NM_023067.4:c.402C>G

FOXL2 · NP_075555.1:p.(Cys134Trp) · NM_023067.4

GRCh37: chr3:138665163 G>C · GRCh38: chr3:138946321 G>C

Gene: FOXL2 Transcript: NM_023067.4

Final call

Likely Pathogenic

PS3 supporting PM1 moderate PM2 moderate PP3 supporting

Variant details

Gene

FOXL2

Transcript

NM_023067.4

Protein

NP_075555.1:p.(Cys134Trp)

gnomAD AF

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_023067.4:c.402C>G (p.Cys134Trp) in FOXL2 is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada v1.0.

The variant alters codon 134 in the forkhead DNA-binding domain wing 2 region, a statistically significant mutational hotspot with 901 somatic occurrences in COSMIC (COSV57725321).

Functional studies in KGN granulosa cell tumor cells demonstrate that C134W mutant FOXL2 fails to upregulate GnRH receptor expression and fails to enhance GnRH-induced apoptosis, whereas wild-type FOXL2 performs both functions, consistent with a loss-of-function effect (PMID:23372819).

REVEL in silico prediction score of 0.884 supports a deleterious effect on protein function.

Applying generic ACMG/AMP 2015 final classification combination rules (PMID:25741868): two moderate criteria (PM1, PM2) and two supporting criteria (PS3, PP3) are met, consistent with a Likely Pathogenic classification.

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 variant (p.Cys134Trp). It does not fall into the default generic PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants per ClinGen SVI PVS1 recommendations (PMC6185798).	pvs1_generic_framework
PS1	N/A	Only one nucleotide substitution (c.402C>G, TGT→TGG) can produce the p.Cys134Trp amino acid change at codon 134. No alternative nucleotide change at this codon yields the same amino acid, precluding a PS1 comparison.
PS2	Not met	No de novo observation of NM_023067.4:c.402C>G with confirmed paternity and maternity was identified in any reviewed publication.
PS3	Met	Functional studies in KGN granulosa cell tumor cells (PMID:23372819) demonstrate that wild-type FOXL2 upregulates GnRH receptor expression and enhances GnRH-induced apoptosis, whereas C134W mutant FOXL2 does not, consistent with a loss-of-function effect. This is a single well-controlled in vitro study in a somatic cell context; applied at supporting strength for germline interpretation.	PMID:23372819
PS4	Not met	No case-control data comparing variant prevalence in germline-affected individuals versus unaffected controls is available. The variant is a known somatic driver in ~97% of adult granulosa cell tumors, but this does not constitute germline case-control evidence.
PS5	Not met	No data on trans configuration with a known pathogenic variant. FOXL2-associated disorders (BPES) are autosomal dominant, and no second pathogenic variant was identified.
PM1	Met	The p.Cys134Trp alteration lies within the forkhead DNA-binding domain wing 2 region, a statistically significant mutational hotspot (cancerhotspots.org) with 901 somatic occurrences in COSMIC (COSV57725321). The C134 residue is critical for FOXL2 protein-protein interactions and transcriptional regulatory function.	PMID:23372819
PM2	Met	This variant is absent from all population databases: gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 (allele frequency 0.0%). This absence from large population cohorts is consistent with a rare pathogenic variant.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	No same-residue missense comparator variants with established pathogenicity were identified; automatic PM5 candidate harvesting could not confirm classic PM5 semantics for this residue.
PM6	Not met	No de novo observation of this variant has been reported, with or without confirmation of paternity and maternity.
PP1	Not met	No co-segregation data is available for this variant in any family.
PP2	Not assessed	HCI prior score is not available for FOXL2, and a formal assessment of the gene's rate of benign missense variation versus pathogenic missense variation cannot be made per the generic ACMG/AMP framework without this data.
PP3	Met	REVEL score of 0.884 predicts a deleterious effect on protein function. BayesDel score of 0.353 is below typical pathogenicity thresholds, and SpliceAI delta score is 0.00 (no splicing impact). The high REVEL score provides one line of in silico evidence supporting a deleterious effect.	revel bayesdel spliceai
PP4	Not met	No patient phenotype or clinical data were provided for this assessment. PP4 requires that the patient's phenotype or family history is highly specific for a disease with a single genetic etiology.
PP5	Not assessed	No reputable source (e.g., clinical diagnostic laboratory) has reported this variant as pathogenic with evidence that is unavailable for independent review. OncoKB classification of Likely Oncogenic is a somatic cancer annotation and does not satisfy PP5 for germline interpretation.
BA1	Not met	This variant is absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada v1.0; allele frequency 0.0%). Does not meet the BA1 threshold of >1% allele frequency.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	This variant is absent from population databases (allele frequency 0.0%). Does not meet the BS1 threshold of >0.3% allele frequency.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	No observation of this variant in a healthy adult individual has been reported for a disorder expected to be fully penetrant. The variant is absent from population databases altogether.
BS3	Not met	The available functional study (PMID:23372819) demonstrates a damaging effect for the C134W mutant (loss of GnRHR upregulation and failure to enhance GnRH-induced apoptosis), which is inconsistent with a benign functional assessment.	PMID:23372819
BS4	Not met	No segregation data is available to assess lack of co-segregation with disease.
BP1	Not met	FOXL2 is associated with blepharophimosis, ptosis, and epicanthus inversus syndrome (BPES) via both truncating and missense germline variants, with over 100 germline variants described. Missense variants are a well-established pathogenic mechanism in this gene, so BP1 does not apply.
BP2	Not met	No observation of this variant in trans with a fully penetrant dominant pathogenic variant has been reported.
BP4	Not met	REVEL score of 0.884 predicts a deleterious effect, contradicting the BP4 requirement that multiple lines of computational evidence suggest no impact. BayesDel (0.353) is inconclusive, and SpliceAI (0.00) shows no splicing effect, but the high REVEL score precludes application of BP4.	revel bayesdel spliceai
BP5	Not met	No observation of this variant in a case with an alternate molecular cause for disease has been reported.
BP6	Not met	No reputable source reports this variant as benign. The variant is absent from ClinVar and no clinical laboratory has classified it as benign.
BP7	N/A	This is a missense variant (c.402C>G, p.Cys134Trp). BP7 applies only to synonymous variants with no predicted splicing impact.
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions; not applicable to a single-nucleotide substitution.
PM3	N/A	PM3 applies to recessive disorders where a pathogenic variant is detected in trans; FOXL2-associated disorders (BPES) are autosomal dominant.
PM4	N/A	PM4 applies to protein length changes from in-frame indels or stop-loss variants; not applicable to a single-nucleotide missense substitution.

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