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Variant interpretation report

ESR1 c.1610A>C, p.Tyr537Ser

NM_000125.4:c.1610A>C NP_000116.2:p.(Tyr537Ser) Missense · exon 8 View identifiers
Classification
Likely pathogenic

Variant description:

The ESR1 NM_000125.4:c.1610A>C (NP_000116.2:p.(Tyr537Ser)) missense variant has previously been reported in somatic cancers (COSMIC; COSV52783938, n = 98 times), and lies in a statistically significant hotspot (cancerhotspots.org). Experimental evidence: Y537S showed approximately 60-fold estrogen-independent ER activity versus wild type, with concordant cellular, xenograft, and biophysical evidence across independent studies. Based on available guidelines, this variant is considered to be Likely Pathogenic.

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 ESR1

ESR1 encodes estrogen receptor alpha (ERα), a nuclear receptor and ligand-activated transcription factor that regulates estrogen-inducible genes involved in growth, metabolism, sexual development, and reproduction. It plays a key role in breast cancer, endometrial cancer, and osteoporosis, and functions as an oncogene whose signaling promotes tumorigenesis. Constitutive receptor activity is a common driver of acquired resistance to estrogen-deprivation therapies in hormone-resistant metastatic breast cancer.

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 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.

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

Met, strong: Y537S showed approximately 60-fold estrogen-independent ER activity versus wild type, with concordant cellular, xenograft, and biophysical evidence across independent studies.

PM2Supporting
PM2 · supporting

Met at supporting strength: the variant is absent from gnomAD v2.1 and v4.1, giving allele frequency 0 versus the <=0.0001 PM2 threshold.

PP3Moderate
PP3 · moderate

Met at moderate strength: missense REVEL score 0.911 exceeds the PP3 moderate threshold of 0.773.

Benign criteria applied · 0

No benign criterion marked as applied in the recorded assessment.

Recorded classification: Likely pathogenic

Likely Pathogenic: PS3 strong plus PM2 supporting satisfy the generic ACMG/AMP Likely Pathogenic rule, with additional PP3 moderate computational evidence.

02The sources

Evidence at a glance

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

No screenshot for this evidence
REVEL score
0.911 recorded score

Recorded REVEL score: 0.911. Refer to the recorded PP3/BP4 rationale for interpretation.

ClinVar submissions
Not recorded

A ClinVar laboratory submission summary was not recorded. ClinVar API review status: criteria provided, single submitter.

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: Oncogenic.

COSMIC
Cancer Hotspots
Somatic evidence
98 recorded samples

This variant has previously been reported in somatic cancers (COSMIC; COSV52783938, n = 98 times).

Cancer Hotspots

This variant lies in a statistically significant hotspot.

For specialists

Technical detail

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: 3 met · 8 not met · 12 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

The available evidence is somatic tumor and functional literature, not germline pedigree evidence; PS2, PM6, and BS4 cannot be assigned, and PP1 is not applicable without an inherited disease pedigree and established disease context.

No VCEP covers ESR1 in this case; the supplied generic ACMG/AMP 2015 definitions govern.

The literature contains affected-patient observations and functional studies but no qualifying case-control enrichment, phenotype-specific single-etiology evidence, alternate molecular basis, or expert-panel ClinVar Pathogenic/Likely pathogenic or Benign/Likely benign assertion for this exact variant.

Generic ACMG/AMP rules govern because no VCEP covers ESR1 in this case.

The variant is missense, so PP3 and BP4 use REVEL only; the SpliceAI result is not combined with or substituted for REVEL.

REVEL 0.911 reaches PP3 moderate >=0.773 but does not meet BP4 supporting <=0.29.

Met · 3

PS3 StrongACMG_2015Met, strong: Y537S showed approximately 60-fold estrogen-independent ER activity versus wild type, with concordant cellular, xenograft, and biophysical evidence across independent studies. Details ▾Hide ▴
Reasoning

PS3 is met at strong strength. The exact ESR1 p.Tyr537Ser variant (NM_000125.4:c.1610A>C) was tested in multiple independent functional systems with wild-type comparators and hormone/antiestrogen controls. In HEK293T ERE-luciferase assays, Y537S showed strong constitutive transcriptional activation without estradiol and two- to fourfold higher 4-hydroxytamoxifen and fulvestrant IC50 values than wild type (PMID:24185510). In SKBR3 cells, activity was approximately 60-fold above wild type without estradiol; the result was reproduced across additional breast and endometrial cell lines, with increased ER-target gene expression in MCF7 cells and hormone-independent tumor growth in xenografts (PMID:24185512). Independent biophysical work showed hormone-independent SRC3 coactivator recruitment by Y537S, with Kd 13.6 +/- 2.0 nM versus no detectable apo recruitment for wild-type ERalpha, and reduced ligand binding (PMID:26836308). The exact Y537S construct was also characterized in recombinant-receptor binding and dissociation assays, although those results alone were not damaging (PMID:11914066). The concordant cellular, transcriptional, in vivo, structural, and biophysical results establish a reproducible damaging gain-of-function effect relevant to ESR1 biology.

Rule
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
Evidence considered
  • PMID:24185510, Results paragraph on the HEK293T ERE-luciferase assay: the exact p.Tyr537Ser mutant had strong constitutive ERE reporter activation without beta-estradiol; 4-hydroxytamoxifen and fulvestrant IC50 values were two- to fourfold higher than wild-type ESR1.
  • PMID:24185512, Results and Figures 2-5: in ER-negative SKBR3 cells, Y537S ERE-luciferase activity was 60X wild-type levels without estradiol; the mutant increased ER-target transcripts, promoted growth after estrogen withdrawal in MCF7 xenografts, and retained greater residual activity under antiestrogen treatment.
  • PMID:26836308, Results and Tables 1-2: purified Y537S ERalpha recruited SRC3 without estradiol with Kd 13.6 +/- 2.0 nM, while wild-type ERalpha showed no apo coactivator recruitment; structural and binding studies supported constitutive activation and reduced antagonist effectiveness.
  • PMID:11914066, Tables 1-2 and molecular-modeling results: recombinant Y537S ESR1 was directly tested in estradiol-binding and dissociation assays, providing an orthogonal characterization of the exact substitution, but not a benign functional conclusion.
  • Assay controls and biological relevance: studies used wild-type ESR1 comparators, estradiol-depleted conditions, estradiol stimulation, antiestrogen dose-response testing, reporter normalization, ER-target transcriptional readouts, and breast-cancer cellular or xenograft models.
Sources
PM2 SupportingACMGMet at supporting strength: the variant is absent from gnomAD v2.1 and v4.1, giving allele frequency 0 versus the <=0.0001 PM2 threshold. Details ▾Hide ▴
Reasoning

PM2 is met at supporting strength. NM_000125.4:c.1610A>C (p.Tyr537Ser) is absent from gnomAD v2.1 and gnomAD v4.1. It is also reported absent from gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes. The observed allele frequency is therefore 0, meeting the supplied generic PM2 supporting threshold of <=0.0001.

Rule
Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
Evidence considered
  • gnomAD v2.1 exome record for 6-152419923-A-C: absent; allele frequency 0.
  • gnomAD v4.1 record for chr6-152098788-A-C: absent; allele frequency 0.
  • The evidence record also reports absence from gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes.
  • The supplied generic PM2 supporting calibration is <=0.0001, identified in the prompt as the ClinGen SVI 2020 recommendation (PMID:25741868).
Sources
PP3 ModerateACMGMet at moderate strength: missense REVEL score 0.911 exceeds the PP3 moderate threshold of 0.773. Details ▾Hide ▴
Reasoning

NM_000125.4:c.1610A>C produces the missense consequence NP_000116.2:p.(Tyr537Ser) in exon 8, so the generic missense path applies: REVEL only. REVEL is 0.911, which reaches the supplied PP3 moderate threshold of >= 0.773 but not the strong threshold of >= 0.932. The SpliceAI max delta of 0.004 and BayesDel score of 0.418913 were not used: SpliceAI is not evidence for a missense PP3 decision, and no generic ACMG-strength calibration is established for BayesDel.

Rule
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only. Its SpliceAI score says nothing about whether the amino-acid substitution is tolerated, so 'no predicted splice impact' is never BP4 support for a missense variant. ... PP3 (moderate): >= 0.773 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
Evidence considered
  • Variant consequence: NM_000125.4:c.1610A>C, NP_000116.2:p.(Tyr537Ser), missense in exon 8; the generic missense REVEL path therefore applies and SpliceAI is not used.
  • Local REVEL lookup: score 0.911.
  • Generic ClinGen SVI REVEL calibration supplied in the governing case instructions: PP3 moderate requires >=0.773 and PP3 strong requires >=0.932; the calibration is attributed to Pejaver et al. 2022, PMID:36413997.
  • BayesDel score 0.418913 was not used because no generic ACMG-strength calibration is established for BayesDel.
Sources
revel

Not met · 8 · evaluated, threshold not reached

PS4 ACMG_2015Not met: affected-cohort reports lack unaffected or population-control counts, OR/RR, and a confidence interval required to establish PS4 enrichment. Details ▾Hide ▴
Reasoning

The governing PS4 rule requires a significantly increased prevalence in affected individuals compared with controls and states that RR or OR must be >5.0 with a confidence interval excluding 1.0. The reviewed variant-specific literature reports affected cancer cohorts, including p.Tyr537Ser in 3 patients in PMID:24185510, p.Tyr537Ser among 14 ESR1-mutant cases in an 80-case cohort in PMID:24185512, and 13 of 95 metastatic breast-cancer patients with somatic ESR1 mutations in PMID:27986707, but none supplies unaffected or population-control counts matched to the case cohort, an OR/RR, or a confidence interval. The two literature-pass PS4 leads, PMID:22918138 and PMID:34131312, were verified from their abstracts as general diagnostic/genome-testing standards and do not report this variant in a case-control study. Therefore no case-control enrichment estimate can be computed and PS4 is not met; no prevalence comparison reaches the required OR/RR >5.0 with CI excluding 1.0.

Rule
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.
Evidence considered
  • PMID:24185510: the exact p.Tyr537Ser alteration was observed in three patients in a six-patient ER-positive metastatic breast-cancer sequencing cohort; the report provides no unaffected or population-control comparison.
  • PMID:24185512: ESR1 ligand-binding-domain mutations were identified in 14 of 80 metastatic ER-positive breast tumors, including p.Tyr537Ser; this is a case series/cohort without a matched control frequency or OR/RR.
  • PMID:27986707: Y537S was reported in 13 of 95 metastatic breast-cancer patients with somatic ESR1 mutations; the cited result is not a case-control comparison and has no control count or confidence interval.
  • PMID:22918138 and PMID:34131312 were the literature-pass PS4 leads; their available abstracts describe general molecular-testing standards, not variant-specific case-control prevalence evidence. These PMIDs are not present as source_registry keys, so they are not placed in evidence_refs.
Still missing
  • A matched case-control study or equivalent control-frequency data for ESR1 p.Tyr537Ser is not available.
  • No OR/RR and 95% confidence interval can be calculated from the available reports.
Sources
PP5 ACMG_2015Not met: ClinVar has only a single-submitter one-star Oncogenic label, not an exact-variant expert-panel Pathogenic or Likely pathogenic classification. Details ▾Hide ▴
Reasoning

The governing PP5 rule concerns a reputable source reporting the variant as pathogenic when the underlying evidence is unavailable for independent evaluation. The exact ClinVar record for NM_000125.4:c.1610A>C (p.Tyr537Ser) has one single-submitter, one-star somatic classification of Oncogenic, with no expert-panel submission and no validated submission-level pathogenic or likely-pathogenic assertion. The available literature reports functional and somatic observations but does not provide a qualifying reputable pathogenic assertion of the type required here. PP5 is therefore not met.

Rule
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
Evidence considered
  • ClinVar variation 3257895 exactly matches NM_000125.4:c.1610A>C (p.Tyr537Ser), but the record has one submission, one-star criteria-provided single-submitter status, somatic origin, and classification Oncogenic rather than an expert-panel Pathogenic or Likely pathogenic assertion.
  • The ClinVar submission audit reports zero expert-panel submissions and zero usable criterion-lead submissions.
Sources
BA1 ACMG_2015Not met: the variant was absent from gnomAD v2.1 and v4.1, far below the generic BA1 allele-frequency threshold of 5%. Details ▾Hide ▴
Reasoning

BA1 is not met. NM_000125.4:c.1610A>C (p.Tyr537Ser) was absent from gnomAD v2.1 and gnomAD v4.1, with no allele frequency approaching the generic stand-alone threshold of >=0.05. The non-cancer gnomAD v2.1 exome and v3.1 genome subsets were also absent. No ancestry-specific elevated frequency was identified.

Rule
Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
Evidence considered
  • gnomAD v2.1 exome record for 6-152419923-A-C: absent; allele frequency 0.
  • gnomAD v4.1 record for chr6-152098788-A-C: absent; allele frequency 0.
  • The evidence record also reports absence from gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes.
  • The supplied generic BA1 calibration is >=0.05, ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868).
Sources
BS1 ACMGNot met: gnomAD v2.1 and v4.1 show no alternate alleles, below the generic BS1 default threshold of 1%. Details ▾Hide ▴
Reasoning

BS1 is not met. The variant was absent from gnomAD v2.1 and v4.1 and therefore does not exceed the supplied generic default BS1 threshold of >=0.01. No ancestry-specific frequency elevation, founder effect, prevalence estimate, penetrance estimate, or allelic-heterogeneity calculation indicates that this variant is more frequent than expected for a disorder. Because no elevated frequency was observed, the reduced-penetrance/late-onset exception does not alter the conclusion.

Rule
Allele frequency is greater than expected for the disorder.
Evidence considered
  • gnomAD v2.1 exome record for 6-152419923-A-C: absent; allele frequency 0.
  • gnomAD v4.1 record for chr6-152098788-A-C: absent; allele frequency 0.
  • The evidence record also reports absence from gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes.
  • The supplied generic BS1 calibration is >=0.01; the prompt identifies Whiffin et al. 2017 (PMID:28518168) as the preferred per-gene maximum-credible-frequency framework when an elevated frequency requires interpretation.
Sources
BS3 ACMG_2015Not met: independent assays show constitutive ER activation and antiestrogen resistance, so the evidence does not demonstrate no damaging effect on ESR1 function or splicing. Details ▾Hide ▴
Reasoning

BS3 is not met. The available functional evidence does not show no damaging effect on ESR1 function or splicing; instead, multiple controlled studies of the exact p.Tyr537Ser substitution demonstrate constitutive estrogen-independent transcription, increased ER-target gene expression, hormone-independent tumor growth, antiestrogen resistance, and hormone-independent coactivator recruitment. PMID:11914066 found near-wild-type estradiol affinity in one binding assay, but that isolated result does not establish absence of damage and does not outweigh the concordant damaging functional findings in independent cellular, in vivo, and biophysical assays.

Rule
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
Evidence considered
  • PMID:24185510, HEK293T ERE-luciferase and antiestrogen dose-response assays: Y537S was constitutively active without estradiol and had higher antiestrogen IC50 values than wild type.
  • PMID:24185512, SKBR3, MCF7, and xenograft experiments: Y537S produced approximately 60X wild-type basal reporter activity, increased ER-target transcription, and supported estrogen-independent tumor growth.
  • PMID:26836308, purified ERalpha biophysical and structural assays: Y537S recruited SRC3 without hormone and altered ligand-binding and agonist/antagonist conformational behavior.
  • PMID:11914066, recombinant-receptor binding assays: Y537S retained similar estradiol affinity to wild type, but this single assay result does not demonstrate absence of damaging effect across ESR1 function and does not evaluate splicing.
Sources
BP4 ACMGNot met: missense REVEL score 0.911 is above the BP4 supporting cutoff of 0.29. Details ▾Hide ▴
Reasoning

NM_000125.4:c.1610A>C produces the missense consequence NP_000116.2:p.(Tyr537Ser), so BP4 must be evaluated on the generic missense REVEL path only. REVEL is 0.911, which is above the supplied BP4 supporting cutoff of <= 0.29 and therefore does not support no impact. The SpliceAI max delta of 0.004 was not substituted because a splice prediction cannot establish BP4 for a missense amino-acid substitution; BayesDel was not used because no generic ACMG-strength calibration is established.

Rule
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) ... Missense variant -> REVEL only. Its SpliceAI score says nothing about whether the amino-acid substitution is tolerated, so 'no predicted splice impact' is never BP4 support for a missense variant. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
Evidence considered
  • Variant consequence: NM_000125.4:c.1610A>C, NP_000116.2:p.(Tyr537Ser), missense in exon 8; the generic missense REVEL path applies and SpliceAI is not used.
  • Local REVEL lookup: score 0.911.
  • Generic ClinGen SVI REVEL calibration supplied in the governing case instructions: BP4 supporting requires <=0.29; the calibration is attributed to Pejaver et al. 2022, PMID:36413997.
  • BayesDel score 0.418913 was not used because no generic ACMG-strength calibration is established for BayesDel.
Sources
revel
BP5 ACMG_2015Not met: no documented case shows this variant alongside an independent alternate molecular basis explaining the disease. Details ▾Hide ▴
Reasoning

The governing BP5 rule requires the variant to be found in a case with an alternate molecular basis for disease. The available evidence documents ESR1 p.Tyr537Ser in somatic breast-cancer cohorts and functional models, but does not document a specific case in which an independent alternate molecular cause explains the disease while this variant is present. BP5 is not met.

Rule
Variant found in a case with an alternate molecular basis for disease.
Evidence considered
  • The reviewed ESR1 literature reports somatic p.Tyr537Ser observations and functional studies, not a case with a separately established alternate molecular basis for disease.
Still missing
  • No case-level alternate pathogenic molecular diagnosis is reported.
BP6 ACMG_2015Not met: no exact-variant expert-panel Benign or Likely benign assertion is present; ClinVar instead reports a single-submitter Oncogenic label. Details ▾Hide ▴
Reasoning

The governing BP6 rule concerns a reputable source reporting the variant as benign when the evidence is unavailable for independent evaluation. The exact ClinVar record is a single-submitter one-star somatic Oncogenic record, not an expert-panel Benign or Likely benign classification, and no qualifying benign reputable-source assertion is present. BP6 is not met.

Rule
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
Evidence considered
  • ClinVar variation 3257895 exactly matches NM_000125.4:c.1610A>C (p.Tyr537Ser), but its one submission is classified Oncogenic with one-star single-submitter status, not Benign or Likely benign.
  • The ClinVar submission audit reports zero expert-panel submissions.
Sources

Not assessed · 12 · no assessment recorded

PS1 ACMG_2015Not assessed: exact p.Tyr537Ser reports are available, but no qualifying previously established pathogenic classification is documented for the generic PS1 comparator. Details ▾Hide ▴
Reasoning

The queried variant is ESR1 p.Tyr537Ser (NM_000125.4:c.1610A>C). The reviewed literature reports this exact amino-acid change, but the available records establish somatic oncogenic or functional observations rather than a previously established pathogenic classification suitable for the generic PS1 comparator requirement. Therefore, the evidence does not establish a qualifying previously pathogenic variant for PS1.

Rule
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.
Evidence considered
  • PMID:24185510 reports p.Tyr537Ser in three metastatic breast-cancer tumors and functional activation, but this is a somatic observation and not a qualifying generic ACMG pathogenic comparator.
  • PMID:24185512 reports recurrent p.Tyr537Ser in metastatic ER-positive breast cancer and functional activity, without establishing a germline or generic ACMG pathogenic classification.
  • ClinVar variation 3257895 is classified Oncogenic with a single somatic submitter and one-star review status; this does not document a previously established pathogenic variant for generic PS1.
Still missing
  • A previously established pathogenic variant record for the same amino-acid change, with an applicable disease context, is not documented.
Sources
PS2 ACMG_2015Not assessed: no germline proband, confirmed maternity and paternity, or documented absence of family history is available for this somatic tumor variant. Details ▾Hide ▴
Reasoning

The available evidence concerns somatic ESR1 p.Tyr537Ser observations in metastatic breast-cancer tumors and provides no germline proband record, no confirmed maternity and paternity, and no documented absence of family history. Therefore, the required de novo evidence for PS2 cannot be assessed.

Rule
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
Evidence considered
  • The available variant-specific literature reports p.Tyr537Ser in metastatic breast-cancer tumors, including tumor-versus-matched-normal sequencing, rather than a germline trio or parental testing.
  • No case evidence documents confirmed maternity, confirmed paternity, or absence of family history.
Still missing
  • Germline testing of the proband is not documented.
  • Maternity and paternity confirmation is not documented.
  • Family-history information is not documented.
Sources
PM1 ACMG_2015Not assessed: Tyr537 is in the ESR1 ligand-binding domain, but domain-wide absence of benign variation required by generic PM1 is not established. Details ▾Hide ▴
Reasoning

ESR1 p.Tyr537Ser lies in the ligand-binding domain, and the literature describes recurrent mutations at Tyr537 and functional importance of this region. However, generic PM1 requires a mutational hotspot and/or critical, well-established functional domain without benign variation. The available evidence does not establish absence of benign variation across the relevant ligand-binding domain, and the cancer-hotspot result is a somatic hotspot record rather than a generic ACMG route that can substitute for the missing domain-level benign-variation evidence. Thus PM1 cannot be assessed as met from the available evidence.

Rule
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
Evidence considered
  • PMID:24185510 places p.Tyr537Ser among ESR1 ligand-binding-domain mutations and reports the variant in metastatic tumors with functional activation.
  • PMID:24185512 describes recurrent ESR1 ligand-binding-domain mutations including Tyr537Ser and functional activity of the variant.
  • PMID:27986707 reports recurrent somatic mutations at Tyr537, including Y537S, Y537C, and Y537N, supporting residue-level recurrence but not domain-wide absence of benign variation.
  • The Cancer Hotspots record reports ESR1 Y537 as a statistically significant somatic hotspot, but the generic rule's required no-benign-variation condition is not resolved by that record.
Still missing
  • A documented critical-domain or hotspot assessment demonstrating no benign variation across the applicable ESR1 region is needed.
Sources
PM3 ACMG_2015Not assessed: tumor reports provide no pathogenic variant in trans or parent/offspring phase testing needed to evaluate PM3. Details ▾Hide ▴
Reasoning

PM3 cannot be assessed because the available evidence concerns somatic ESR1 p.Tyr537Ser observations in metastatic breast tumors and provides no recessive-disease context, pathogenic allele in trans, or parent/offspring phase testing. The study reports tumor sequencing relative to matched normal DNA and transcriptome corroboration, but does not establish allelic phase with another pathogenic variant.

Rule
PM3: For recessive disorders, detected in trans with a pathogenic variant ... Note: This requires testing of parents (or offspring) to determine phase.
Evidence considered
  • PMID:24185510 reports p.Tyr537Ser in metastatic breast-cancer tumors using tumor whole-exome sequencing relative to matched normal DNA and transcriptome corroboration; it provides no report of a pathogenic second allele or phase testing.
  • The available case evidence is somatic oncology evidence and does not establish a recessive ESR1 disease model for applying PM3.
Still missing
  • A defined recessive ESR1 disorder context is not available.
  • No pathogenic second allele is reported.
  • No parent, offspring, or other valid phase testing is reported.
Sources
PM5 ACMG_2015Not assessed: alternate Tyr537 substitutions are reported, but none is documented as a previously determined pathogenic missense comparator. Details ▾Hide ▴
Reasoning

The reviewed evidence identifies alternate missense substitutions at Tyr537, including Y537C and Y537N, but does not establish either alternate as a previously determined pathogenic missense variant under the generic ACMG/AMP framework. Somatic recurrence and functional activity alone do not satisfy the required pathogenic comparator. Therefore PM5 is not assessed.

Rule
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.
Evidence considered
  • PMID:27986707 reports alternate somatic Tyr537 substitutions Y537C and Y537N alongside Y537S, but does not provide a qualifying pathogenic classification for those comparators.
  • PMID:24185512 reports recurrent Tyr537Ser and other ESR1 ligand-binding-domain mutations, but the available extraction does not establish a different pathogenic missense comparator at the same residue.
Still missing
  • A different missense variant at Tyr537 with an established pathogenic classification is not documented.
Sources
PM6 ACMG_2015Not assessed: no germline proband evidence or observation of a de novo variant without parental testing is documented. Details ▾Hide ▴
Reasoning

The available evidence concerns somatic ESR1 p.Tyr537Ser observations in metastatic breast-cancer tumors and provides no germline proband record or evidence that the variant arose de novo without parental testing. PM6 therefore cannot be assessed.

Rule
Assumed de novo, but without confirmation of paternity and maternity.
Evidence considered
  • The available variant-specific literature reports tumor-associated ESR1 p.Tyr537Ser in metastatic breast cancer and does not report a germline de novo observation or parental testing.
  • No case evidence documents that the variant was assumed de novo.
Still missing
  • Germline testing of the proband is not documented.
  • A de novo observation is not documented.
  • Parental testing status is not documented.
Sources
PP2 ACMG_2015Not assessed: gene-level low benign-missense rate and common missense disease mechanism are not established together for generic PP2. Details ▾Hide ▴
Reasoning

The available case evidence documents ESR1 somatic gain-of-function mutations and absence of this variant from gnomAD, but it does not establish both requirements for generic PP2: a low rate of benign missense variation for the gene and missense variation as a common disease mechanism in the applicable disease context. The individual variant's population absence and functional or oncogenic reports cannot substitute for those gene-level prerequisites.

Rule
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
Evidence considered
  • gnomAD v2.1 and v4.1 report the queried variant as absent, which is variant-level evidence and does not quantify ESR1's benign missense rate.
  • PMID:24185510 and PMID:24185512 describe recurrent somatic ESR1 activating mutations, but do not establish the generic PP2 gene-level requirements for the applicable disease context.
Still missing
  • Gene-level evidence quantifying a low rate of benign missense variation is unavailable.
  • Applicable disease-context evidence that missense variants are a common mechanism of disease is unavailable.
Sources
PP4 ACMG_2015Not assessed: no patient-level phenotype or family history is provided to show a highly specific disease with a single genetic etiology. Details ▾Hide ▴
Reasoning

The governing PP4 rule requires the patient's phenotype or family history to be highly specific for a disease with a single genetic etiology. The available case materials identify an ESR1 p.Tyr537Ser somatic cancer variant and literature context involving metastatic ER-positive breast cancer, but they do not provide a patient-level phenotype or family history demonstrating a highly specific single-gene disorder. The criterion therefore cannot be assessed from the available clinical phenotype information.

Rule
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
Evidence considered
  • The case summary identifies a somatic ESR1 p.Tyr537Ser variant and metastatic ER-positive breast-cancer literature context, but does not provide the patient's detailed phenotype or family history.
Still missing
  • Patient-level phenotype and family-history details are not available.
  • A disease context with a demonstrably single genetic etiology is not established for this somatic ESR1 finding.
BS2 ACMG_2015Not assessed: no verified healthy adult carrying the variant, zygosity, inheritance model, and full early-age penetrance information are available. Details ▾Hide ▴
Reasoning

BS2 was not assessed. The available population records show the variant is absent from gnomAD v2.1, gnomAD v4.1, and the reported non-cancer subsets, but they do not provide a verified healthy-adult observation, zygosity, inheritance mode, disease prevalence, or penetrance assessment for ESR1-related disease. Absence from population databases cannot establish or exclude the specific BS2 healthy-adult observation requirement.

Rule
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.
Evidence considered
  • gnomAD v2.1 and v4.1 report the variant as absent; these records do not document a healthy-adult carrier or zygosity.
  • The evidence record also reports absence from gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes; these results likewise do not establish the BS2 observation requirement.
Still missing
  • A verified observation of this variant in a healthy adult with documented zygosity and relevant inheritance model.
  • A defined ESR1-related disorder with expected full penetrance at an early age.
Sources
BS4 ACMG_2015Not assessed: no affected relatives, familial genotypes, or segregation observations are available to demonstrate lack of segregation. Details ▾Hide ▴
Reasoning

No affected family members were evaluated for the variant, and no familial genotypes or phenotypes are available. Consequently, lack of segregation cannot be determined and BS4 is not assessed.

Rule
Lack of segregation in affected members of a family.
Evidence considered
  • The case contains no affected-family segregation data or non-segregation observations.
Still missing
  • No family pedigree is documented.
  • No affected-relative testing is documented.
  • No familial genotype-phenotype comparison is documented.
BP1 ACMG_2015Not assessed: primarily truncating ESR1 disease causation is not established, so the generic BP1 gene-level premise remains unresolved. Details ▾Hide ▴
Reasoning

The available evidence does not establish that ESR1 disease is caused primarily by truncating variants, nor does it provide a validated gene-disease spectrum showing missense variants are generally not the disease mechanism. The reports in this case concern somatic ESR1 missense gain-of-function mutations and cannot establish the generic BP1 gene-level premise.

Rule
Missense variant in a gene for which primarily truncating variants are known to cause disease.
Evidence considered
  • PMID:24185510 and PMID:24185512 report somatic ESR1 missense activating mutations in metastatic breast cancer, but do not establish that the relevant disease is primarily caused by truncating variants.
Still missing
  • A validated gene-disease variant spectrum demonstrating that ESR1 disease is caused primarily by truncating variants is unavailable.
Sources
BP2 ACMG_2015Not assessed: no constitutional cis or trans phase observation with a pathogenic variant is reported for this variant. Details ▾Hide ▴
Reasoning

BP2 cannot be assessed because no affected-proband or family observation documents NM_000125.4:c.1610A>C in trans with a pathogenic variant or in cis with a pathogenic variant. The available literature reports somatic tumor observations and functional studies, not constitutional cis/trans phase relationships.

Rule
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.
Evidence considered
  • PMID:24185510 reports the variant in somatic metastatic breast-cancer tumors and does not report constitutional cis/trans phase with another pathogenic variant.
  • No available case source documents the queried variant in an affected proband with a pathogenic allele in trans or cis.
Still missing
  • No affected-proband or family genotype is reported with a second pathogenic variant.
  • No cis/trans phase result is available.
  • No evidence establishes a fully penetrant dominant ESR1 disorder for the BP2 trans pathway.
Sources
Not applicable · 5· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANot applicable: PVS1 requires a null variant (nonsense, frameshift, canonical splice, start-loss or stop-loss), and this is a missense variant. Details ▾Hide ▴
Reasoning

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_000125.4:c.1610A>C in ESR1 is a missense substitution predicted to produce NP_000116.2:p.(Tyr537Ser). 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 ESR1, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.

Rule
deterministic_prefilter: requires_null_variant_class
Evidence considered
  • Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
  • VCEP criterion policy: absent
Sources
pvs1_generic_framework ↗generic_acmg_combination_rules
PM4 N/ANot applicable: PM4 requires a protein-length change, and this is a missense variant. Details ▾Hide ▴
Reasoning

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_000125.4:c.1610A>C in ESR1 is a missense substitution predicted to produce NP_000116.2:p.(Tyr537Ser). 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 ESR1, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.

Rule
deterministic_prefilter: requires_stop_loss_or_nonrepeat_indel
Evidence considered
  • Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
  • VCEP criterion policy: absent
Sources
pvs1_generic_framework ↗generic_acmg_combination_rules
PP1 N/ANot applicable: no inherited disease pedigree or affected-family segregation is available, and the evidence concerns somatic metastatic breast-cancer tumors. Details ▾Hide ▴
Reasoning

The available evidence is from somatic metastatic breast-cancer studies and includes no affected family members, meioses, or segregation analysis. The case provides no evidence that this variant is being evaluated in a definitively established inherited disease caused by ESR1, so the PP1 applicability condition is not met.

Rule
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.
Evidence considered
  • The reviewed studies describe recurrent ESR1 p.Tyr537Ser in metastatic breast-cancer tumors and functional assays, not familial co-segregation.
  • No affected relatives, informative meioses, or familial genotype-phenotype relationships are reported for this case.
Still missing
  • No affected family members or pedigree are documented.
  • No informative meioses or segregation analysis are documented.
  • A definitive inherited ESR1 disease context is not documented.
Sources
BP3 N/ANot applicable: BP3 requires an in-frame indel in a repeat region, and this is a missense variant. Details ▾Hide ▴
Reasoning

BP3 (Richards et al. 2015, PMID:25741868) applies to in-frame insertions/deletions located in a repetitive region without a known function. NM_000125.4:c.1610A>C in ESR1 is a missense substitution predicted to produce NP_000116.2:p.(Tyr537Ser). 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 ESR1, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.

Rule
deterministic_prefilter: requires_repeat_region_indel
Evidence considered
  • Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
  • VCEP criterion policy: absent
Sources
pvs1_generic_framework ↗generic_acmg_combination_rules
BP7 N/ANot applicable: BP7 requires a synonymous variant, and this is a missense variant. Details ▾Hide ▴
Reasoning

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_000125.4:c.1610A>C in ESR1 is a missense substitution predicted to produce NP_000116.2:p.(Tyr537Ser). 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 ESR1, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.

Rule
deterministic_prefilter: requires_synonymous
Evidence considered
  • Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
  • VCEP criterion policy: absent
Sources
generic_acmg_combination_rules

Identifiers

Gene
ESR1
Transcript
NM_000125.4
Coding (HGVS c.)
NM_000125.4:c.1610A>C
Protein (HGVS p.)
NP_000116.2:p.(Tyr537Ser)
GRCh38
chr6:152098788 A>C
GRCh37
chr6:152419923 A>C
Location and type
Exon 8 · missense
ClinVar
3257895
COSMIC
COSV52783938

Gene diagram

Every interpreted variant in ESR1, mapped onto the exon structure of NM_000125.4. Select a row to find it on the plot.

ESR1NM_000125.4
Fetching transcript structure from UCSC…
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

SpliceAI acceptor lossat -56 bp
0.004
SpliceAI acceptor gainat +134 bp
0.000
SpliceAI donor lossat -356 bp
0.000
SpliceAI donor gainat +132 bp
0.004
Pangolin splice lossmagnitude shown
-0.004
Pangolin splice gain
0.004

Other predictors

REVEL
0.911
BayesDel
0.419

How the predictions were used

PP3 ModerateACMGMet at moderate strength: missense REVEL score 0.911 exceeds the PP3 moderate threshold of 0.773. Details ▾Hide ▴
Reasoning

NM_000125.4:c.1610A>C produces the missense consequence NP_000116.2:p.(Tyr537Ser) in exon 8, so the generic missense path applies: REVEL only. REVEL is 0.911, which reaches the supplied PP3 moderate threshold of >= 0.773 but not the strong threshold of >= 0.932. The SpliceAI max delta of 0.004 and BayesDel score of 0.418913 were not used: SpliceAI is not evidence for a missense PP3 decision, and no generic ACMG-strength calibration is established for BayesDel.

Rule
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only. Its SpliceAI score says nothing about whether the amino-acid substitution is tolerated, so 'no predicted splice impact' is never BP4 support for a missense variant. ... PP3 (moderate): >= 0.773 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
Evidence considered
  • Variant consequence: NM_000125.4:c.1610A>C, NP_000116.2:p.(Tyr537Ser), missense in exon 8; the generic missense REVEL path therefore applies and SpliceAI is not used.
  • Local REVEL lookup: score 0.911.
  • Generic ClinGen SVI REVEL calibration supplied in the governing case instructions: PP3 moderate requires >=0.773 and PP3 strong requires >=0.932; the calibration is attributed to Pejaver et al. 2022, PMID:36413997.
  • BayesDel score 0.418913 was not used because no generic ACMG-strength calibration is established for BayesDel.
Sources
revel
BP4 ACMGNot met: missense REVEL score 0.911 is above the BP4 supporting cutoff of 0.29. Details ▾Hide ▴
Reasoning

NM_000125.4:c.1610A>C produces the missense consequence NP_000116.2:p.(Tyr537Ser), so BP4 must be evaluated on the generic missense REVEL path only. REVEL is 0.911, which is above the supplied BP4 supporting cutoff of <= 0.29 and therefore does not support no impact. The SpliceAI max delta of 0.004 was not substituted because a splice prediction cannot establish BP4 for a missense amino-acid substitution; BayesDel was not used because no generic ACMG-strength calibration is established.

Rule
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) ... Missense variant -> REVEL only. Its SpliceAI score says nothing about whether the amino-acid substitution is tolerated, so 'no predicted splice impact' is never BP4 support for a missense variant. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
Evidence considered
  • Variant consequence: NM_000125.4:c.1610A>C, NP_000116.2:p.(Tyr537Ser), missense in exon 8; the generic missense REVEL path applies and SpliceAI is not used.
  • Local REVEL lookup: score 0.911.
  • Generic ClinGen SVI REVEL calibration supplied in the governing case instructions: BP4 supporting requires <=0.29; the calibration is attributed to Pejaver et al. 2022, PMID:36413997.
  • BayesDel score 0.418913 was not used because no generic ACMG-strength calibration is established for BayesDel.
Sources
revel
BP7 N/ANot applicable: BP7 requires a synonymous variant, and this is a missense variant. Details ▾Hide ▴
Reasoning

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_000125.4:c.1610A>C in ESR1 is a missense substitution predicted to produce NP_000116.2:p.(Tyr537Ser). 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 ESR1, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.

Rule
deterministic_prefilter: requires_synonymous
Evidence considered
  • Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
  • VCEP criterion policy: absent
Sources
generic_acmg_combination_rules

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.911. BayesDel score = 0.418913.

7 paper records listed. 4 cited in the classification.

Cited in the classification

  • Mutations of tyrosine 537 in the human estrogen receptor-alpha selectively alter the receptor's affinity for estradiol and the kinetics of the interaction.
    The paper experimentally studied ESR1 Y537S and the alternate same-residue substitution Y537F in recombinant receptor assays. It characterized altered ligand-binding kinetics and local conformational effects near residue 537, but did not establish Y537F as a pathogenic clinical variant.
    → PS3 · strong Names this variant
    PMID 11914066 ↗
    Source detail
    The hormone-binding affinities of the wt ER, the Y537F, and the Y537S mutant did not differ.

    Location Results, Equilibrium Binding of [3H]E2 to the wt and Y537 Mutant ERs; Tables 1 and 2; Molecular Modeling of the wt and Mutant ERs

    Context Site-directed mutagenesis of human ESR1 cDNA; recombinant wild-type and mutant estrogen receptors expressed in Sf9 insect cells; estradiol equilibrium-binding and dissociation assays; molecular modeling of the ligand-binding domain.

  • Activating ESR1 mutations in hormone-resistant metastatic breast cancer.
    Robinson DR et al. · 2013 Dec
    The paper explicitly reports ESR1 p.Tyr537Ser in the ligand-binding domain, observed in three patients with ER-positive metastatic breast cancer. Tumor sequencing was corroborated by transcriptome sequencing, and functional assays showed constitutive transcriptional activation.
    → PS3 · strong Names this variant
    PMID 24185510 ↗
    Source detail
    The six index patients MO_1031, MO_1051, MO_1069, MO_1129, MO_1167 and MO_1185 had mutations encoding p.Leu536Gln, p.Tyr537Ser, p.Asp538Gly, p.Tyr537Ser, p.Asp538Gly and p.Tyr537Ser alterations in the LBD, respectively.

    Location Results, paragraph describing the six index patients with ESR1 ligand-binding-domain mutations

    Context Six-patient ER-positive metastatic breast cancer sequencing cohort; tumor versus matched-normal whole-exome sequencing corroborated by whole-transcriptome sequencing; HEK293T ERE-luciferase functional assays.

  • ESR1 ligand-binding domain mutations in hormone-resistant breast cancer.
    Toy W et al. · 2013 Dec
    The paper explicitly studied ESR1 p.Tyr537Ser and reports recurrent ligand-binding-domain mutations in metastatic ER-positive breast cancer. Y537S showed strong ligand-independent receptor activity and promoted tumor growth after estrogen withdrawal in model systems.
    → PS3 · strong Names this variant
    PMID 24185512 ↗
    Source detail
    Mutation of Tyr537 to serine was previously demonstrated to promote the ER agonist conformation and activation of its transcriptional functions14,15.

    Location Results, “ERα LBD mutations promote estrogen-independent receptor activation” and Discussion

    Context Targeted sequencing of metastatic ER-positive breast-cancer samples; ESR1 reporter assays in SKBR3 and MCF7 cells; ER target-gene and phosphorylation assays; MCF7 xenograft estrogen-withdrawal model.

  • Estrogen receptor alpha somatic mutations Y537S and D538G confer breast cancer endocrine resistance by stabilizing the activating function-2 binding conformation.
    The paper studied ERalpha Y537S using purified ligand-binding-domain assays and structural methods. Y537S recruited SRC3 in the absence of estradiol with Kd 13.6 +/- 2.0 nM, whereas wild-type ERalpha showed no apo coactivator recruitment; additional binding and structural results supported constitutive activity and reduced antagonist effectiveness.
    → PS3 · strong Does not name this variant
    PMID 26836308 ↗
    Source detail
    In contrast, the SRC3 NRD bound to Y537S and D538G ERa in the absence of E2, with affinities of 13.6 +/- 2.0 nM and 151 +/- 20 nM, respectively

    Location Results, "Y537S and D538G promote constitutive coactivator binding to ERalpha"; Table 1; ligand-binding and structural analyses

    Context Purified ERalpha ligand-binding-domain tr-FRET SRC3 coactivator-binding assays; radioligand estradiol and 4-hydroxytamoxifen binding; hydrogen/deuterium exchange mass spectrometry; X-ray crystallography; molecular dynamics.

Other recorded publications

  • Activating ESR1 Mutations Differentially Affect the Efficacy of ER Antagonists.
    The paper reports recurrent somatic ESR1 ligand-binding-domain mutations at Tyr537, including Y537S, Y537C, and Y537N, with Y537S showing strong constitutive activity in cellular and model-system assays.
    Names this variant
    PMID 27986707 ↗
    Quoted passage
    Among the most frequent mutations in this series were D538G (n=34), Y537S (n=13), E380Q (n=20), Y537C (n=6), Y537N (n=5), and L536H (n=4).

    Results, “Novel ESR1 LBD mutations in hormone-resistant breast cancer patients”

  • Efficacy of SERD/SERM Hybrid-CDK4/6 Inhibitor Combinations in Models of Endocrine Therapy-Resistant Breast Cancer.
    Wardell SE et al. · 2015
    No paper-specific finding is recorded.
    PMID 25991817 ↗
  • Systematic Functional Annotation of Somatic Mutations in Cancer.
    Ng PK et al. · 2018
    No paper-specific finding is recorded.
    PMID 29533785 ↗

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

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

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 = 3257895)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.911. BayesDel score = 0.418913.

Functional

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

Somatic

This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV52783938, n = 98 times).

Cancer Hotspots

This variant lies in a statistically significant hotspot.