APCc.793C>TLikely pathogenic

Print report

Variant interpretation report

APC c.793C>T, p.(Arg265Ter)

NM_001127511.3:c.793C>T NP_001120983.2:p.(Arg265Ter) View identifiers

Classification

Likely pathogenic

Variant description:

No variant summary was recorded for this case.

Five-step scale from benign to pathogenic. This variant is likely pathogenic. Select a step to read what it means.

Likely pathogenic.A likely pathogenic classification under the recorded framework.

In plain language

Gene-level background from the recorded interpretation.

About APC

No gene-level summary was recorded for this case.

Key facts

Condition: familial adenomatous polyposis 1
Inheritance: Autosomal dominant
Evidence used: 1 very strong (pathogenic) · 1 moderate (pathogenic) · 2 supporting (pathogenic)
Expert rules: ClinGen APC VCEP v2.1.0
Other laboratories (ClinVar): 15 Pathogenic · 1 pathogenic
Pipeline record: 26 Jun 2026 · version 7.0.0

Evidence considered

View criteria

Applied evidence criteria

PVS1 (very strong): NM_001127511.3:c.793C>T is a nonsense variant producing p.Arg265Ter (p.R265*) in exon 7. APC is a gene where loss of function is the established mechanism of disease (InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP v2.1.0). The premature termination codon at position 265 occurs well upstream of the last exon, and nonsense-mediated decay is expected. Under the APC VCEP modified PVS1 decision tree (Figure 1), this null variant meets PVS1 at Very Strong strength.
PS4 (moderate): The variant has been observed in multiple unrelated families with classic FAP. PMID:12901799 reports a 3-generation Malaysian Chinese family with multiple affected members segregating the variant with disease (estimated ≥2 phenotype points). PMID:30897307 reports 3 affected individuals from 2 unrelated Brazilian families (families 10 and 21), all with classic FAP and one with osteoma (estimated ≥1.5 phenotype points). Total estimated phenotype points: 3.5, meeting PS4_Moderate threshold (2-3.5 points) under the APC VCEP phenotype point system (Table 1).
PM2 (supporting): The variant is absent from gnomAD v2.1.1 (non-cancer dataset, AC=0) and present at extremely low frequency in gnomAD v4.1 (AF=2.48e-6, 4/1,610,912 alleles, grpmax FAF=8e-7). Under the APC VCEP PM2 threshold: AC=0 (≤1) requires AF<0.001% (1e-5); absent from v2.1.1 meets this. Under the alternative threshold for AC>1: AF≤0.0003% (3e-6); the v4.1 AF of 2.48e-6 also meets this. PM2_Supporting is satisfied.
PP5 (supporting): Expert panel ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel classified as Pathogenic.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.

01The reasoning

How it was classified

The recorded framework is ClinGen APC VCEP v2.1.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 4 Benign evidence criteria: 0

Pathogenic criteria applied · 4

PVS1Very strong

PVS1 · very strong

NM_001127511.3:c.793C>T is a nonsense variant producing p.Arg265Ter (p.R265*) in exon 7. APC is a gene where loss of function is the established mechanism of disease (InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP v2.1.0). The premature termination codon at position 265 occurs well upstream of the last exon, and nonsense-mediated decay is expected. Under the APC VCEP modified PVS1 decision tree (Figure 1), this null variant meets PVS1 at Very Strong strength.

PS4Moderate

PS4 · moderate

The variant has been observed in multiple unrelated families with classic FAP. PMID:12901799 reports a 3-generation Malaysian Chinese family with multiple affected members segregating the variant with disease (estimated ≥2 phenotype points). PMID:30897307 reports 3 affected individuals from 2 unrelated Brazilian families (families 10 and 21), all with classic FAP and one with osteoma (estimated ≥1.5 phenotype points). Total estimated phenotype points: 3.5, meeting PS4_Moderate threshold (2-3.5 points) under the APC VCEP phenotype point system (Table 1).

PM2Supporting

PM2 · supporting

The variant is absent from gnomAD v2.1.1 (non-cancer dataset, AC=0) and present at extremely low frequency in gnomAD v4.1 (AF=2.48e-6, 4/1,610,912 alleles, grpmax FAF=8e-7). Under the APC VCEP PM2 threshold: AC=0 (≤1) requires AF<0.001% (1e-5); absent from v2.1.1 meets this. Under the alternative threshold for AC>1: AF≤0.0003% (3e-6); the v4.1 AF of 2.48e-6 also meets this. PM2_Supporting is satisfied.

PP5Supporting

PP5 · supporting

Expert panel ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel classified as Pathogenic.

Benign criteria applied · 0

No benign criterion marked as applied in the recorded assessment.

Recorded classification: Likely pathogenic

ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for APC Version 2.1.0 v2.1.0 criteria-combination framework: matched Rule18 (1 Pathogenic.Very Strong + 1 Pathogenic.Moderate) with applied criteria: PVS1 very strong, PS4 moderate, PM2 supporting, PP5 supporting; maps to Likely Pathogenic.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

gnomAD v4.1

gnomAD v2.1

Population frequency

4 / 1,610,912 alleles

gnomAD v4.1: 4 / 1,610,912 alleles. Recorded AF 2.48307e-06. Recorded homozygote count 0.

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

Applied · PM2 →

gnomAD v4.1 ↗gnomAD v2.1 ↗gnomAD-Canada ↗

SpliceAI score

0.190 maximum delta

Recorded SpliceAI maximum delta score: 0.190. Refer to the recorded PP3/BP4 rationale for interpretation.

No listed criterion applied SpliceAI ↗

ClinVar submissions

16 reported laboratory submissions

15 Pathogenic · 1 pathogenic.

Applied · PP5 → ClinVar ↗

Functional evidence

Statement recorded

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.

No listed criterion applied OncoKB ↗

COSMIC

Cancer Hotspots

Somatic evidence

No matching record reported

This variant has not previously been reported in somatic cancers (COSMIC).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

Context only

COSMIC ↗Cancer Hotspots ↗

For specialists

Technical detail

ACMG/AMP criteria under ClinGen APC VCEP v2.1.0, with the data and sources behind each one.

29 criteria with recorded statuses: 4 met · 3 not met · 8 not assessed · 14 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic

PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 PS5

Benign

BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7

Met Not met Not assessed Not applicable

NM_001127511.3:c.793C>T (p.Arg265Ter) is a nonsense variant in exon 7 of APC, a gene where loss of function is the established disease mechanism for familial adenomatous polyposis.

The variant meets PVS1 at Very Strong strength: null variant in a LOF-established gene, expected to trigger nonsense-mediated decay (InSiGHT VCEP v2.1.0 modified decision tree).

The variant has been observed in multiple unrelated families with classic FAP: a 3-generation Malaysian Chinese family (PMID:12901799) and 3 affected individuals from 2 Brazilian families (PMID:30897307), meeting PS4 at Moderate strength (estimated 3.5 phenotype points).

The variant is absent from gnomAD v2.1.1 and present at extremely low frequency in gnomAD v4.1 (AF=2.48e-6, grpmax FAF=8e-7), meeting PM2 at Supporting strength under APC VCEP population thresholds.

Under the APC VCEP v2.1.0 combination rules (Rule 22): one Very Strong criterion (PVS1) + one Moderate criterion (PS4) + one Supporting criterion (PM2) reaches Pathogenic classification. The ClinGen InSiGHT expert panel independently classified this variant as Pathogenic (ClinVar variation 184999).

Met · 4

PVS1 Very strongNM_001127511.3:c.793C>T is a nonsense variant producing p.Arg265Ter (p.R265*) in exon 7. APC is a gene where loss of function is the established mechanism of disease (InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP v2.1.0). The premature termination codon at position 265 occurs well upstream of the last exon, and nonsense-mediated decay is expected. Under the APC VCEP modified PVS1 decision tree (Figure 1), this null variant meets PVS1 at Very Strong strength. Details ▾Hide ▴

Evidence considered

Nonsense variant c.793C>T producing p.Arg265Ter in exon 7 of APC
APC is a gene where LOF is the predominant disease mechanism per InSiGHT VCEP v2.1.0
Premature termination at codon 265 expected to trigger NMD
Variant reported as causative of FAP in a 3-generation Malaysian Chinese family (PMID:12901799)
Variant identified in 3 Brazilian FAP patients from 2 families (PMID:30897307)

Sources

cspec ↗pvs1_gene_contextpvs1_variant_assessmentPMID:12901799 ↗PMID:30897307 ↗

PS4 ModerateThe variant has been observed in multiple unrelated families with classic FAP. PMID:12901799 reports a 3-generation Malaysian Chinese family with multiple affected members segregating the variant with disease (estimated ≥2 phenotype points). PMID:30897307 reports 3 affected individuals from 2 unrelated Brazilian families (families 10 and 21), all with classic FAP and one with osteoma (estimated ≥1.5 phenotype points). Total estimated phenotype points: 3.5, meeting PS4_Moderate threshold (2-3.5 points) under the APC VCEP phenotype point system (Table 1). Details ▾Hide ▴

Evidence considered

PMID:12901799: 3-generation FAP family
variant segregated with affected members (≥2 phenotype points)
PMID:30897307: 3 individuals from 2 families with classic FAP
one with osteoma (≥1.5 phenotype points)
ClinVar variation 184999: reviewed by expert panel as Pathogenic
17 clinical submissions

Still missing

Exact phenotype point counts require expert panel curation with individual-level polyp counts

Sources

clinvar ↗PMID:12901799 ↗PMID:30897307 ↗

PM2 SupportingThe variant is absent from gnomAD v2.1.1 (non-cancer dataset, AC=0) and present at extremely low frequency in gnomAD v4.1 (AF=2.48e-6, 4/1,610,912 alleles, grpmax FAF=8e-7). Under the APC VCEP PM2 threshold: AC=0 (≤1) requires AF<0.001% (1e-5); absent from v2.1.1 meets this. Under the alternative threshold for AC>1: AF≤0.0003% (3e-6); the v4.1 AF of 2.48e-6 also meets this. PM2_Supporting is satisfied. Details ▾Hide ▴

Evidence considered

Absent from gnomAD v2.1.1 (non-cancer
AC=0)
gnomAD v4.1: 4/1
610
912 alleles
AF=2.48e-6
grpmax FAF=8e-7

Sources

gnomad_v2 ↗gnomad_v4 ↗cspec ↗

PP5 SupportingExpert panel ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel classified as Pathogenic. Details ▾Hide ▴

Evidence considered

ClinVar expert panel classification

Sources

cspec ↗clinvar ↗

Not met · 3 · evaluated, threshold not reached

PP1 PMID:12901799 reports segregation of the variant with disease in a 3-generation FAP family, representing approximately 2-3 meioses in one family. The minimum threshold for PP1_Supporting under the APC VCEP is 3-4 meioses in at least one family. The available evidence falls below this threshold. Details ▾Hide ▴

Evidence considered

PMID:12901799: variant segregated with FAP in a 3-generation family (estimated 2-3 meioses)
PMID:30897307: family 21 had 2 affected members but meioses not explicitly documented

Still missing

Exact meioses count not documented
additional segregation data from other families may elevate PP1

Sources

PMID:12901799 ↗PMID:30897307 ↗

BA1 Under the APC VCEP, BA1 requires gnomAD Popmax Filtering AF ≥0.1% (0.001). The variant's grpmax FAF in gnomAD v4.1 is 8e-7 (0.00008%), far below the BA1 threshold. The variant is absent from gnomAD v2.1 entirely. Details ▾Hide ▴

Evidence considered

gnomAD v4.1 grpmax FAF=8e-7
well below BA1 threshold of 0.1%
Absent from gnomAD v2.1

Sources

gnomad_v2 ↗gnomad_v4 ↗cspec ↗

BS1 Under the APC VCEP, BS1 requires gnomAD Popmax Filtering AF ≥0.001% (1e-5). The variant's grpmax FAF in gnomAD v4.1 is 8e-7 (0.00008%), which is below the BS1 threshold. Details ▾Hide ▴

Evidence considered

gnomAD v4.1 grpmax FAF=8e-7
below BS1 threshold of 0.001% (1e-5)

Sources

gnomad_v4 ↗cspec ↗

Not assessed · 8 · no assessment recorded

PS2 No de novo observations have been reported for this variant in the available literature or databases. PS2 requires confirmed de novo occurrence with confirmed maternity and paternity. Details ▾Hide ▴

Still missing

No de novo data available in literature or ClinVar submissions for this variant

PS3 No well-established in vitro or in vivo functional studies have been performed for this variant. The APC VCEP PS3 criteria require RNA assays demonstrating a premature stop codon with defined full-length transcript levels, or specific protein assay evidence. OncoKB's 'Likely Loss-of-function' annotation is a computational inference, not experimental functional evidence for germline PS3. Details ▾Hide ▴

Evidence considered

OncoKB annotates as Likely Loss-of-function (computational inference only
not experimental)

Still missing

No RNA or protein functional assay data available for this variant

Sources

oncokb ↗

PM6 No assumed or confirmed de novo observations have been reported for this variant. PM6 requires de novo occurrence data (with or without parental confirmation) scored per the APC VCEP Tables 1 and 2. Details ▾Hide ▴

Still missing

No de novo data available

BS2 No documented observations of this variant in healthy adults meeting the APC VCEP criteria (age ≥50 years, <5 adenomatous polyps, no FAP features) have been reported. The 4 alleles in gnomAD v4.1 lack phenotype data and cannot be assumed to represent healthy individuals for BS2. Details ▾Hide ▴

Still missing

No documented healthy adult carriers with sufficient phenotype data

BS3 No well-established functional studies demonstrating a benign effect have been reported for this variant. The APC VCEP BS3 criteria require RNA assays showing no mRNA aberration in constitutional patient samples, or specific protein assay evidence; none are available. Details ▾Hide ▴

Still missing

No functional data showing benign effect available

BS4 No evidence of affected family members lacking the variant has been reported. BS4 requires documentation of affected individuals without the variant meeting specific phenotype point thresholds. Details ▾Hide ▴

Still missing

No non-segregation data available

BP2 No evidence of this variant occurring in trans with a (likely) pathogenic APC variant or in unknown phase with multiple different (likely) pathogenic APC variants has been reported. Details ▾Hide ▴

Still missing

No trans/phase co-occurrence data available

BP5 No evidence of an alternate molecular basis for the colorectal polyposis phenotype (e.g., pathogenic variants in POLD1, POLE, MUTYH, NTHL1, or MSH3) has been reported in individuals carrying this variant. Details ▾Hide ▴

Still missing

No alternate molecular basis investigation data available

Not applicable · 14· recorded as not applicable Show reasons ▾Hide reasons ▴

PS1 N/APS1 applies to missense or splice variants with the same amino acid change as a previously established Pathogenic/Likely Pathogenic variant. This variant is a nonsense change (p.Arg265Ter); PS1 is not applicable to nonsense variants under the APC VCEP framework. Details ▾Hide ▴

Sources

cspec ↗

PM1 VCEPPM1 is designated 'Not Applicable' by the APC VCEP v2.1.0. No mutational hotspot or functional domain criteria are defined within this framework. Details ▾Hide ▴

Sources

cspec ↗

PM3 VCEPPM3 is for recessive disorders. FAP/APC is autosomal dominant; PM3 is not applicable. Details ▾Hide ▴

Sources

cspec ↗

PM4 VCEPPM4 is for protein length changes due to in-frame deletions/insertions or stop-loss. This is a substitution (nonsense), not an in-frame change or stop-loss. VCEP also designates PM4 as not used. Details ▾Hide ▴

Sources

cspec ↗

PM5 N/APM5 is applicable only to missense variants under the APC VCEP. This is a nonsense variant (p.Arg265Ter). The PM5 candidate scan confirmed no eligible same-residue missense comparators. Details ▾Hide ▴

Sources

cspec ↗pm5_candidates

PP2 VCEPPP2 is designated 'Not Applicable' by the APC VCEP v2.1.0. Missense variants are not a frequent mechanism of disease in APC. Details ▾Hide ▴

Sources

cspec ↗

PP3 N/AUnder the APC VCEP v2.1.0, PP3 is applicable only to missense variants (for in silico splicing predictor evaluation) and non-canonical splicing variants. This is a nonsense variant producing a premature termination codon; the pathogenic mechanism is loss of normal protein function through truncation and NMD. Computational prediction is not relevant to this established null effect. SpliceAI max delta score is 0.19, consistent with no cryptic splice effect. Details ▾Hide ▴

Evidence considered

SpliceAI max delta 0.19 — no significant splice impact

Sources

cspec ↗spliceai ↗

PP4 VCEPPP4 is designated 'Not Applicable' by the APC VCEP v2.1.0. Phenotype specificity is already captured by the PS4 phenotype point system and therefore PP4 is not used. Details ▾Hide ▴

Sources

cspec ↗

BP1 N/ABP1 is a criterion for missense variants in genes where primarily truncating variants cause disease. This variant is itself a truncating (nonsense) variant; BP1 is not applicable to nonsense variants. Details ▾Hide ▴

Sources

cspec ↗

BP3 VCEPBP3 is not applicable to substitution variants (in-frame deletion/insertion in repetitive region). Variant is a substitution. Details ▾Hide ▴

No further detail was recorded.

BP4 N/AUnder the APC VCEP v2.1.0, BP4 is not applicable to missense variants and is used only for synonymous (silent) or intronic variants where multiple splicing predictors suggest no impact. This is a nonsense variant. Details ▾Hide ▴

Sources

cspec ↗

BP6 VCEPBP6 is designated 'Not Applicable for this VCEP' by the ClinGen InSiGHT VCEP v2.1.0. Not used. Details ▾Hide ▴

Sources

cspec ↗

BP7 N/ABP7 is applicable to synonymous (silent) or intronic variants at or beyond +7/-21 for which multiple splicing prediction algorithms predict no impact. This is a nonsense variant (c.793C>T, p.Arg265Ter); BP7 does not apply. Details ▾Hide ▴

Sources

cspec ↗

PS5 N/APS5 is not defined within the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP v2.1.0 framework for APC. Not used. Details ▾Hide ▴

Sources

cspec ↗

Identifiers

Gene: APC
Transcript: NM_001127511.3
Coding (HGVS c.): NM_001127511.3:c.793C>T
Protein (HGVS p.): NP_001120983.2:p.(Arg265Ter)
GRCh38: chr5:112815507 C>T
GRCh37: chr5:112151204 C>T
ClinVar: 184999

Gene diagram

Every interpreted variant in APC, mapped onto the exon structure of NM_001127511.3. Select a row to find it on the plot.

APCNM_001127511.3

Fetching transcript structure from UCSC…

Exons

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Transcript span

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Strand

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Variants mapped

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Source

UCSC ncbiRefSeqCurated

All variants in APC — Select a row to find it on the plot; use the link to open its page.

	Protein	Location	Classification	Link

gnomAD v4.1 4 / 1,610,912 alleles AF 2.48e-06 · 0 homozygotes · FAF 8e-07

gnomAD v2.1 Allele count data not recorded

gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 2.5e-06 · 4 / 1,610,912 alleles · 0 hom · FAF 8e-07

European (non-Finnish)4 / 1,177,804

3.4e-06

0 alternate alleles recorded in 9 other groups: Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American.

Statements

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 2.48307e-06; MAF= 0.00025%, 4/1610912 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 3.39615e-06; MAF= 0.00034%, 4/1177804 alleles, homozygotes = 0); grpmax FAF= 8e-07.

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

SpliceAI and Pangolin

SpliceAI acceptor lossat -12 bp

0.190

SpliceAI acceptor gainat +6 bp

0.000

SpliceAI donor lossat +86 bp

0.150

SpliceAI donor gainat -12 bp

0.000

Pangolin splice lossmagnitude shown

-0.080

Pangolin splice gain

0.000

Other predictors

REVEL: Not available
BayesDel: 0.660

How the predictions were used

Evidence considered

SpliceAI max delta 0.19 — no significant splice impact

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.19). BayesDel score = 0.66.

8 paper records listed. 2 cited in the classification.

Cited in the classification

A nonsense mutation in exon 8 of the APC gene (Arg283Ter) causes clinically variable FAP in a Malaysian Chinese family.

Mohamed Z et al. · 2003 Aug

A nonsense mutation in exon 8 of APC (NM_000038.6:c.847C>T, p.Arg283Ter) — identical to NM_001127511.3:c.793C>T under alternate transcript nomenclature — was identified as causative in a 3-generation Malaysian Chinese family with FAP. The variant segregated with disease in affected family members. SSCP analysis confirmed heterozygous C>T transition. Computational analysis predicted possible disruption of splicing enhancer motifs.
→ PS4 Names this variant
PMID 12901799 ↗
Source detail

Sequence analysis revealed that the affected individuals are heterozygous for a C847T transition, whilst all the unaffected family members and control individuals are homozygous C at the same position. This nucleotide substitution generates a stop codon at amino acid position 283, in place of the usual arginine (Arg283Ter).

Location Abstract; Results paragraph describing sequencing confirmation
Genotype-phenotype correlation in 99 familial adenomatous polyposis patients: A prospective prevention protocol.

de Oliveira JC et al. · 2019 May

In a Brazilian cohort of 99 FAP patients from 35 families, the variant NM_000038.6:c.847C>T (p.Arg283Ter) — identical to NM_001127511.3:c.793C>T — was identified in 3 individuals from 2 unrelated families (families 10 and 21). All affected individuals exhibited classic FAP; one individual had osteoma. The variant was among 26 different APC pathogenic variants characterized in the study.
→ PVS1 → PS4 Names this variant
PMID 30897307 ↗
Source detail

p.Arg283Ter(c.847C>T) 1 (Family 10) ... p.Arg283Ter(c.847C>T) 2 (Family 21)

Location Table 1 (families 10 and 21); Table 7 (codon 283 phenotypic correlations)

Context Prospective single-center cohort study; clinical phenotyping by colonoscopy, UGIE, CT, MRI, Doppler ultrasound, ophthalmoscopy

Other recorded publications

Expression of beta-catenin and full-length APC protein in normal and neoplastic colonic tissues.

This paper examines expression of beta-catenin and full-length APC protein in normal and neoplastic colonic tissues. It discusses APC mutations generally in colorectal carcinogenesis but does not mention NM_001127511.3:c.793C>T or any specific nonsense variant.
Does not name this variant
PMID 11062151 ↗
The ABC of APC.

A review article ('The ABC of APC') describing APC gene structure, function, and role in colorectal tumorigenesis. Discusses APC mutations at gene level; does not mention NM_001127511.3:c.793C>T.
Does not name this variant
PMID 11257105 ↗
Truncating APC mutations have dominant effects on proliferation, spindle checkpoint control, survival and chromosome stability.

This paper examines dominant effects of truncating APC mutations on proliferation, spindle checkpoint control, survival, and chromosome stability in cell models. It does not reference NM_001127511.3:c.793C>T or any specific patient variant.
Does not name this variant
PMID 15561772 ↗
Screening for germ-line mutations in familial adenomatous polyposis patients: 61 new patients and a summary of 150 unrelated patients.

Nagase H et al. · 1992

No paper-specific finding is recorded.

PMID 1338764 ↗
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.

This is the ACMG/AMP standards and guidelines for variant interpretation consensus paper. It provides the generic framework for criteria definition and combination rules but does not discuss NM_001127511.3:c.793C>T or any specific APC variant.
Does not name this variant
PMID 25741868 ↗
A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

This paper describes a standardized DNA variant scoring system (rules-based) for pathogenicity assessment in Mendelian disorders. It does not discuss NM_001127511.3:c.793C>T or any specific APC variant.
Does not name this variant
PMID 26467025 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

gnomAD v4.1 4 / 1,610,912 recorded alleles Open source ↗

gnomAD v2.1 Captured gnomAD v2.1 source record Open source ↗

SpliceAI Lookup Recorded maximum delta 0.190 Open source ↗

ClinVar 15 Pathogenic · 1 pathogenic Open source ↗

COSMIC Captured COSMIC source record Open source ↗

Cancer hotspots Captured Cancer Hotspots source record Open source ↗

OncoKB Captured OncoKB source record Open source ↗

ClinGen CSpec Captured ClinGen CSpec source record Open source ↗

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

ClinVar

Error retrieving ClinVar entry.

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.19). BayesDel score = 0.66.

Functional

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.

Somatic

This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.