FGFR3 c.1118A>G, p.Tyr373Cys

Reasoning

PS3 is met at strong strength. The exact FGFR3 Y373C variant was experimentally tested in NIH 3T3 focus-formation assays with equal transfection amounts and appropriate comparators: Y373C produced transformation equivalent to the known activating K650E mutant, whereas wild-type FGFR3 and F384L did not induce foci. Independent in vivo studies of the corresponding Fgfr3Y367C/+ mouse allele, explicitly stated to correspond to human c.1118A>G (p.Tyr373Cys), demonstrated constitutive FGFR3-related skeletal, skull, growth-plate, and ossification abnormalities in heterozygous animals compared with wild-type controls. These concordant, biologically relevant cellular and in vivo findings support a damaging gain-of-function effect, although they are research assays rather than validated clinical diagnostic-laboratory tests.

Rule

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

Evidence considered

• Guan et al. 2001, PMID:11157491: FGFR3 Y373C was cloned and tested in NIH 3T3 focus-formation assays; with equal transfection amounts, Y373C and the activating K650E control induced the same number of foci, while wild-type FGFR3 and F384L did not induce transformation.
• Lorget et al. 2012, PMID:23200862: the heterozygous Fgfr3Y367C/+ mouse model was identified as corresponding to human c.1118A>G (p.Tyr373Cys) and showed skeletal, skull, foramen-magnum, and growth-plate abnormalities in phenotypic, imaging, histologic, ex vivo, and in vivo studies.
• Lorget et al. 2014, PMID:24419316: heterozygous Fgfr3Y367C/+ mice carrying the orthologous activating allele corresponding to human p.Tyr373Cys showed abnormal endochondral and membranous ossification, cranial-suture/skull-base abnormalities, and craniofacial changes compared with wild-type littermates.

Sources

Reasoning

The variant is p.Tyr373Cys in FGFR3 and the Cancer Hotspots result identifies FGFR3 Y373 as a statistically significant hotspot. No VCEP covers FGFR3 and vcep_materials.json has no domain table, so the generic PM1 rule applies. The hotspot evidence provides the generic mutational-hotspot route; the extraction warns that the row was only partially parsed, so the result warrants human confirmation. The exact variant is absent from gnomAD v2.1 and v4.1, with no benign population observation supplied for this site.

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

• Cancer Hotspots query FGFR3 Y373: result found; evidence sentence states 'This variant lies in a statistically significant hotspot'; record row FGFR3 Y373 was only partially parsed.
• gnomAD v2.1: exact variant absent.
• gnomAD v4.1: exact variant absent.
• vcep_materials.json: no VCEP-specific framework and domain_tables is empty; generic ACMG/AMP PM1 governs.

Still missing

• Cancer Hotspots extraction was partial and should be confirmed from the retained screenshot or live record.

Sources

Reasoning

PM2 is met at supporting strength. The exact variant was absent from gnomAD v2.1 and gnomAD v4.1 all-comers datasets and from the available gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer searches. This is consistent with the supplied generic PM2 threshold of <=0.0001, including the stronger absent-from-controls observation; no population-specific VCEP source rule applies because no VCEP covers FGFR3.

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 reported the exact GRCh37 variant as absent.
• gnomAD v4.1 reported the exact GRCh38 variant as absent.
• The gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer searches also reported the exact variant as absent; no alternative non-cancer frequency is needed because both searches were negative.
• The supplied generic PM2 calibration is <=0.0001, with absent-from-controls qualifying as the strongest form of rarity under that threshold.

Sources

Reasoning

PMID:24476948 reports the exact FGFR3 c.1118A>G (p.Tyr373Cys) variant as de novo in fetus F23, whose lethal skeletal dysplasia phenotype is consistent with the known disorder. The study sequenced the fetus and parents and validated the candidate variant, but did not document confirmation of maternity and paternity; this supports PM6 rather than PS2.

Rule

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

Evidence considered

• PMID:24476948 states that fetus F23 had lethal skeletal dysplasia features and carried FGFR3 c.1118A>G (p.373Y>C), identified as a de novo missense variant; the study analyzed fetuses or neonates along with their parents and validated candidate de novo variants by capillary sequencing.
• The source does not document biological parentage confirmation, so the evidence fits assumed de novo status without confirmed maternity and paternity.

Still missing

• Explicit confirmation of biological maternity and paternity is not documented.

Sources

Reasoning

The variant is a missense substitution, NM_000142.5:c.1118A>G (p.Tyr373Cys), so the governing generic rule selects the REVEL path only; SpliceAI is not used for this missense assessment. REVEL is 0.80, meeting the generic PP3 moderate threshold of >= 0.773 from the ClinGen SVI calibration by Pejaver et al. 2022 (PMID:36413997). BayesDel has no established generic ACMG-strength calibration and is not used. Therefore PP3 is met at moderate strength.

Rule

Missense variant -> REVEL only. ... PP3 (moderate): >= 0.773 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• Variant consequence is missense: NM_000142.5:c.1118A>G, NP_000133.1:p.(Tyr373Cys), exon 9.
• Local REVEL lookup reports a score of 0.80 for the variant.
• The supplied generic calibration assigns PP3 moderate at REVEL >= 0.773; this threshold is from Pejaver et al. 2022, ClinGen SVI REVEL calibration (PMID:36413997).
• SpliceAI max delta is 0.023, but the governing missense path is REVEL only, so the splice score is not counted for PP3.
• BayesDel score 0.343469 is not used because no generic ACMG-strength calibration is established for BayesDel.

Sources

Reasoning

The variant is NP_000133.1:p.(Tyr373Cys), and the reviewed reports establish this exact c.1118A>G change as pathogenic. However, PS1 requires the same amino-acid change from a previously established pathogenic variant regardless of nucleotide change; the available reports document the same nucleotide change, not an alternative nucleotide change producing Tyr373Cys. Therefore PS1 is not met.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.

Evidence considered

• Trujillo-Tiebas et al. 2009, Results paragraph 2/Table 2: one TD-I case carried 1118A>G [Y373C].
• Exome sequencing study, Results paragraph beginning 'Two of the de novo missense variants are highly likely to be pathogenic': fetus F23 carried c.1118A>G (p.373Y>C), described as known to cause thanatophoric dysplasia.
• ClinVar variation 16342: exact variant NM_000142.5(FGFR3):c.1118A>G (p.Tyr373Cys), classified Pathogenic with multiple submitters and no conflicts.

Still missing

• No validated report of an alternative nucleotide change producing p.Tyr373Cys was identified.

Sources

Reasoning

The exact FGFR3 c.1118A>G (p.Tyr373Cys) variant was reported as de novo in fetus F23 with features consistent with lethal skeletal dysplasia, after exome sequencing of the fetus and parents and capillary-sequencing validation. However, the report does not document confirmation of both maternity and paternity, so the full PS2 definition is not satisfied.

Rule

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

Evidence considered

• PMID:24476948 reports fetus F23 with lethal skeletal dysplasia features carrying FGFR3 c.1118A>G (p.373Y>C), identified as a de novo missense variant; the cohort included fetal-neonatal samples and their parents, and candidate variants were validated by capillary sequencing.
• The report does not state that biological maternity and paternity were independently confirmed.

Still missing

• Explicit confirmation of biological maternity and paternity is not documented.

Sources

Reasoning

The governing rule concerns a reputable source reporting the exact variant as pathogenic when the underlying evidence is unavailable for independent evaluation. ClinVar contains exact-variant Pathogenic submissions, but the audit records zero expert-panel submissions; the available assertions are ordinary laboratory, curation, literature-only, or otherwise non-expert records. Under the required generic PP5 restriction, these assertions do not 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 exact variant NM_000142.5(FGFR3):c.1118A>G (p.Tyr373Cys), variation ID 16342: Pathogenic aggregate classification with 20 clinical laboratories, but the submission audit reports expert_panel_submissions = 0; no expert-panel classification was identified.

Sources

Reasoning

BA1 is not met. NM_000142.5:c.1118A>G (FGFR3 p.Tyr373Cys) was absent from gnomAD v2.1 and gnomAD v4.1, including the available non-cancer searches, so no allele frequency reaches the generic stand-alone threshold of >=0.05. The variant's established pathogenic disease association does not create a BA1 exception here because the required high frequency is absent.

Rule

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

Evidence considered

• gnomAD v2.1 reported the exact GRCh37 variant 4-1806099-A-G as absent.
• gnomAD v4.1 reported the exact GRCh38 variant 4-1804372-A-G as absent.
• The generic BA1 calibration supplied for this case is >=0.05; no qualifying allele frequency was observed.

Sources

Reasoning

BS1 is not met. The variant was absent from gnomAD v2.1, gnomAD v4.1, gnomAD v2.1 non-cancer, and gnomAD v3.1 non-cancer, so there is no observed allele frequency greater than expected for the disorder. The generic 0.01 default and any maximum-credible-frequency comparison are therefore not reached.

Rule

Allele frequency is greater than expected for the disorder.

Evidence considered

• The exact variant was absent from gnomAD v2.1 and gnomAD v4.1 all-comers datasets.
• The exact variant was also reported absent from the gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer searches; no exome-only non-cancer frequency was available because the variant was absent.
• The generic BS1 default supplied for this case is >=0.01, but no observed allele frequency is available to support BS1.

Sources

Reasoning

BS3 is not met. The reviewed functional evidence does not show an absence of damaging effect; instead, the exact Y373C variant produced cellular transformation, and independent studies of the corresponding Fgfr3Y367C/+ allele demonstrated disease-relevant skeletal and ossification abnormalities. No well-established benign functional assay or validated neutral splicing result was identified that could support BS3.

Rule

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

Evidence considered

• Guan et al. 2001, PMID:11157491: the exact Y373C variant induced NIH 3T3 focus formation at the level of the activating K650E comparator, unlike wild-type FGFR3 and F384L.
• Lorget et al. 2012, PMID:23200862: the corresponding Fgfr3Y367C/+ mouse model showed skeletal and growth-plate abnormalities relevant to constitutive FGFR3 activity.
• Lorget et al. 2014, PMID:24419316: the corresponding heterozygous mouse allele produced abnormal ossification and craniofacial phenotypes compared with wild-type littermates.

Sources

Reasoning

BP1 is not supported because the available FGFR3 disease literature describes activating missense variants as the mechanism for skeletal dysplasia, including p.Tyr373Cys and other activating FGFR3 substitutions. This is contrary to a gene for 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

• Chesi et al. 2001: FGFR3 Y373C induced cellular transformation in NIH 3T3 focus-formation assays, matching the activating FGFR3 mechanism.
• Lorget et al. 2012: achondroplasia is described as caused by a gain-of-function FGFR3 mutation, and the human p.Tyr373Cys mutation is modeled in mice.
• FGFR3 mutation study: the p.Tyr373Cys-equivalent mouse mutation is used to model constitutive FGFR3 activation and skeletal disease.

Sources

Reasoning

The variant is a missense substitution, so BP4 must be assessed through the REVEL path only; the SpliceAI result cannot substitute for an indeterminate or non-supportive REVEL result. REVEL is 0.80, which is above the strongest generic BP4 supporting cutoff of <= 0.29 and therefore does not support no impact. The SpliceAI max delta of 0.023 is excluded because SpliceAI is not the governing path for a missense variant. BayesDel is not usable because no generic ACMG-strength calibration is established. Therefore BP4 is not met.

Rule

Missense variant -> REVEL only. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• Variant consequence is missense: NM_000142.5:c.1118A>G, NP_000133.1:p.(Tyr373Cys), exon 9.
• Local REVEL lookup reports a score of 0.80 for the variant.
• The supplied generic calibration assigns BP4 supporting at REVEL <= 0.29; this threshold is from Pejaver et al. 2022, ClinGen SVI REVEL calibration (PMID:36413997).
• SpliceAI max delta is 0.023, but the governing missense path is REVEL only and this splice prediction is not evidence for BP4 here.
• BayesDel score 0.343469 is not used because no generic ACMG-strength calibration is established for BayesDel.

Sources

Reasoning

The governing rule concerns a reputable source recently reporting the exact variant as benign when the evidence is unavailable for independent evaluation. ClinVar's exact-variant aggregate classification is Pathogenic, not benign, and the submission audit identifies zero expert-panel submissions; no exact-variant expert-panel benign or likely benign classification is present. Therefore 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 exact variant NM_000142.5(FGFR3):c.1118A>G (p.Tyr373Cys), variation ID 16342: aggregate classification Pathogenic; the submission audit reports expert_panel_submissions = 0 and no benign/likely benign expert-panel assertion.

Sources

Reasoning

The governing ACMG/AMP rule requires a case-control relative risk or odds ratio greater than 5.0 with a confidence interval excluding 1.0. The literature packet's PS4-triaged paper PMID:9677066 reports 91 affected thanatophoric dysplasia cases with genotype-phenotype correlations, but the available abstract does not provide unaffected or population control counts for c.1118A>G/p.Tyr373Cys, an odds ratio, or a confidence interval. PMID:19789973 independently reports the exact variant in one affected fetus, but is a prenatal case series without a control comparison. The variant is absent from gnomAD v2.1 and v4.1, but no matched case and control denominators are available to compute the required estimate and confidence interval. Therefore PS4 cannot be assessed from the available quantitative evidence.

Rule

The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Note 1: 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:9677066 abstract: the International Skeletal Dysplasia Registry examined 91 affected thanatophoric dysplasia cases and correlated findings with specific FGFR3 mutations; no unaffected/population control comparison, OR, or CI for c.1118A>G/p.Tyr373Cys is reported in the available abstract.
• PMID:19789973, Results paragraph 2/Table 2: one of three TD-I cases carried 1118A>G [Y373C] in a 54-sample prenatal/abortus cohort; this is affected-case evidence without controls.
• gnomAD v2.1 and gnomAD v4.1: the exact variant is absent, but the available records provide no matched control denominator or allele count suitable for the required case-control calculation.

Still missing

• A case-control comparison or sufficient case and matched-control counts to calculate an odds ratio and 95% confidence interval is unavailable.

Sources

Reasoning

The variant affects residue Tyr373 and is p.Tyr373Cys. The available PM5 candidate artifact contains zero same-residue candidates and explicitly states that classic same-residue PM5 semantics could not be safely confirmed. The reviewed paper extracts establish the exact Tyr373Cys variant but do not establish a different pathogenic missense substitution at Tyr373. Evidence is therefore insufficient to assess PM5 rather than sufficient to call it not met.

Rule

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.

Evidence considered

• pm5_candidates.json: total_candidates_seen=0 and same_residue_candidates=0; artifact recommends manual review and says not to apply PM5 from it alone.
• ClinVar variation 16342 documents the exact p.Tyr373Cys variant but does not provide a different missense substitution at residue 373.

Still missing

• A validated pathogenic FGFR3 missense variant at Tyr373 with an amino-acid change different from cysteine is needed.

Sources

Reasoning

The available evidence reports the variant in affected fetuses but provides no family-level segregation analysis with multiple affected relatives, no meiosis count, and no transmission data. PP1 therefore cannot be assessed.

Rule

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

Still missing

• No affected relatives with variant status are documented.
• No informative meioses or family-level segregation analysis is available.

Reasoning

The evidence bundle documents that FGFR3 disease-associated variants can have gain-of-function effects, but it does not provide a validated gene-wide estimate or reference establishing both a low rate of benign missense variation and missense as a common disease mechanism under the supplied PP2 rule. The exact variant's absence from gnomAD is not sufficient to establish the required gene-level benign missense rate.

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

• The available evidence describes FGFR3 gain-of-function missense disease variants, but supplies no gene-wide benign missense rate or equivalent PP2 dataset.
• gnomAD absence of this single variant cannot establish the gene-wide low rate of benign missense variation required by PP2.

Still missing

• Validated FGFR3 gene-wide benign missense constraint and disease-mechanism evidence are required.

Reasoning

The governing rule requires the patient's phenotype or family history to be highly specific for a disease with a single genetic etiology. The case summary provides no patient phenotype, family history, or alternate diagnostic information. Literature reports that this exact variant occurs in thanatophoric dysplasia, including one fetus with micromelia and a hypoplastic thorax (PMID:19789973), but published phenotype observations from other individuals cannot establish that this patient's phenotype is highly specific. Therefore PP4 is not assessed.

Rule

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

Evidence considered

• PMID:19789973, Results paragraph 2/Table 2: the exact variant was found in a fetus with micromelia and a hypoplastic thorax and classified as type I thanatophoric dysplasia; this is literature phenotype evidence, not the current patient's phenotype.

Still missing

• Patient phenotype and family history sufficiently specific for a single-gene disorder are not provided.

Sources

Reasoning

BS2 cannot be assessed from the available evidence. The population records establish absence from gnomAD but provide no observation of this variant in a healthy adult, no homozygote or hemizygote count, and no ascertainment information demonstrating an unaffected adult with the relevant inheritance state. Absence from population databases is not evidence that BS2 is met.

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 reported the variant as absent; these records do not document a healthy-adult observation or provide a BS2-qualifying genotype count.
• The case evidence contains no independently documented healthy adult with FGFR3 p.Tyr373Cys and no relevant homozygote or hemizygote observation.

Still missing

• A documented healthy adult carrying the variant in the inheritance state relevant to the disorder is unavailable.
• No homozygote or hemizygote observation and no adult age/phenotype ascertainment data are available.

Sources

Reasoning

The available evidence does not describe affected family members who were tested for the variant and found not to carry it. No non-segregation observation is available, so BS4 cannot be assessed.

Rule

Lack of segregation in affected members of a family.

Still missing

• No affected relatives with variant-negative testing are documented.
• No family structure or segregation data are available to evaluate phenocopies or multiple pathogenic variants.

Reasoning

The exact variant has been reported as de novo in an affected fetus, but the available evidence does not establish whether another pathogenic variant is present in cis or trans in any individual. No parental/offspring phase data, haplotype data, or documented pathogenic allele paired with this variant are available to assess BP2.

Rule

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

• The exact FGFR3 c.1118A>G (p.373Y>C) variant was reported as a de novo missense variant in fetus F23 after whole-exome sequencing of fetuses/neonates and their parents; this establishes de novo status but does not establish cis or trans phase with another pathogenic variant.
• No source reviewed for this group documents a second pathogenic variant paired with c.1118A>G or provides phase information sufficient for BP2.

Still missing

• Need parental or offspring testing, or equivalent haplotype/phase data, and documentation of a second pathogenic variant to evaluate cis/trans status.

Sources

Reasoning

The governing rule requires the variant to be found in a case with an alternate molecular basis for disease. The case materials do not document an alternate molecular diagnosis for the current patient. A literature abstract describes a dual diagnosis involving an FGFR3 pathogenic variant and EFTUD2-related mandibulofacial dysostosis, but the available material does not establish that the FGFR3 variant in that report is the exact c.1118A>G/p.Tyr373Cys variant. The criterion therefore cannot be assessed for this case.

Rule

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

Evidence considered

• The available literature packet mentions a dual diagnosis involving a maternally inherited pathogenic FGFR3 variant and EFTUD2-related mandibulofacial dysostosis, but does not identify that FGFR3 variant as c.1118A>G/p.Tyr373Cys; it cannot be used as exact-variant BP5 evidence.
• The current case materials do not provide a patient-level alternate molecular diagnosis.

Still missing

• Documentation that this exact variant occurred in a case with a confirmed alternate molecular basis for disease is unavailable.