exact-variant ClinVar expert-panel classification. ClinVar contains exact-variant pathogenic and likely pathogenic submissions, but the case audit reports zero expert-panel submissions; the record is a multiple-submitter record without an expert-panel assertion. Therefore the required PP5 trigger is absent.
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
BS1 is not met on the available population evidence. The default generic threshold is 0.01, whereas the all-comers gnomAD v4.1 allele frequency is 0.0004207304 and the non-cancer genome-only v3.1 frequency is 0.0006763154; the gnomAD v2.1 non-cancer exome-only frequency is 0.0002497037. The Amish subgroup frequency is 0.0679824561, but this is confined to a founder ancestry and no maximum-credible-frequency calculation using disorder prevalence, penetrance, and allelic heterogeneity is available; the overall and non-cancer frequencies do not support BS1 from the default alone.
BS1: Allele frequency is greater than expected for the disorder; the 1% figure is only a default. Before applying it, ask whether the disorder's prevalence, penetrance and allelic heterogeneity allow this frequency (maximum credible allele frequency, Whiffin et al. 2017, PMID 28518168).
The variant is a missense variant, NP_000375.3:p.(Arg3527Gln), so the governing generic rule selects REVEL only; the SpliceAI result cannot establish BP4 for a missense substitution. REVEL is 0.735, which does not meet any supplied BP4 threshold (supporting <= 0.29, moderate <= 0.183, or strong <= 0.016). BayesDel is not usable because no generic ACMG-strength calibration is established. Therefore BP4 is not met.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc). ... Missense variant -> REVEL only. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
Not met. The governing rule is that a reputable source recently reports the variant as benign when the evidence is unavailable for independent evaluation. Under the specified generic rule for this interpretation, BP6 is restricted to an exact-variant ClinVar expert-panel classification of benign or likely benign. ClinVar contains no exact-variant expert-panel submission; its record is pathogenic/likely pathogenic from non-expert submissions, with expert-panel count 0. Therefore the required BP6 trigger is absent.
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
No patient-level de novo observation is documented for NM_000384.3:c.10580G>A (p.Arg3527Gln). The available literature concerns a different APOB Arg3500Gln variant, and the case evidence contains no proband phenotype, family-history assessment, or confirmed maternity and paternity results; therefore PS2 cannot be assessed.
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
The APOB VCEP specification is listed but has no released criteria, and vcep_materials.json contains no APOB domain-table entries. The available literature describes a hotspot at APOB amino acid 3500, not the variant's residue 3527; cancerhotspots.org returned no hotspot for APOB R3527. No qualifying critical domain or hotspot evidence meeting the generic PM1 definition is available.
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
The variant is Arg3527Gln. The reviewed literature reports APOB Thr3492Ile and Arg3500Gln at different residues, while the PM5 candidate file contains no candidates and no same-residue pathogenic alternate missense variant was established. The available evidence is therefore insufficient to assess PM5.
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.
No patient-level assumed de novo observation is documented for NM_000384.3:c.10580G>A (p.Arg3527Gln). The available literature concerns a different APOB Arg3500Gln variant, and the case evidence contains no parental testing or other evidence establishing de novo occurrence; therefore PM6 cannot be assessed.
Assumed de novo, but without confirmation of paternity and maternity.
No auditable family-level genotype and phenotype data are available for NM_000384.3:c.10580G>A (p.Arg3527Gln), including affected relatives, informative meioses, or a quantitative segregation analysis. PMID:2563166 describes segregation of a different APOB Arg3500Gln variant and cannot be transferred to this variant; therefore PP1 cannot be assessed.
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.
The available evidence does not provide a gene-level assessment demonstrating both a low rate of benign APOB missense variation and that missense variation is a common disease mechanism. A single variant frequency and disease reports for individual variants cannot establish both PP2 premises.
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
Not assessed. The governing PP4 rule requires the patient's phenotype or family history to be highly specific for a disease with a single genetic etiology, but the supplied case evidence does not provide a patient-specific phenotype or family-history description that can be adjudicated against this requirement.
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
BS2 cannot be assessed from the available data. gnomAD reports one homozygote in the all-comers v2.1 and v4.1 datasets and one homozygote in the non-cancer v3.1 genome dataset, but these records do not establish that the individuals were healthy adults, nor do they document age, phenotype, or expected full early-age penetrance. The presence of a homozygote alone therefore does not satisfy the complete BS2 definition.
Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.
BS3 is not assessed. The available variant-specific functional evidence is damaging rather than benign: the exact Arg3500Gln/Arg3527Gln variant was associated with defective LDL-receptor binding. No well-established in vitro or in vivo study demonstrating no damaging effect on APOB protein function or splicing was identified.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
No affected relative documented to lack NM_000384.3:c.10580G>A (p.Arg3527Gln) is available, and there is no auditable pedigree or variant-specific non-segregation analysis. PMID:2563166 reports segregation of a different APOB Arg3500Gln variant and does not provide BS4 evidence for this case; therefore BS4 cannot be assessed.
Lack of segregation in affected members of a family.
The available evidence does not establish that APOB disease is caused primarily by truncating variants. General familial hypercholesterolemia background statements about loss-of-function mechanisms are not an APOB-specific variant-spectrum analysis and cannot establish the BP1 premise.
Missense variant in a gene for which primarily truncating variants are known to cause disease.
BP2 requires documented allelic phase: the variant must be observed in trans with a pathogenic variant in a fully penetrant dominant gene/disorder, or in cis with a pathogenic variant in any inheritance pattern. The available case evidence establishes the APOB variant as a heterozygous disease-associated allele in the literature but does not document a second pathogenic variant in the same individual, parental/offspring testing, or cis/trans phase. The criterion cannot be adjudicated from the available evidence.
BP2: Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.
Not assessed. BP5 requires the variant to be found in a case with an alternate molecular basis for disease. The supplied case evidence does not document an alternate pathogenic molecular diagnosis in the patient, so the criterion cannot be adjudicated.
Variant found in a case with an alternate molecular basis for disease.
PVS1 (ClinGen SVI PVS1 recommendations, PMC6185798, pvs1_generic_framework) applies only to null variant classes — nonsense, frameshift, canonical ±1/2 splice-consensus, translation-initiation-codon loss, and stop-loss variants — each expected to trigger nonsense-mediated decay or otherwise abolish normal protein function. NM_000384.3:c.10580G>A in APOB is a missense substitution predicted to produce NP_000375.3:p.(Arg3527Gln). As a result, no null-variant mechanism (nonsense-mediated decay, truncation, or canonical splice disruption) is triggered by this variant class, so PVS1's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PVS1 for APOB, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_null_variant_class
The case is evaluated for APOB-related hypercholesterolemia, whose available framework context is semidominant/autosomal dominant rather than a recessive disorder. PM3 is therefore not applicable under the governing definition, which restricts it to recessive disorders with the variant detected in trans with a pathogenic variant. No PM3 strength is assigned.
PM3: For recessive disorders, detected in trans with a pathogenic variant
PM4 (Richards et al. 2015, PMID:25741868) applies to protein length changes: in-frame insertions/deletions in a non-repetitive region, or stop-loss variants that extend the protein past the reference stop codon. NM_000384.3:c.10580G>A in APOB is a missense substitution predicted to produce NP_000375.3:p.(Arg3527Gln). As a result, no change in protein length occurs, so there is nothing for this criterion to evaluate, so PM4's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PM4 for APOB, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_stop_loss_or_nonrepeat_indel
BP3 (Richards et al. 2015, PMID:25741868) applies to in-frame insertions/deletions located in a repetitive region without a known function. NM_000384.3:c.10580G>A in APOB is a missense substitution predicted to produce NP_000375.3:p.(Arg3527Gln). As a result, the variant does not alter protein length within a repeat region, so there is nothing for this criterion to evaluate, so BP3's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP3 for APOB, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_repeat_region_indel
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_000384.3:c.10580G>A in APOB is a missense substitution predicted to produce NP_000375.3:p.(Arg3527Gln). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for APOB, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
Every interpreted variant in APOB, mapped onto the exon structure of NM_000384.3. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| Amish62 / 912 | 0.068 |
| European (non-Finnish)582 / 1,179,964 | 0.000491 hom |
| Remaining individuals16 / 62,480 | 0.00026 |
| African/African American9 / 74,880 | 0.00012 |
| Admixed American7 / 59,988 | 0.00012 |
| East Asian2 / 44,888 | 4.5e-05 |
| European (Finnish)1 / 63,982 | 1.6e-05 |
| European (non-Finnish)76 / 128,568 | 0.000591 hom |
| Remaining individuals2 / 7,208 | 0.00028 |
| African/African American3 / 24,948 | 0.00012 |
| European (Finnish)1 / 25,116 | 4e-05 |
| Admixed American1 / 35,416 | 2.8e-05 |
This variant is present in gnomAD v4.1 (AF= 0.00042073; MAF= 0.04207%, 679/1613860 alleles, homozygotes = 1) and has highest observed frequency in the Amish population (AF= 0.0679825; MAF= 6.79825%, 62/912 alleles, homozygotes = 0); grpmax FAF= 0.00045981.
This variant is present in gnomAD v2.1 (AF= 0.000294157; MAF= 0.02942%, 83/282162 alleles, homozygotes = 1) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000591127; MAF= 0.05911%, 76/128568 alleles, homozygotes = 1); grpmax FAF= 0.00049843.
This variant is present in gnomAD-Canada v1.0 (AF= 0.00016290182450043442, 3/18416 alleles, homozygotes = 0).
The variant is a missense variant, NP_000375.3:p.(Arg3527Gln), so the governing generic rule selects the REVEL path only; SpliceAI is not used for PP3/BP4 in this situation. The REVEL score is 0.735, which meets the supplied ClinGen SVI supporting PP3 threshold of >= 0.644 (Pejaver et al. 2022, PMID:36413997). BayesDel is not used because no generic ACMG-strength calibration is established. Therefore PP3 is met at supporting strength.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only. ... PP3 (supporting): >= 0.644 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
The variant is a missense variant, NP_000375.3:p.(Arg3527Gln), so the governing generic rule selects REVEL only; the SpliceAI result cannot establish BP4 for a missense substitution. REVEL is 0.735, which does not meet any supplied BP4 threshold (supporting <= 0.29, moderate <= 0.183, or strong <= 0.016). BayesDel is not usable because no generic ACMG-strength calibration is established. Therefore BP4 is not met.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc). ... Missense variant -> REVEL only. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_000384.3:c.10580G>A in APOB is a missense substitution predicted to produce NP_000375.3:p.(Arg3527Gln). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for APOB, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.735. BayesDel score = 0.264919.
9 paper records listed. 2 cited in the classification.
The mutation reported here changes the codon for amino acid 3500 and correlates with hypercholesterolemia and with defective LDL binding to the receptor.
Location Discussion, paragraph 3
Context DNA sequencing of APOB exon 26; PCR with allele-specific oligonucleotide probes for family segregation; LDL receptor-binding assays using normal human fibroblasts; three probands and affected relatives from two families, plus four additional unrelated individuals.
While many of the different software programs use different algorithms for their predictions, they have similarities in their underlying basis; therefore, the combination of predictions from different in-silico tools are considered as a single piece of evidence in sequence interpretation as opposed to independent pieces of evidence.
Location Computational (In Silico) Predictive Programs
Context ACMG/AMP sequence-variant interpretation guidance; not an experimental variant study.
The Thr3492Ile mutation is situated in close proximity of the typical Arg3500Gln one.
Results, paragraph describing patient P132; Table 2; Discussion, paragraph 5
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
This variant is present in gnomAD v4.1 (AF= 0.00042073; MAF= 0.04207%, 679/1613860 alleles, homozygotes = 1) and has highest observed frequency in the Amish population (AF= 0.0679825; MAF= 6.79825%, 62/912 alleles, homozygotes = 0); grpmax FAF= 0.00045981.
This variant is present in gnomAD v2.1 (AF= 0.000294157; MAF= 0.02942%, 83/282162 alleles, homozygotes = 1) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000591127; MAF= 0.05911%, 76/128568 alleles, homozygotes = 1); grpmax FAF= 0.00049843.
This variant is present in gnomAD-Canada v1.0 (AF= 0.00016290182450043442, 3/18416 alleles, homozygotes = 0).
This variant has been reported in ClinVar as Pathogenic (53 clinical laboratories) and as Likely pathogenic (4 clinical laboratories) and as pathogenic (1 clinical laboratory). (ClinVarID = 17890)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.735. BayesDel score = 0.264919.
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.