About CTNNB1
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
CTNNB1 c.110C>T, p.(Ser37Phe)
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.
Words with a dotted underline have a short definition. Hover or tap them.
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 Not recorded. 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: 3
Benign evidence criteria: 0
Pathogenic criteria applied · 3
PS3Strong
PS3 · strong
Saturation genome editing (PMID:41629672) systematically characterized all 342 possible missense mutations in the CTNNB1 exon 3 degron hotspot (positions 31–48), directly including p.Ser37Phe, and demonstrated gain-of-function signaling activation via an endogenous-locus reporter assay. Independently, PMID:22815287 directly tested the β-catenin S37F variant in luciferase reporter assays, chromatin immunoprecipitation, and IL-10 induction experiments in human melanoma cell lines, confirming constitutive Wnt pathway activation. PMID:10192393 independently identified S37F as a β-catenin-stabilizing mutation in pilomatricomas. Two or more independent publications provide systematic functional evidence supporting a gain-of-function pathogenic effect for this variant.
PM1Moderate
PM1 · moderate
Ser37 is a critical GSK3β phosphorylation residue within the N-terminal β-TRCP degron motif (DpSGXXpS, residues 32–37). This well-characterized functional domain mediates phosphorylation-dependent ubiquitination and degradation of β-catenin. Saturation mutagenesis (PMID:41629672) confirms this position is essential for degron function, and the variant lies within a statistically significant cancer mutational hotspot (cancerhotspots.org). Missense variants in this domain are a recognized gain-of-function mechanism.
PM2Moderate
PM2 · moderate
The variant is absent from all population databases: gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 (allele frequency = 0). This meets the non-VCEP PM2 threshold of <0.1%.
Benign criteria applied · 0
No benign criterion marked as applied in the recorded assessment.
Recorded classification: Likely pathogenic
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PS3 strong, PM1 moderate, PM2 moderate; combination = 1 strong + 2 moderate, which 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
Not recorded
gnomAD v4.1 allele counts were not recorded for this variant.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI score
0.000 maximum delta
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
No listed criterion applied
SpliceAI ↗
ClinVar submissions
Not recorded
A ClinVar laboratory submission summary was not recorded. ClinVar API review status: no assertion criteria provided.
Context only
ClinVar ↗
Functional evidence
Statement recorded
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Likely Oncogenic.
COSMIC
Cancer Hotspots
Somatic evidence
410 recorded samples
This variant has previously been reported in somatic cancers (COSMIC; COSV62687856, n = 410 times).
Cancer Hotspots
This variant lies in a statistically significant hotspot.
Context only
For specialists
Technical detail
ACMG/AMP criteria under Not recorded, with the data and sources behind each one.
27 criteria with recorded statuses: 3 met · 19 not met · 0 not assessed · 5 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
NM_001098209.2:c.110C>T (p.Ser37Phe) in CTNNB1 is absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada), meeting PM2 at moderate strength.
Ser37 is a critical phosphorylation residue within the N-terminal β-TRCP degron motif (DpSGXXpS, residues 32-37), a well-characterized functional domain mediating β-catenin ubiquitination and degradation. This position is a statistically significant cancer mutational hotspot, meeting PM1 at moderate strength.
Saturation genome editing across all 342 possible missense substitutions in the CTNNB1 exon 3 degron (positions 31-48) demonstrated that p.Ser37Phe confers gain-of-function Wnt pathway activation (PMID:41629672). Independently, direct functional testing of β-catenin S37F in melanoma cell lines confirmed constitutive TCF/LEF transcriptional activity, IL-10 induction, and immune suppression (PMID:22815287). Two or more independent publications with systematic functional characterization meet PS3 at strong strength.
Combined classification: PS3 (strong) + PM1 (moderate) + PM2 (moderate) = Likely Pathogenic per generic ACMG/AMP 2015 combination rules (1 strong + 2 moderate).
No criteria match.
Met · 3
PS3 StrongSaturation genome editing (PMID:41629672) systematically characterized all 342 possible missense mutations in the CTNNB1 exon 3 degron hotspot (positions 31–48), directly including p.Ser37Phe, and demonstrated gain-of-function signaling activation via an endogenous-locus reporter assay. Independently, PMID:22815287 directly tested the β-catenin S37F variant in luciferase reporter assays, chromatin immunoprecipitation, and IL-10 induction experiments in human melanoma cell lines, confirming constitutive Wnt pathway activation. PMID:10192393 independently identified S37F as a β-catenin-stabilizing mutation in pilomatricomas. Two or more independent publications provide systematic functional evidence supporting a gain-of-function pathogenic effect for this variant. Details ▾Hide ▴
Evidence considered
- Saturation mutagenesis of CTNNB1 exon 3 degron (positions 31-48) in mouse ES cells at endogenous Ctnnb1 locus
- S37F assigned a high mutational effect score confirming gain-of-function signaling activation.
- Direct functional testing of β-catenin S37F in melanoma cell lines: luciferase reporter assays
- ChIP confirmation of TCF/LEF binding
- IL-10 induction
- and in vivo DC suppression.
- S37F identified as a β-catenin-stabilizing activating mutation in pilomatricomas with demonstration of impaired phosphorylation-dependent degradation.
Sources
PM1 ModerateSer37 is a critical GSK3β phosphorylation residue within the N-terminal β-TRCP degron motif (DpSGXXpS, residues 32–37). This well-characterized functional domain mediates phosphorylation-dependent ubiquitination and degradation of β-catenin. Saturation mutagenesis (PMID:41629672) confirms this position is essential for degron function, and the variant lies within a statistically significant cancer mutational hotspot (cancerhotspots.org). Missense variants in this domain are a recognized gain-of-function mechanism. Details ▾Hide ▴
Evidence considered
- Ser37 is a phosphorylation site within the β-TRCP degron docking motif (residues 32-37)
- a critical functional domain for β-catenin degradation.
- cancerhotspots.org identifies this position as a statistically significant mutational hotspot.
- Saturation mutagenesis confirms functional importance of all positions in the 31-48 degron region.
Sources
PM2 ModerateThe variant is absent from all population databases: gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 (allele frequency = 0). This meets the non-VCEP PM2 threshold of <0.1%. Details ▾Hide ▴
Evidence considered
- Absent from gnomAD v2.1 (exomes).
- Absent from gnomAD v4.1 (exomes).
- Absent from gnomAD-Canada v1.0 (genomes).
Sources
Not met · 19 · evaluated, threshold not reached
PS2 No de novo occurrence report for this variant was identified in the reviewed literature. Details ▾Hide ▴
Evidence considered
- No de novo data found.
Still missing
- No clinical de novo testing data available.
PS4 No case-control or prevalence data comparing affected vs. unaffected individuals was identified. The literature_pass indexed PMIDs 23788249 and 25356965 for PS4, but these are ACMG policy statements, not patient cohort studies. Details ▾Hide ▴
Evidence considered
- No case-control or cohort prevalence data available.
Still missing
- No systematic case-control study for this variant in a specific disease cohort.
PM5 Automated PM5 candidate harvesting (pm5_candidates.json) returned zero same-residue comparator variants. Although S37C (TCT→TGT) was identified as a somatic activating mutation in pilomatricomas (PMID:10192393), it has not been established as a pathogenic germline variant through ClinVar or other curated databases with sufficient evidence to serve as a PM5 comparator for germline classification. Details ▾Hide ▴
Evidence considered
- No same-residue pathogenic comparator with a different amino acid change identified in ClinVar or curated databases.
Still missing
- S37C reported in somatic context (PMID:10192393) but lacks ClinVar germline pathogenic classification as a comparator.
PM6 No de novo occurrence report for this variant was identified in the reviewed literature. Details ▾Hide ▴
Evidence considered
- No de novo data found.
Still missing
- No clinical de novo testing data available.
PP1 No segregation data or family studies were identified in the reviewed literature. Details ▾Hide ▴
Evidence considered
- No segregation or family cosegregation data available.
Still missing
- No family-based segregation studies available.
PP2 CTNNB1 germline disease (CTNNB1 syndrome, MIM 615075) is primarily caused by loss-of-function variants (nonsense, frameshift). The p.Ser37Phe variant is a gain-of-function missense change not characteristic of the LoF disease mechanism. PP2 (missense variants are a common mechanism of disease with low rate of benign missense variation) does not apply in this context. Details ▾Hide ▴
Evidence considered
- CTNNB1 syndrome is primarily a LoF disorder
- S37F is a GoF variant with a distinct mechanism.
PP3 Computational evidence is equivocal and does not reach consensus support for a deleterious effect. REVEL score is 0.586 (borderline, below the typical 0.7 damaging threshold). BayesDel score is 0.143 (low, predicted benign). SpliceAI max delta score is 0.00 (no splicing impact). Only one of three predictors is borderline, and in silico tools are not optimized for gain-of-function mechanisms such as the β-catenin stabilization caused by S37F. Details ▾Hide ▴
Evidence considered
- REVEL: 0.586 (borderline).
- BayesDel: 0.143 (low/predicted benign).
- SpliceAI max delta: 0.00 (no splice impact).
Still missing
- In silico predictors are not calibrated for gain-of-function variants
- scores may underestimate pathogenicity.
Sources
PP4 No specific patient phenotype or clinical data were provided for this case to assess whether the variant's phenotype is highly specific for a disease. Details ▾Hide ▴
Evidence considered
- No patient phenotype data available for this case.
Still missing
- Patient phenotype not provided.
PP5 The ClinVar classification is 'Pathogenic' from OMIM (SCV000039439) with 'no assertion criteria provided' and somatic disease context (pilomatricoma). This does not constitute a reputable source with transparent evidence suitable for PP5 application in germline classification. Details ▾Hide ▴
Evidence considered
- ClinVar OMIM submission (SCV000039439) lacks assertion criteria and is somatic in origin.
BA1 Variant is absent from gnomAD (allele frequency = 0), well below the BA1 threshold of >1%. Details ▾Hide ▴
Evidence considered
- AF = 0 in gnomAD v2.1
- v4.1
- and gnomAD-Canada
- far below the 1% BA1 threshold.
Sources
BS1 Variant is absent from gnomAD (allele frequency = 0), well below the BS1 threshold of >0.3%. Details ▾Hide ▴
Evidence considered
- AF = 0 in all gnomAD cohorts
- far below the 0.3% BS1 threshold.
Sources
BS2 No observation of this variant in healthy adults has been documented. The variant is absent from gnomAD and no unaffected carriers have been reported. Details ▾Hide ▴
Evidence considered
- No healthy adult carriers identified.
Still missing
- No systematic screening of healthy adults for this variant.
BS3 Functional evidence from saturation mutagenesis (PMID:41629672) and direct testing (PMID:22815287) demonstrates gain-of-function — constitutive Wnt pathway activation — rather than a benign or normal functional effect. No evidence supports that the variant does not alter protein function. Details ▾Hide ▴
Evidence considered
- Functional studies demonstrate gain-of-function activation
- not benign effect.
Sources
BS4 No cosegregation data in affected families is available to assess lack of segregation with disease. Details ▾Hide ▴
Evidence considered
- No family segregation data available.
Still missing
- No family-based cosegregation studies available.
BP1 Although CTNNB1 syndrome (MIM 615075) is primarily caused by loss-of-function truncating variants, p.Ser37Phe is a well-characterized gain-of-function missense variant with a distinct functional mechanism (β-catenin stabilization) rather than a variant of uncertain significance. BP1 does not apply when the missense variant has an established alternative pathogenic mechanism. Details ▾Hide ▴
Evidence considered
- S37F has an established gain-of-function mechanism distinct from the LoF mechanism of CTNNB1 syndrome
- BP1 is not applicable for variants with known alternative pathogenic mechanisms.
Sources
BP2 No observation in trans with a pathogenic variant has been reported. Details ▾Hide ▴
Evidence considered
- No trans-phase data available.
BP4 Computational evidence is equivocal and does not provide multiple consistent lines supporting no impact. While BayesDel (0.143) and SpliceAI (0.00) suggest benign/no impact, REVEL (0.586) is borderline. The lack of consensus and the known gain-of-function mechanism (not captured by these tools) preclude application of BP4. Details ▾Hide ▴
Evidence considered
- BayesDel: 0.143 (predicted benign).
- SpliceAI: 0.00 (no splice impact).
- REVEL: 0.586 (borderline
- conflicting with benign prediction).
Still missing
- In silico tools are not designed to assess gain-of-function mechanisms.
Sources
BP5 No alternative molecular cause for the disease has been identified in this case to support BP5. Details ▾Hide ▴
Evidence considered
- No alternative molecular cause documented.
Still missing
- Clinical case context and alternative diagnoses not provided.
PS5 No independent reputable source with transparent evidence has classified this variant as pathogenic. The ClinVar OMIM submission (SCV000039439) lacks assertion criteria and is derived from a single literature-only review of somatic pilomatricoma data. Details ▾Hide ▴
Evidence considered
- ClinVar OMIM submission has no assertion criteria provided
- not sufficient as an independent reputable source.
Not applicable · 5· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANM_001098209.2:c.110C>T (p.Ser37Phe) is a missense variant and does not fall into the generic PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants per ClinGen SVI PVS1 recommendations (PMC6185798). Details ▾Hide ▴
PS1 N/AThe only single-nucleotide substitution producing p.Ser37Phe from the TCT codon is c.110C>T, which is the query variant itself. No alternative nucleotide change yielding the same amino acid change has been established as pathogenic, so a comparator for PS1 does not exist. Details ▾Hide ▴
Evidence considered
- Only one nucleotide substitution path to p.Ser37Phe exists (c.110C>T)
- no independent PS1 comparator available.
BP3 N/ASKIP: trivially not applicable (in-frame indel criteria). Details ▾Hide ▴
No further detail was recorded.
BP6 N/ABP6 applies to synonymous variants with no predicted splice impact. This is a missense variant. Details ▾Hide ▴
Evidence considered
- Missense variant
- BP6 criterion is for synonymous variants.
BP7 N/ABP7 applies to synonymous variants with no predicted splice impact. This is a missense variant. Details ▾Hide ▴
Evidence considered
- Missense variant
- BP7 criterion is for synonymous variants.
Identifiers
- Gene
- CTNNB1
- Transcript
- NM_001098209.2
- Coding (HGVS c.)
- NM_001098209.2:c.110C>T
- Protein (HGVS p.)
- NP_001091679.1:p.(Ser37Phe)
- GRCh38
- chr3:41224622 C>T
- GRCh37
- chr3:41266113 C>T
- ClinVar
- 17586
- COSMIC
- COSV62687856
Gene diagram
Every interpreted variant in CTNNB1, mapped onto the exon structure of NM_001098209.2. Select a row to find it on the plot.
CTNNB1NM_001098209.2
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 CTNNB1
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Select a row to find it on the plot; use the link to open its page.
| Protein | Location | Classification | Link |
|---|
gnomAD v4.1
Allele count data not recorded
gnomAD v2.1
Allele count data not recorded
gnomAD-Canada v1.0
Allele count data not recorded
Statements
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
Other predictors
- REVEL
- 0.586
- BayesDel
- 0.143
How the predictions were used
PP3 Computational evidence is equivocal and does not reach consensus support for a deleterious effect. REVEL score is 0.586 (borderline, below the typical 0.7 damaging threshold). BayesDel score is 0.143 (low, predicted benign). SpliceAI max delta score is 0.00 (no splicing impact). Only one of three predictors is borderline, and in silico tools are not optimized for gain-of-function mechanisms such as the β-catenin stabilization caused by S37F. Details ▾Hide ▴
Evidence considered
- REVEL: 0.586 (borderline).
- BayesDel: 0.143 (low/predicted benign).
- SpliceAI max delta: 0.00 (no splice impact).
Still missing
- In silico predictors are not calibrated for gain-of-function variants
- scores may underestimate pathogenicity.
Sources
BP4 Computational evidence is equivocal and does not provide multiple consistent lines supporting no impact. While BayesDel (0.143) and SpliceAI (0.00) suggest benign/no impact, REVEL (0.586) is borderline. The lack of consensus and the known gain-of-function mechanism (not captured by these tools) preclude application of BP4. Details ▾Hide ▴
Evidence considered
- BayesDel: 0.143 (predicted benign).
- SpliceAI: 0.00 (no splice impact).
- REVEL: 0.586 (borderline
- conflicting with benign prediction).
Still missing
- In silico tools are not designed to assess gain-of-function mechanisms.
Sources
BP7 N/ABP7 applies to synonymous variants with no predicted splice impact. This is a missense variant. Details ▾Hide ▴
Evidence considered
- Missense variant
- BP7 criterion is for synonymous variants.
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.586. BayesDel score = 0.14345.
7 paper records listed. 3 cited in the classification.
Cited in the classification
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PMID 10192393 ↗A common human skin tumour is caused by activating mutations in beta-catenin.Chan EF et al. · 1999 AprCTNNB1 exon 3 was sequenced in 16 human pilomatricomas. S37F (TCT→TTT) was one of eight distinct missense mutations identified. All mutations mapped to the N-terminal phosphorylation-dependent degradation domain. S37F was characterized as a β-catenin-stabilizing activating mutation that ablates a GSK3β phosphorylation site essential for ubiquitin-mediated degradation.→ PS3 → PM1 Names this variant
Source detail
S37C (TCT→TGT), S37F (TCT→TTT) and T41I (ACC→ATC)
Location Results paragraphs describing Figure 3; Figure 5a (schematic of mutations)
Context PCR amplification and direct sequencing of exon 3 from microdissected formalin-fixed paraffin-embedded pilomatricoma tissue; HinfI restriction endonuclease confirmation
-
PMID 22815287 ↗Immune suppression and resistance mediated by constitutive activation of Wnt/β-catenin signaling in human melanoma cells.Yaguchi T et al. · 2012 Sep 1β-catenin S37F, identified as a melanoma antigen recognized by T cells, was directly tested in functional assays. Overexpression of β-catenin-S37F in human melanoma cell lines (397mel, 938mel) induced high IL-10 production, suppressed dendritic cell maturation, promoted regulatory DC generation, and inhibited melanoma-specific CTL function both in vitro and in vivo. β-catenin/TCF was shown to directly bind and transactivate the IL-10 promoter via a TCF binding element at -2438 bp. The S37F mutation was characterized as resistant to degradation and constitutively activating Wnt/β-catenin signaling.→ PS3 Names this variant
Source detail
We have previously identified a mutation of β-catenin (S37F) as a melanoma Ag recognized by T cells.
Location Abstract line 137; Results sections 'High IL-10 expression', 'b-catenin directly promotes IL-10 expression', 'DC impairment', 'CTL impairment'; Figures 2, 4, 5, 6
Context Human melanoma cell lines (624mel, 888mel, 397mel, 928mel, 938mel); luciferase reporter assays in HeLa and HEK293T cells; ChIP in 888mel; in vivo xenograft models in nude and NOG mice
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PMID 41629672 ↗Mutational scanning reveals oncogenic CTNNB1 mutations have diverse effects on signaling.Saturation genome editing quantified signaling activity for all 342 possible missense mutations in the CTNNB1 exon 3 degron motif (positions 31-48). Ser37 substitutions, including S37F, were among the most activating mutations in the hotspot. The screen was conducted at the endogenous mouse Ctnnb1 locus (100% conserved with human at amino acid level) using a Tcf/Lef-H2B-GFP reporter in mouse ES cells. Mutational effect scores correlated with endogenous β-catenin target gene expression in both mouse ES cells and human HCC cohorts.→ PS3 → PM1 Names this variant
Source detail
Residues T41 and S45 were most frequently affected, comprising 27% and 25% of hotspot missense mutations, respectively, followed by S37, S33, D32 and G34.
Location Figure 1e, Figure 2a (heatmap), Figure 3a, Results section 'Mutational scanning reveals diverse consequences of Ctnnb1 hotspot mutations'
Context Saturation genome editing (CRISPR HDR) in mouse ES cells; Tcf/Lef-H2B-GFP fluorescent reporter assay quantifying Wnt pathway activation
Other recorded publications
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PMID 17531558 ↗Genomic stability prevails in North-African hepatocellular carcinomas.In a cohort of 42 North-African hepatocellular carcinomas, CTNNB1 exon 3 was sequenced. One patient (M012) carried a c.110C>T (Ser37Phe) missense mutation. CTNNB1 mutations were identified in 4 of 42 cases (9%). The study characterized the genomic landscape of HCC in a previously unstudied North-African population.Names this variant
Quoted passage
M012: c→t, 37, Ser→Phe
Table 2: Patient M012, exon 3, c→t, codon 37, Ser→Phe
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PMID 18500270 ↗Clinicopathological and molecular analysis of endometrial carcinoma associated with tamoxifen.Analysis of endometrial carcinomas associated with tamoxifen exposure and ovarian hyperthecosis. Two patients in the ovarian hyperthecosis control group (Cases 1 and 6) carried the CTNNB1 c.110C>T (Ser37Phe) mutation, confirmed by direct sequencing. Both cases showed nuclear β-catenin immunostaining. CTNNB1 mutations were significantly more frequent in estrogen-driven endometrial carcinomas compared to random controls.Names this variant
Quoted passage
Ser(TCT)37(TTT)Phe
Table 4: Cases 1 and 6, Ser(TCT)37(TTT)Phe; Figure 2d
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PMID 9065403 ↗Stabilization of beta-catenin by genetic defects in melanoma cell lines.Discusses β-catenin stabilization by genetic defects in melanoma cell lines. The study identified CTNNB1 mutations in 6 of 26 melanoma lines but the specific variant NM_001098209.2:c.110C>T (p.Ser37Phe) was not confirmed as mentioned in the abstract or accessible text. The paper demonstrates the general mechanism of β-catenin stabilization through exon 3 mutations.Does not name this variant
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PMID 10347231 ↗The ubiquitin-proteasome pathway and serine kinase activity modulate adenomatous polyposis coli protein-mediated regulation of beta-catenin-lymphocyte enhancer-binding factor signaling.Examined APC-mediated regulation of β-catenin/LEF signaling using luciferase reporter assays. The study focused on the general mechanism of β-catenin degradation by the ubiquitin-proteasome pathway. The specific variant NM_001098209.2:c.110C>T (p.Ser37Phe) was not identified in the abstract or accessible content.Does not name this variant
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
Captured gnomAD v4.1 source record
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.000
Open source ↗
ClinVar
Captured ClinVar source record
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 ↗
All source links
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/variation/17586/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/3-41266113-C-T?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr3-41224622-C-T?dataset=gnomad_r4
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/3-41224622-C-T
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_001098209.2%3Ac.1…
- OncoKB ↗www.oncokb.org/gene/CTNNB1/S37F
- COSMIC ↗cancer.sanger.ac.uk/cosmic/mutation/overview?id=223262011
- Cancer hotspots ↗www.cancerhotspots.org/
Statements for reports
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar but submission details could not be extracted. (ClinVarID = 17586)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.586. BayesDel score = 0.14345.
Functional
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Likely Oncogenic.
Somatic
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV62687856, n = 410 times).
Cancer Hotspots
This variant lies in a statistically significant hotspot.