Variant classification summary

NM_001122740.1:c.1613A>G

ESR1 · NP_001116212.1:p.(Asp538Gly) · NM_001122740.1

GRCh37: chr6:152419926 A>G · GRCh38: chr6:152098791 A>G

Gene: ESR1 Transcript: NM_001122740.1

Final call

Likely Pathogenic

PS3 strong PM1 moderate PM2 moderate PP3 supporting

Variant details

Gene

ESR1

Transcript

NM_001122740.1

Protein

NP_001116212.1:p.(Asp538Gly)

gnomAD AF

ClinVar

Oncogenic

OncoKB

Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_001122740.1:c.1613A>G (p.Asp538Gly) in ESR1 is a missense variant in exon 9 encoding a substitution in helix 12 of the ligand-binding domain.

2

This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases, satisfying PM2 (moderate).

3

The variant is located at a statistically significant mutational hotspot within helix 12 of the ESR1 ligand-binding domain, a critical functional domain, satisfying PM1 (moderate).

4

Multiple independent functional studies demonstrate that p.Asp538Gly confers constitutive, ligand-independent transcriptional activity, promotes coactivator recruitment in the absence of estrogen, and confers resistance to antiestrogen therapies. Evidence includes luciferase reporter assays, co-immunoprecipitation, X-ray crystallography, HDX-MS, and cell proliferation assays across multiple laboratories, satisfying PS3 (strong).

5

The REVEL meta-predictor score of 0.914 supports a deleterious effect, satisfying PP3 (supporting).

6

Caveat: all functional evidence derives from somatic cancer studies of acquired endocrine resistance; no germline-specific functional or clinical evidence is available. The variant has not been reported as a germline pathogenic variant. Classification should be interpreted with the understanding that this variant's clinical significance in a germline context is uncertain.

7

PVS1 is not applicable as this is a missense variant. PS1, PS2, PS4, PS5, PM5, PM6, PP1, PP4, PP5, BA1, BS1, BS2, BS3, BS4, BP1, BP2, BP4, BP5, BP6, and BP7 are not met or not applicable.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Pathogenic classification based on the observed combination of pathogenic criteria.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	This is a missense substitution (NM_001122740.1:c.1613A>G; p.Asp538Gly). PVS1 requires a null variant (nonsense, frameshift, canonical ±1,2 splice site, initiation codon, or exon deletion). This variant does not fall into any PVS1 null-variant bucket per the ClinGen SVI PVS1 decision tree (PMC6185798).	pvs1_generic_framework
PS1	Not met	No prior germline pathogenic or likely pathogenic classification exists for p.Asp538Gly in ClinVar or the literature. The ClinVar entry (VariationID 3764845) is classified as 'Oncogenic' in a somatic context only, which does not satisfy the PS1 requirement for a germline pathogenic assertion at the same amino acid change.	clinvar
PS2	N/A	No de novo data are available for this variant. All documented occurrences are in somatic tumor samples (metastatic breast and endometrial cancers), not in germline de novo contexts.
PS3	Met	Well-established functional studies from multiple independent research groups consistently demonstrate that p.Asp538Gly (D538G) confers constitutive, ligand-independent transcriptional activity of ESR1, promotes coactivator recruitment in the absence of estrogen, and confers resistance to antiestrogen therapies. Evidence includes luciferase reporter assays in MCF-7, MDA-MB-231, and HEK293T cells (PMIDs: 24185510, 24185512, 24217577), X-ray crystallography and hydrogen-deuterium exchange mass spectrometry demonstrating stabilized agonist conformation of helix 12 (PMID: 26836308), co-immunoprecipitation showing constitutive SRC-1 binding (PMID: 24217577), and CRISPR/Cas9-engineered heterozygous D538G endometrial cancer cell models (PMID: 31362937). The functional data are replicated across five independent laboratories and multiple orthogonal assays. Caveat: all functional evidence derives from somatic cancer studies; germline-specific functional data are not available.	PMID:24185510 PMID:24185512 PMID:24217577 PMID:24398047 PMID:26836308 PMID:31362937 oncokb
PS4	Not met	No germline case-control data are available. The variant has been observed 162 times in COSMIC (somatic cancers), but these are tumor-acquired mutations and do not constitute germline case-control prevalence evidence for PS4.
PS5	N/A	PS5 is not a defined criterion in the generic ACMG/AMP 2015 framework (Richards et al., PMID:25741868). This criterion does not exist in the standard ACMG/AMP classification schema.	generic_acmg_combination_rules
PM1	Met	p.Asp538 is located in helix 12 of the ESR1 ligand-binding domain (LBD), a critical functional domain governing receptor activation and coactivator recruitment. The residue lies within a statistically significant mutational hotspot (cancerhotspots.org). Multiple structural studies confirm that D538G alters the conformation of helix 12, and the residue is part of a well-characterized cluster of gain-of-function somatic mutations (Y537S, Y537N, Y537C, D538G) that constitutively activate ESR1.	PMID:26836308 PMID:24217577 PMID:24185512
PM2	Met	This variant is absent from all population databases, including gnomAD v2.1 (exomes), gnomAD v4.1 (exomes/genomes), and gnomAD-Canada v1.0 (genomes). Under non-VCEP generic ACMG guidance, PM2 is applied when allele frequency is below 0.1% in population databases.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	The pm5_candidates automated assessment was unable to confirm classic same-residue PM5 semantics. No comparator missense variants at residue 538 with a confirmed germline pathogenic classification were identified for PM5 evaluation.	pm5_candidates
PM6	N/A	No de novo observation data are available for this variant. All documented occurrences are somatic, acquired mutations in tumor tissue.
PP1	N/A	No family segregation data are available. This variant has only been documented as a somatic, acquired mutation in tumor samples, not in family-based germline studies.
PP2	Not assessed	PP2 requires gene-specific calibration (low rate of benign missense variation where missense variants are a common disease mechanism). No CSPEC/VCEP framework or HCI prior score is available for ESR1 to establish whether PP2 applies in a germline context. The variant is a well-established gain-of-function somatic mutation, but germline missense constraint data are absent.
PP3	Met	The REVEL meta-predictor score of 0.914 strongly supports a deleterious effect. SpliceAI predicts no splicing impact (max delta score = 0.00). BayesDel score of 0.346 is below typical pathogenicity thresholds. While BayesDel does not reach the damaging threshold, REVEL (which integrates multiple individual predictors including conservation, evolutionary, and protein-level features) strongly supports a deleterious effect, satisfying PP3 at supporting level.	revel bayesdel spliceai
PP4	Not assessed	No patient phenotype or clinical history is available for the proband. PP4 requires evaluation of whether the patient's phenotype or family history is highly specific for a disease with a single genetic etiology. Without clinical data, this criterion cannot be assessed.
PP5	Not met	No reputable source has reported this variant as germline pathogenic or likely pathogenic. The ClinVar entry (VariationID 3764845) is classified as 'Oncogenic' in the somatic context only, which does not constitute a germline pathogenic assertion for PP5.	clinvar
BA1	Not met	The variant is absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada). Under non-VCEP generic ACMG guidance, BA1 requires an allele frequency >1%. The observed frequency of 0% does not meet this threshold.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	The variant is absent from all population databases. Under non-VCEP generic ACMG guidance, BS1 requires an allele frequency >0.3%. The observed frequency of 0% does not meet this threshold.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	N/A	No data are available regarding observation of this variant in healthy adult individuals for a fully penetrant dominant disorder. The variant is absent from gnomAD and has only been observed as a somatic mutation in tumor tissue.
BS3	Not met	Multiple well-established functional studies (see PS3) demonstrate that p.Asp538Gly is a gain-of-function mutation conferring constitutive ligand-independent transcriptional activity and antiestrogen resistance. These studies do not show a benign or neutral effect; rather, they consistently demonstrate a damaging functional alteration.	PMID:24185510 PMID:24185512 PMID:24217577 PMID:26836308
BS4	N/A	No family segregation data are available. This variant has only been documented as a somatic acquired mutation; no germline family studies exist.
BP1	N/A	BP1 applies when a missense variant occurs in a gene for which primarily truncating variants are known to cause disease. No CSPEC/VCEP framework defines BP1 for ESR1. The ESR1 germline disease mechanism is not established as exclusively truncating; regulatory variants and missense mutations may also contribute to disease predisposition per the available literature.
BP2	N/A	No data are available regarding observation of this variant in trans with a pathogenic variant for a fully penetrant dominant disorder.
BP4	Not met	BP4 requires multiple lines of computational evidence suggesting no impact on the gene or gene product. The REVEL meta-predictor score of 0.914 strongly supports a deleterious effect, contradicting BP4. SpliceAI is neutral (max delta = 0.00). BP4 is not satisfied because the strongest computational evidence points toward pathogenicity.	revel spliceai bayesdel
BP5	N/A	No data are available regarding observation of this variant in a case with an alternate molecular basis for disease. No proband clinical data or genetic workup results are available.
BP6	N/A	No reputable source has reported this variant as benign. BP6 cannot be applied without a benign assertion from a trusted source.
BP7	N/A	BP7 applies to synonymous (silent) variants for which splicing prediction algorithms predict no impact. This is a missense variant (p.Asp538Gly), not a synonymous variant.

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