NM_023067.4:c.469C>G

FOXL2 · NP_075555.1:p.(Pro157Ala) · NM_023067.4

GRCh37: chr3:138665096 G>C · GRCh38: chr3:138946254 G>C

Gene: FOXL2 Transcript: NM_023067.4

Final call

VUS

PM1 supporting PM2 supporting BP4 supporting benign

Variant details

Gene

FOXL2

Transcript

NM_023067.4

Protein

NP_075555.1:p.(Pro157Ala)

gnomAD AF

5.66166636680804e-06 (v4.1)

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_023067.4:c.469C>G (p.Pro157Ala) is a missense variant in the forkhead DNA-binding domain of FOXL2.

This variant is extremely rare in population databases (gnomAD v2.1: 1/203,794 alleles, AF=4.9e-06; v4.1: 9/1,589,638 alleles, AF=5.66e-06), meeting PM2 at supporting strength.

Pro157 resides within the forkhead domain, a critical and well-established functional domain required for FOXL2 DNA-binding and transcriptional activity, meeting PM1 at supporting strength.

Multiple computational predictors do not support a deleterious effect: REVEL score 0.291 (below pathogenic threshold), BayesDel score -0.188 (predicted benign), and SpliceAI max delta 0.00, meeting BP4 at supporting benign strength.

This variant has been observed in somatic cancers (COSMIC: n=6) but lacks germline pathogenicity evidence. It is absent from ClinVar and no publications have directly characterized p.Pro157Ala.

The evidence profile includes two pathogenic supporting criteria (PM1, PM2) and one benign supporting criterion (BP4), resulting in an indeterminate classification (Variant of Uncertain Significance) under the generic ACMG/AMP 2015 framework.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

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	Missense variant (p.Pro157Ala); does not fall into null-variant buckets (nonsense, frameshift, or canonical ±1,2 splice consensus). Not eligible for PVS1 under ClinGen SVI PVS1 decision tree (PMC6185798).	pvs1_variant_assessment pvs1_generic_framework
PS1	Not met	No previously established pathogenic variant at this amino acid position (Pro157) has been identified in ClinVar or the literature.	clinvar
PS2	Not met	No de novo occurrence data available for this variant. No parental testing or trio sequencing results in the case record or literature.
PS3	Not met	No variant-specific functional studies identified. OncoKB reports Unknown Oncogenic Effect with no curated functional evidence. Literature search returned no publications evaluating the functional impact of p.Pro157Ala. COSMIC somatic occurrence (n=6) does not constitute functional evidence.	oncokb
PS4	Not met	No case-control or prevalence data comparing affected individuals to controls for this variant is available.
PS5	Not met	No well-established, validated functional assay demonstrating a pathogenic effect for this variant is available in a clinical diagnostic setting.
PM1	Met	Located at codon 157 within the forkhead DNA-binding domain of FOXL2 (approximately residues 152–256), a critical and well-established functional domain required for transcription factor activity. Population data show extreme constraint (gnomAD AF ~5e-06), consistent with absence of benign variation in this domain. Residue-specific hotspot not identified at cancerhotspots.org, but domain-level application is supported.	gnomad_v2 gnomad_v4
PM2	Met	Extremely low allele frequency in population databases, well below the 0.1% PM2 threshold. gnomAD v2.1: 1/203,794 alleles (AF=4.9e-06); gnomAD v4.1: 9/1,589,638 alleles (AF=5.66e-06); absent from gnomAD-Canada v1.0. No homozygotes observed.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	No pathogenic missense variant at the same codon (Pro157) identified in ClinVar or literature. PM5 candidate harvesting returned no eligible comparators.	pm5_candidates clinvar
PM6	Not met	No de novo status confirmed for this variant. No trio data or de novo reports available.
PP1	Not met	No co-segregation data available for this variant. No family studies identified.
PP2	Not assessed	FOXL2 missense variants are a known mechanism for blepharophimosis, ptosis, and epicanthus inversus syndrome (BPES) and premature ovarian insufficiency. However, gene-level missense constraint metrics (e.g., Z-score, gnomAD missense o/e) were not retrieved. Cannot definitively apply PP2 without quantitative constraint data.
PP3	Not met	Multiple computational predictors do not support a deleterious effect. REVEL score 0.291 (below typical pathogenic threshold of 0.5). BayesDel score -0.188 (negative, predicting benign). SpliceAI max delta 0.00 (no splicing impact). No HCI prior score available for FOXL2.	revel bayesdel spliceai
PP4	Not met	No patient phenotype or family history data available in the case record to evaluate phenotype specificity for FOXL2-related disorders.
PP5	Not met	This variant is absent from ClinVar; no reputable source has classified it as pathogenic.	clinvar
BA1	Not met	gnomAD allele frequency is far below the 1% BA1 threshold. v2.1 AF=4.9e-06, v4.1 AF=5.66e-06.	gnomad_v2 gnomad_v4
BS1	Not met	gnomAD allele frequency is far below the 0.3% BS1 threshold. v2.1 AF=4.9e-06, v4.1 AF=5.66e-06.	gnomad_v2 gnomad_v4
BS2	Not met	No evidence of this variant being observed in healthy adults with complete penetrance for a dominant disorder. gnomAD carriers lack phenotype annotation.
BS3	Not met	No well-established functional studies demonstrating no damaging effect for this variant. No functional data available in OncoKB or the literature.
BS4	Not met	No segregation data available to evaluate lack of segregation with disease.
BP1	Not met	FOXL2-related disease (BPES, POI) is known to be caused by missense variants; this is not a gene where only truncating variants cause disease.
BP2	Not met	No evidence of this variant observed in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant for a recessive disorder.
BP4	Met	Multiple lines of computational evidence suggest no significant impact. REVEL score 0.291 (below 0.5 pathogenic threshold), BayesDel score -0.188 (predicted benign), and SpliceAI max delta 0.00 (no splicing impact). HCI prior not available.	revel bayesdel spliceai
BP5	Not met	No alternate molecular basis for disease has been identified in the case record.
BP6	Not met	This variant is absent from ClinVar; no reputable source has classified it as benign.	clinvar
BP7	N/A	Missense variant (c.469C>G, p.Pro157Ala), not synonymous or intronic. BP7 is reserved for synonymous variants without splice impact.	spliceai
BP3	N/A	Skipped: variant is a substitution, not an in-frame indel in a non-repetitive region.
PM3	N/A	Skipped: FOXL2-related disorders are autosomal dominant; PM3 is for recessive disorders.
PM4	N/A	Skipped: variant is a substitution, not a protein-length-altering change (indel/stop-loss).

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.