FGFR2 c.758C>G, p.Pro253Arg

Reasoning

The variant is NM_000141.5:c.758C>G, p.Pro253Arg. This same amino-acid change is previously established as pathogenic in ClinVar and is explicitly reported in the functional and clinical literature. The rule does not require a different nucleotide change; it states that the same amino-acid change qualifies regardless of nucleotide change. The reported effect is protein-level rather than a splice effect: SpliceAI max delta score is 0.001.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.

Evidence considered

• ClinVar variation 13273 identifies the exact NM_000141.5(FGFR2):c.758C>G (p.Pro253Arg) variant and reports Pathogenic/Likely pathogenic classifications.
• Ibrahimi et al. explicitly studied FGFR2 Pro253Arg, corresponding to the case variant; this is the same nucleotide/amino-acid variant, not a different nucleotide change yielding the same amino-acid substitution.
• The prenatal case report explicitly reports heterozygous FGFR2 c.758C>G (CCT>CGT), p.Pro253Arg.
• SpliceAI max delta score is 0.001, providing no significant predicted splice impact.

Sources

Reasoning

PS3 is met at moderate strength. PMID:11390973 directly studied FGFR2 p.Pro253Arg, corresponding to NM_000141.5:c.758C>G, using X-ray crystallography of wild-type and mutant FGFR2(IIIc)-FGF2 complexes, with the mutant structure refined to 2.3 Å. Arg253 formed three additional hydrogen bonds with FGF2, and the paper cited biochemical data showing an approximately 1.5-fold decrease in the FGF2 dissociation rate relative to wild type, supporting increased ligand-receptor affinity and an activating damaging effect. The exact variant, wild-type comparator, structural assay, and biochemical functional readout support PS3; moderate rather than strong strength is used because the available evidence is from a published research study and does not document validation and reproducibility in a clinical diagnostic laboratory setting.

Rule

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.

Evidence considered

• Structural basis for fibroblast growth factor receptor 2 activation in Apert syndrome, Results subsection ‘FGF2 in Complex with Pro253Arg Mutant FGFR2’ and Discussion subsection ‘Implications for Ligand Binding’: the exact p.Pro253Arg variant was studied in FGFR2(IIIc)-FGF2 complexes; Arg253 made three additional hydrogen bonds with FGF2.
• The same study reports a Pro253Arg structure refined to 2.3 Å and cites prior biochemical measurements showing an approximately 1.5-fold decrease in FGF2 dissociation rate relative to wild-type FGFR2.
• The ACMG/AMP functional criterion definition was applied to the exact variant-specific structural and biochemical evidence.

Still missing

• No independent clinical-diagnostic-laboratory validation and reproducibility data were identified for the exact functional assay evidence.

Sources

Reasoning

PM2 is met at supporting strength. NM_000141.5:c.758C>G (FGFR2 p.Pro253Arg) is absent from gnomAD v2.1 and gnomAD v4.1, and the non-cancer subsets are also reported absent. This is below the supplied generic PM2 threshold of <=0.0001 and supports rarity in reference populations; no VCEP-specific population source rule applies.

Rule

Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium. ... PM2 (supporting): <= 0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868)

Evidence considered

• gnomAD v2.1 (exome, GRCh37): variant absent.
• gnomAD v4.1 (exome, GRCh38): variant absent.
• GNOMAD_V2_1_NON_CANCER and GNOMAD_V3_1_NON_CANCER were also reported absent; no non-cancer allele frequency was available.
• Generic calibration supplied in the governing instructions: PM2 supporting threshold <=0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868).

Sources

Reasoning

PMID:23915865 reports the exact heterozygous FGFR2 c.758C>G (p.Pro253Arg) variant in a fetus with Apert syndrome and states that molecular testing of both parents did not detect the variant. Because parental testing supports de novo occurrence but confirmed maternity and paternity are not documented, this meets PM6 rather than PS2.

Rule

Assumed de novo, but without confirmation of paternity and maternity.

Evidence considered

• PMID:23915865 explicitly reports heterozygous FGFR2 c.758C>G (CCT>CGT), p.Pro253Arg, in a fetus diagnosed with Apert syndrome; testing of both parents did not detect the variant and the authors described it as de novo.
• The available report does not document confirmed maternity or paternity, which is why the evidence is assigned to PM6 rather than PS2.

Sources

Reasoning

The variant is a missense substitution, NM_000141.5:c.758C>G (p.Pro253Arg), so the generic missense path uses REVEL only. REVEL is 0.724, which meets the generic PP3 supporting threshold of >= 0.644. SpliceAI is not used for PP3 in this missense situation, and BayesDel is not available for generic ACMG/AMP strength assignment.

Rule

PP3: Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... Missense variant -> REVEL only. ... PP3 (supporting): >= 0.644 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• NM_000141.5:c.758C>G is an exonic missense variant producing p.Pro253Arg in FGFR2; the applicable generic computational path is REVEL only.
• Local REVEL lookup reports a score of 0.724 for this variant.
• The supplied ClinGen SVI REVEL calibration assigns PP3 supporting at >= 0.644 (Pejaver et al. 2022, Am J Hum Genet, PMID:36413997); 0.724 meets that threshold.
• The available SpliceAI max delta score of 0.001 was not used because splice prediction is not the applicable path for a missense variant; BayesDel has no established generic ACMG-strength calibration in the supplied rules.

Sources

Reasoning

The exact variant is reported in a fetus with Apert syndrome and its characteristic craniosynostosis-related craniofacial abnormalities and bilateral syndactyly of the hands and feet. PMID:23915865 directly identifies NM_000141.5:c.758C>G (p.Pro253Arg) in that affected fetus and reports frontal bossing, midface hypoplasia, hypertelorism, and bilateral syndactyly. PMID:11390973 describes Apert syndrome as craniosynostosis with severe syndactyly and identifies Pro253Arg as one of the recurrent activating FGFR2 substitutions accounting for nearly all known Apert syndrome cases. This phenotype is highly specific for the disease under the generic PP4 definition.

Rule

Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.

Evidence considered

• PMID:23915865 reports heterozygous FGFR2 c.758C>G (p.Pro253Arg) in a female fetus with Apert syndrome, frontal bossing, midface hypoplasia, hypertelorism, and bilateral syndactyly of the hands and feet; parental testing did not detect the variant.
• PMID:11390973 describes Apert syndrome as craniosynostosis with severe syndactyly and identifies FGFR2 Pro253Arg among the two activating substitutions associated with nearly all known Apert syndrome cases.

Sources

Reasoning

The governing rule concerns a reputable pathogenic report whose underlying evidence is unavailable for independent evaluation. Under the supplied generic PP5 instruction, application requires an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic. ClinVar variation 13273 exactly matches NM_000141.5:c.758C>G (p.Pro253Arg), but the audited record contains zero expert-panel submissions; its pathogenic and likely pathogenic assertions are ordinary laboratory or other non-expert submissions. They therefore cannot trigger PP5.

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 13273 exactly matches NM_000141.5(FGFR2):c.758C>G (p.Pro253Arg), but the record reports 0 expert-panel submissions and only individual or other non-expert submissions, including 21 Pathogenic and 1 Likely pathogenic laboratory assertions.

Sources

Reasoning

BA1 is not met. NM_000141.5:c.758C>G (FGFR2 p.Pro253Arg) is absent from gnomAD v2.1 and gnomAD v4.1, so no filtering allele frequency or grpmax FAF reaches the generic stand-alone threshold of >=0.05. The non-cancer subsets are also reported absent, and no VCEP-specific population source rule applies because no VCEP covers FGFR2.

Rule

Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v2.1 (GRCh37, 10-123279674-G-C): absent; no allele count, allele number, AF, FAF, or homozygote count was reported.
• gnomAD v4.1 (GRCh38, 10-121520160-G-C): absent; no allele count, allele number, AF, FAF, or homozygote count was reported.
• GNOMAD_V2_1_NON_CANCER and GNOMAD_V3_1_NON_CANCER were also reported absent; no non-cancer frequency was available to exceed the threshold.
• Generic calibration supplied in the governing instructions: BA1 stand-alone threshold >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868).

Sources

Reasoning

BS1 is not met. The variant is absent from gnomAD v2.1 and gnomAD v4.1, so no filtering allele frequency or grpmax FAF is greater than the generic default threshold of >=0.01. Because there is no elevated frequency to interpret, a maximum-credible-allele-frequency calculation incorporating disease prevalence, penetrance, and allelic heterogeneity is not needed for this negative assessment.

Rule

Allele frequency is greater than expected for the disorder.

Evidence considered

• gnomAD v2.1: variant absent; therefore no filtering allele frequency or grpmax FAF is available.
• gnomAD v4.1: variant absent; therefore no filtering allele frequency or grpmax FAF is available.
• The governing instructions require the filtering allele frequency (grpmax FAF), not the popmax point estimate, for BS1; no grpmax FAF was reported in either dataset.
• Generic calibration supplied in the governing instructions: BS1 default threshold >=0.01; maximum-credible-allele-frequency considerations are attributed to Whiffin et al. 2017 (PMID:28518168).

Sources

Reasoning

BP1 is not supported for FGFR2. The available disease literature describes recurrent activating missense substitutions, including Pro253Arg and Ser252Trp, as the principal molecular basis of Apert syndrome and demonstrates a gain-of-function effect for Pro253Arg. This is inconsistent with a gene in which primarily truncating variants are known to cause disease.

Rule

Missense variant in a gene for which primarily truncating variants are known to cause disease.

Evidence considered

• Ibrahimi et al. state that two activating FGFR2 mutations, Ser252Trp and Pro253Arg, account for nearly all known Apert syndrome cases and show increased ligand-receptor affinity for Pro253Arg.
• ClinVar records the exact variant as Pathogenic/Likely pathogenic and includes Apert syndrome among associated conditions, consistent with the established missense disease mechanism.

Sources

Reasoning

The variant is a missense substitution, so BP4 must be judged on the generic REVEL path only. REVEL is 0.724, which is above the generic BP4 supporting cutoff of <= 0.29; therefore BP4 is not met. The SpliceAI max delta of 0.001 is not substituted into the missense path, and BayesDel is not available for generic ACMG/AMP strength assignment.

Rule

BP4: Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc) ... Missense variant -> REVEL only. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• NM_000141.5:c.758C>G is an exonic missense variant producing p.Pro253Arg in FGFR2; the applicable generic computational path is REVEL only.
• Local REVEL lookup reports a score of 0.724 for this variant.
• The supplied ClinGen SVI REVEL calibration assigns BP4 supporting at <= 0.29 (Pejaver et al. 2022, Am J Hum Genet, PMID:36413997); 0.724 does not meet that cutoff.
• The available SpliceAI max delta score of 0.001 was not used because splice prediction is not the applicable path for a missense variant; BayesDel has no established generic ACMG-strength calibration in the supplied rules.

Sources

Reasoning

The governing rule concerns a reputable benign report whose underlying evidence is unavailable for independent evaluation. Under the supplied generic BP6 instruction, application requires an exact-variant ClinVar expert-panel classification of Benign or Likely benign. ClinVar variation 13273 exactly matches NM_000141.5:c.758C>G (p.Pro253Arg), but the audited record reports zero expert-panel submissions and no benign or likely benign classification. Ordinary laboratory submissions and aggregate labels cannot trigger BP6.

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 13273 exactly matches NM_000141.5(FGFR2):c.758C>G (p.Pro253Arg), reports 0 expert-panel submissions, and contains no Benign or Likely benign submission in the audited record.

Sources

Reasoning

The published prenatal case reports the exact heterozygous FGFR2 c.758C>G (p.Pro253Arg) variant in a fetus with Apert syndrome and states that testing of both parents did not detect the variant, supporting a de novo event. However, the available report does not document confirmed maternity and paternity or establish absence of a family history, so the full PS2 definition cannot be assessed.

Rule

De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.

Evidence considered

• PMID:23915865 reports a heterozygous FGFR2 c.758C>G (p.Pro253Arg) variant in a fetus with Apert syndrome; molecular testing of both parents did not detect the variant and the authors described it as de novo.
• The report does not provide documentation confirming maternity and paternity or explicitly state that there was no family history.

Still missing

• Confirmed maternity and paternity are not documented.
• Absence of family history is not documented.

Sources

Reasoning

The governing ACMG/AMP rule requires a case-control comparison with RR or OR >5.0 and a confidence interval that does not include 1.0. The literature_pass packet specifically classified PMID:8651276 as a PS4 candidate; its verified abstract reports 70 unrelated affected patients, including 25 with Pro253Arg, but no unaffected or population-control count or matched-ancestry control frequency. The available gnomAD records report absence but provide no usable matched-ancestry denominator or allele-frequency estimate for this calculation. Therefore an OR/RR and 95% confidence interval cannot be computed, so the required inequalities OR/RR > 5.0 and CI excluding 1.0 cannot be evaluated.

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

• The literature_pass packet classified PMID:8651276 as a PS4 candidate; its verified abstract reports analysis of 70 unrelated Apert syndrome patients and the recurrent Ser252Trp/Pro253Arg substitutions, with 25 Pro253Arg cases, but no unaffected or population-control group, OR/RR, or confidence interval.
• gnomAD v2.1 and v4.1 report the exact variant absent, but the available records do not provide a matched-ancestry control denominator or allele frequency suitable for an OR/RR and 95% confidence-interval calculation.

Still missing

• Unaffected or matched-ancestry population-control count or allele frequency for NM_000141.5:c.758C>G is unavailable.
• A case-control OR/RR and 95% confidence interval cannot be calculated from the available data.

Reasoning

p.Pro253Arg lies in the conserved linker between FGFR2 Ig-like domains 2 and 3, a region involved in ligand binding and receptor activation. Published structural work shows that Arg253 creates additional FGF2 hydrogen bonds and increases ligand-receptor affinity, while recurrent disease-associated substitutions at adjacent residues support regional functional importance. However, the available evidence does not establish the required absence of benign variation across this region. The cancer-hotspot result cannot independently establish generic PM1 here because the generic rule does not specify that somatic hotspot source as an applicable route.

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

• Ibrahimi et al. place Pro253Arg in the highly conserved linker between FGFR2 Ig-like domains 2 and 3 and describe this region as involved in receptor activation and ligand binding.
• The same study reports three additional hydrogen bonds between Arg253 and FGF2 and an almost 1.5-fold decrease in FGF2 koff relative to wild type, supporting altered ligand-receptor function.
• ClinVar records the exact variant as Pathogenic/Likely pathogenic, but does not provide a curated benign-variation survey for the entire region.
• Cancer Hotspots reports an FGFR2 P253 hotspot, but its partially parsed record is not used as a standalone generic PM1 route.

Still missing

• A curated assessment demonstrating no benign variation across the FGFR2 IgII–IgIII linker or qualifying hotspot is needed.

Sources

Reasoning

The variant is a novel missense change at residue 253 for purposes of PM5 evaluation, but the available case evidence does not provide a confirmed, independently established pathogenic different missense substitution at Pro253. The collected PM5 candidate artifact contains zero same-residue candidates, so PM5 cannot be applied from the available evidence.

Rule

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.

Evidence considered

• The PM5 candidate record reports zero total candidates and zero same-residue candidates for FGFR2 Pro253.
• ClinVar evidence in this case establishes p.Pro253Arg itself, not a different pathogenic missense change at residue 253.

Still missing

• A validated pathogenic alternate missense variant at FGFR2 residue Pro253 is needed.

Sources

Reasoning

The available evidence reports one affected fetus and parental non-detection of the variant, but does not provide affected relatives, multiple affected family members, or informative meioses demonstrating co-segregation. Therefore, PP1 cannot be assessed.

Rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.

Evidence considered

• The reviewed case report documents a single affected fetus and parental testing, not multiple affected family members with genotype and phenotype data.

Still missing

• Family pedigree and phenotype information are not available.
• No multiple affected relatives with genotype data are documented.
• No informative meioses or segregation counts are documented.

Sources

Reasoning

FGFR2 has well-documented disease-associated activating missense variants, including recurrent Pro253Arg and Ser252Trp substitutions. However, the available case evidence does not provide a gene-level assessment demonstrating both a low rate of benign missense variation and that missense variants are a common disease mechanism under the generic PP2 definition. The absence of this individual variant from gnomAD is not sufficient to establish the gene-level benign-missense criterion.

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

• Ibrahimi et al. describe the recurrent activating FGFR2 substitutions Ser252Trp and Pro253Arg in Apert syndrome and demonstrate altered ligand binding for Pro253Arg.
• The exact case variant is absent from gnomAD v2.1 and v4.1, but single-variant absence does not establish the gene-level rate of benign missense variation required for PP2.

Still missing

• A gene-level benign missense variation constraint assessment and documented missense-mechanism frequency are needed.

Sources

Reasoning

BS2 was not assessed because the available evidence does not document the exact variant in a healthy adult individual. Population databases report the variant as absent, while the reviewed variant-specific literature describes affected individuals or functional studies rather than an unaffected adult carrier. FGFR2-related Apert syndrome is early-onset and autosomal dominant, but no verified healthy-carrier observation with age and phenotype information is available for the exact variant.

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, which does not document a healthy adult carrier or establish BS2.
• The reviewed exact-variant literature includes affected Apert syndrome cases and functional studies, but no verified healthy adult carrier observation was identified.
• The governing BS2 definition requires observation in a healthy adult and specifies full penetrance expected at an early age; the available evidence does not provide the required healthy-carrier observation and associated age/phenotype documentation.

Still missing

• A verified report of the exact variant in a healthy adult, with age and phenotype information, is required to assess BS2.

Sources

Reasoning

BS3 was not assessed because no exact-variant in vitro or in vivo study in the reviewed evidence provides a well-established result showing no damaging effect on FGFR2 protein function or splicing. The available exact-variant functional evidence supports an activating effect rather than a benign functional result.

Rule

Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.

Still missing

• No exact-variant functional or splicing assay demonstrating preserved FGFR2 function was identified.

Reasoning

No affected family members with genotype results are documented, and there is no evidence that the variant fails to segregate with disease in an informative family. BS4 therefore cannot be assessed.

Rule

Lack of segregation in affected members of a family.

Evidence considered

• The reviewed evidence contains no affected-relative genotype data or family-level analysis showing that the variant does not segregate with disease.

Still missing

• No informative affected relatives with genotype data are documented.
• No family-level non-segregation analysis is available.

Sources

Reasoning

BP2 requires an observation showing either that the evaluated variant is in trans with a pathogenic variant in a fully penetrant dominant disorder or that it is in cis with a pathogenic variant in any inheritance pattern. PMID:23915865 documents a heterozygous de novo FGFR2 c.758C>G (p.Pro253Arg) observation and negative testing in both parents, but does not report a second pathogenic variant or establish cis/trans phase with one. The available evidence therefore does not permit assessment of BP2.

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:23915865 reports the exact variant as heterozygous and de novo in a fetus with Apert syndrome; both parents tested negative for the variant.
• The report does not identify a second pathogenic variant and does not provide a cis/trans phase result for the evaluated variant.
• Because neither BP2 pathway is documented, BP2 cannot be assessed from the available evidence.

Still missing

• No documented pathogenic variant in cis or trans with FGFR2 c.758C>G (p.Pro253Arg).
• No phase-resolved testing of a second pathogenic variant is available.

Sources

Reasoning

The governing rule requires the variant to be found in a case with an alternate molecular basis for disease. The verified exact-variant case report documents Apert syndrome with the FGFR2 variant but does not document an independent molecular diagnosis explaining the same phenotype. The available COSMIC somatic count and a literature association with bladder carcinoma do not establish an alternate molecular basis for the relevant germline disease case. Because no sufficiently detailed case record establishes or excludes such an alternate cause, BP5 cannot be adjudicated from the available evidence.

Rule

Variant found in a case with an alternate molecular basis for disease.

Evidence considered

• PMID:23915865 documents Apert syndrome with the FGFR2 variant and does not report an alternate molecular basis.
• COSMIC somatic occurrence and a bladder-carcinoma association do not establish an alternate molecular basis for the Apert syndrome phenotype.

Still missing

• A case report or series documenting the exact variant together with an independent molecular diagnosis for the same disease is unavailable.

Sources