FGFR3 c.1138G>A, p.Gly380Arg

Reasoning

The assessed variant is FGFR3 p.Gly380Arg (c.1138G>A). The same amino-acid substitution is established from the alternate c.1138G>C change: the literature describes either 1138G>A or 1138G>C at codon 380 as producing Gly380Arg in achondroplasia. This directly satisfies PS1 because the alternate nucleotide change produces the same pathogenic amino-acid change.

Rule

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

Evidence considered

• Clinical hypochondroplasia in a family caused by a heterozygous double mutation in FGFR3, Introduction: either 1138G>A or 1138G>C at codon 380 is described as producing Gly380Arg in achondroplasia.
• Paternal age effect mutations and selfish spermatogonial selection, Table 1 and review text: c.1138G>A and c.1138G>C are the FGFR3 achondroplasia substitutions, with the encoded p.Gly380Arg protein explicitly identified.

Sources

Reasoning

PS3 is met at strong strength. The exact FGFR3 c.1138G>A (p.Gly380Arg; G380R) variant was evaluated in multiple orthogonal functional systems with wild-type comparators and assay controls. In mammalian-cell phosphorylation assays, G380R increased mature FGFR3 phosphorylation in the absence of ligand and at low FGF1 concentrations, with an approximately 2.5-fold higher phosphorylation probability and no increase in receptor expression, membrane localization, or cross-linking (PMID:20624921). In stable chondrocytic cells, the mutant showed constitutive kinase activity, severe growth inhibition, reduced differentiation, and altered adhesion and cytoskeletal phenotypes (PMID:10646125). A heterodimerization/phosphorylation study independently demonstrated altered WT/G380R receptor behavior across ligand concentrations (PMID:21324899). These reproducible, variant-specific results across biochemical, cellular, and disease-relevant chondrocyte assays directly support a damaging gain-of-function effect. No validated clinical diagnostic-laboratory assay or formal interlaboratory replication was documented, so no higher-than-strong calibration is assigned.

Rule

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

Evidence considered

• Physical basis behind achondroplasia, PMID:20624921: in CHO and HEK 293 cells, full-length FGFR3/G380R had significantly higher mature-receptor phosphorylation without ligand and at low FGF1; the mutation did not alter receptor expression, membrane localization, or cross-linking, and the authors estimated an approximately 2.5-fold higher phosphorylation probability within unliganded dimers.
• Expression of FGFR3 with the G380R achondroplasia mutation inhibits proliferation and maturation of CFK2 chondrocytic cells, PMID:10646125: stable rat CFK2 cells expressing FGFR3Ach showed partial constitutive kinase activity, severe reduction in proliferation and growth, reduced differentiation markers, altered integrin expression and adhesion, and altered actin organization compared with vector and wild-type controls.
• FGFR3 heterodimerization in achondroplasia, PMID:21324899: HEK 293 functional heterodimerization and phosphorylation assays using full-length wild-type, G380R, and A391E controls showed lower-probability WT/G380R heterodimer formation at low ligand concentration and variant-specific receptor phosphorylation behavior.

Still missing

• The reviewed studies do not document validation and reproducibility in a clinical diagnostic laboratory setting.
• No directly tested benign control variant or functional assay showing preserved FGFR3 function was identified for BS3.
• The studies characterize molecular and cellular consequences rather than a single standardized quantitative clinical cutoff.

Sources

Reasoning

FGFR3 p.Gly380Arg lies at codon 380 in the transmembrane domain and in a statistically significant FGFR3 hotspot. The literature reports codon 380 as the recurrent achondroplasia site, with approximately 98% of achondroplasia cases caused by nucleotide 1138 changes, and the Cancer Hotspots result identifies G380 as a statistically significant hotspot. No benign-variation assessment for the full region is available, but the generic PM1 hotspot route is supported by the documented hotspot evidence.

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 result for FGFR3 G380: the variant lies in a statistically significant hotspot; the extraction warning states that the G380 row was only partially parsed.
• Rapid detection of G1138A and G1138C mutations of FGFR3, abstract: nearly 98% of achondroplasia cases are caused by nucleotide 1138 mutations, including c.1138G>A and c.1138G>C.
• Novel FGFR3 mutations in bladder cancer, Results and Discussion: G380R affects the transmembrane domain and replaces glycine with arginine.

Still missing

• The Cancer Hotspots extraction is flagged as partially parsed; confirm the G380 hotspot row from the archived screenshot or source record.

Sources

Reasoning

PM2 is met at supporting strength under the supplied generic SVI threshold. gnomAD v4.1 shows a total allele frequency of 4.33931e-06 from 7/1613160 alleles, with grpmax FAF=1.24e-06; both are below the <=0.0001 PM2 supporting threshold. gnomAD v2.1 exomes show complete absence, 0/250348 alleles. The result is therefore extremely rare in the default all-comers population sources; no VCEP-specific non-cancer or exome-only rule governs this gene.

Rule

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

Evidence considered

• gnomAD v4.1: total AF=4.33931e-06 from 7/1,613,160 alleles, homozygotes=0, and grpmax FAF=1.24e-06; these values are below the supplied PM2 supporting threshold of <=0.0001.
• gnomAD v2.1 exomes: 0/250,348 alleles, AF=0, homozygotes=0.
• The case has no governing VCEP specification; generic all-comers gnomAD v2.1 and v4.1 are therefore the default sources.

Sources

Reasoning

The assessed p.Gly380Arg variant is a missense substitution at residue 380. The literature reports a different missense substitution at the same residue, p.Gly380Lys, in a mother-daughter family with hypochondroplasia and describes it as the disease-causing mutation; this is a previously observed pathogenic alternate missense change at the same amino-acid residue.

Rule

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

Evidence considered

• Clinical hypochondroplasia in a family caused by a heterozygous double mutation in FGFR3, title and Discussion: the family carried p.Gly380Lys at codon 380 and the report attributes hypochondroplasia to that alternate missense change; the paper contrasts it with classical p.Gly380Arg achondroplasia.

Sources

Reasoning

PMID:16411219 reports the exact FGFR3 c.1138G>A (p.G380R) variant in a child with achondroplasia, with the variant absent from both clinically unaffected parents and considered de novo. Because the report does not document confirmed maternity and paternity, the evidence supports assumed de novo occurrence under PM6 rather than PS2. The concurrent p.L377R variant was in cis and limits attribution of the severe complications, but does not negate the reported parental non-detection of c.1138G>A.

Rule

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

Evidence considered

• PMID:16411219, Results/Mutational Analysis: the exact c.1138G>A (p.G380R) variant was detected in a child with achondroplasia and was not detected in either parent.
• PMID:16411219, Discussion: both FGFR3 mutations were considered de novo; c.1138G>A and c.1130T>G (p.L377R) were on the same allele (cis).
• The report does not document confirmed maternity and paternity, so PM6 is used instead of PS2.

Sources

Reasoning

The variant is a missense substitution, NP_000133.1:p.(Gly380Arg), so the governing computational path is REVEL only. REVEL is 0.696, which meets the generic PP3 supporting threshold of >=0.644 from the ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997). SpliceAI is not used for PP3 in this missense situation, and the BayesDel score is not available for generic ACMG strength calibration.

Rule

Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).

Evidence considered

• Local REVEL predictor lookup: REVEL score 0.696 for FGFR3 NM_000142.5:c.1138G>A, NP_000133.1:p.(Gly380Arg).
• ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997): generic PP3 supporting threshold >=0.644.

Sources

Reasoning

PMID:16411219 reports the exact FGFR3 c.1138G>A (p.G380R) variant in an affected child and states that it was not detected in the clinically unaffected parents and was considered de novo. However, the report does not document confirmation of both maternity and paternity. Under the generic PS2 definition, parental non-detection without confirmed maternity and paternity is insufficient for PS2.

Rule

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

Evidence considered

• PMID:16411219, Results/M เหutational Analysis and Discussion: the exact c.1138G>A (p.G380R) variant was found in a child with achondroplasia, was not detected in either clinically unaffected parent, and was considered de novo.
• The report provides parental testing but does not state that both maternity and paternity were confirmed.

Still missing

• Documented confirmation of both maternity and paternity is absent.

Sources

Reasoning

The exact FGFR3 p.Gly380Arg variant is described as associated with achondroplasia in PMID:12461689 and in other reviewed literature, but the evidence is available for independent evaluation through the paper extracts and full text. ClinVar has no expert-panel submission for the exact variant: the audit reports zero expert-panel submissions and only ordinary/literature-only submissions, which are explicitly ineligible under the requested PP5 safeguard. Thus PP5 is not met.

Rule

PP5: Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• PMID:12461689, Results and Discussion, reports FGFR3 G380R in bladder cancer and describes it as an activating germline mutation associated with achondroplasia; the exact variant was independently extracted from the full text.
• The ClinVar submission audit reports expert_panel_submissions = 0; the exact-match submission is OMIM, has no assertion criteria, is not an expert-panel submission, and is unusable for criterion leads.
• Under the requested generic PP5 safeguard, ordinary laboratory submissions, aggregate labels, and non-expert assertions cannot trigger PP5, and the reviewed paper evidence is available for independent evaluation.

Sources

Reasoning

BA1 is not met. Under the generic stand-alone threshold of >=0.05, the relevant gnomAD v4.1 filtering frequency is grpmax FAF=1.24e-06, far below 0.05. The highest observed subpopulation point estimate, 1/62480 alleles (1.60e-05) in Remaining individuals, is not used for BA1 because the governing instruction requires grpmax FAF rather than popmax AF. gnomAD v2.1 showed 0/250348 alleles, and gnomAD v4.1 showed 7/1613160 total alleles with zero homozygotes.

Rule

BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868) ... BA1: Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v4.1: total 7/1,613,160 alleles, AF=4.33931e-06, homozygotes=0; grpmax FAF=1.24e-06.
• gnomAD v4.1 highest observed subpopulation point estimate: Remaining individuals, 1/62,480 alleles (AF=1.60051e-05); this popmax point estimate was not used for BA1.
• gnomAD v2.1 exomes: 0/250,348 alleles, AF=0, homozygotes=0.

Sources

Reasoning

BS1 is not met on the available population evidence. The generic default threshold is >=0.01, while gnomAD v4.1 grpmax FAF is 1.24e-06. The largest relevant observed subpopulation point estimate is only 1/62480 alleles (1.60e-05), and it must not replace the filtering FAF. No prevalence, penetrance, or allelic-heterogeneity calculation is needed to rescue BS1 because the filtering frequency is already many orders of magnitude below the default threshold.

Rule

BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168) ... BS1: Allele frequency is greater than expected for the disorder.

Evidence considered

• gnomAD v4.1 filtering frequency: grpmax FAF=1.24e-06; total AF=4.33931e-06 from 7/1,613,160 alleles.
• gnomAD v4.1 highest observed subpopulation point estimate: Remaining individuals, 1/62,480 alleles (AF=1.60051e-05); this popmax point estimate was not used for BS1.
• The generic BS1 default of >=0.01 is supplied in the case calibration thresholds; the observed filtering FAF is below it by more than four orders of magnitude.

Sources

Reasoning

BS3 is not met. The available exact-variant functional studies do not show no damaging effect; instead, they report increased FGFR3 phosphorylation and constitutive kinase activity, impaired proliferation and chondrocyte differentiation, and altered receptor heterodimerization. The assays used wild-type comparators and relevant cellular systems, so the evidence directly weighs against a benign functional interpretation. No well-established assay demonstrating preserved protein function or splicing for p.Gly380Arg was identified.

Rule

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

Evidence considered

• PMID:20624921: G380R increased mature FGFR3 phosphorylation in the absence of ligand and at low ligand concentrations compared with wild type.
• PMID:10646125: FGFR3Ach/G380R showed constitutive kinase activity, reduced chondrocyte proliferation and differentiation, and altered cellular adhesion phenotypes compared with controls.
• PMID:21324899: functional assays found lower-probability WT/G380R heterodimer formation at low ligand concentration and variant-specific receptor phosphorylation behavior, not preserved normal function.

Still missing

• No well-established functional study demonstrating no damaging effect on FGFR3 protein function or splicing was identified.

Sources

Reasoning

BP1 does not apply because the supplied gene-specific evidence describes FGFR3 disease-associated variants as activating missense substitutions, including p.Gly380Arg and p.Gly380Lys, rather than showing a gene in which disease is primarily caused by truncating variants.

Rule

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

Evidence considered

• Clinical hypochondroplasia in a family caused by a heterozygous double mutation in FGFR3: codon-380 missense substitutions are linked to achondroplasia or hypochondroplasia and constitutive receptor activation.
• OncoKB FGFR3 G380R record: biological-effect context is gain of function.

Sources

Reasoning

The variant is a missense substitution, so BP4 must use the REVEL path only. REVEL is 0.696, outside the generic BP4 supporting range of <=0.29 and therefore not supportive of a tolerated missense effect. The SpliceAI max delta of 0.052 is not used for BP4 because splice predictions are not the governing path for a missense variant; BayesDel has no generic ACMG-strength calibration.

Rule

Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)

Evidence considered

• Local REVEL predictor lookup: REVEL score 0.696 for FGFR3 NM_000142.5:c.1138G>A, NP_000133.1:p.(Gly380Arg).
• ClinGen SVI REVEL calibration (Pejaver et al. 2022, PMID:36413997): generic BP4 supporting threshold <=0.29; the REVEL result is not within the BP4 range.
• SpliceAI result was not counted for this missense BP4 path; reported max delta 0.052 is outside the applicable predictor scope.

Sources

Reasoning

PMID:16411219 reports exact p.G380R together with p.L377R in cis in a child with achondroplasia, with both variants absent from the unaffected parents. However, the paper states that the additional effect of p.L377R could not be established and that the severe phenotype could reflect p.G380R alone. This does not establish that the case has an alternate molecular basis for disease, so BP5 is not met.

Rule

BP5: Variant found in a case with an alternate molecular basis for disease.

Evidence considered

• PMID:16411219, Results and Discussion, reports p.G380R and p.L377R on the same allele in a child with achondroplasia, but explicitly states that the additional effect of p.L377R could not be established and that the phenotype could reflect p.G380R alone.

Still missing

• Human review could determine whether independent evidence establishes p.L377R as the alternate molecular basis for the reported disease in this case.

Sources

Reasoning

The exact-variant ClinVar record is Pathogenic, not benign or likely benign, and the ClinVar audit reports zero expert-panel submissions. No exact-variant ClinVar expert-panel benign or likely-benign classification is present, so the requested BP6 safeguard is not satisfied.

Rule

BP6: Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• The exact-variant ClinVar record is classified Pathogenic with review status criteria provided, multiple submitters, no conflicts; the audit reports expert_panel_submissions = 0.
• Under the requested generic BP6 safeguard, only an exact-variant ClinVar expert-panel classification of Benign or Likely benign can trigger BP6; ordinary submissions and aggregate labels cannot.

Sources

Reasoning

The literature_pass.json criterion index lists PMID:11186939, PMID:20301650, and PMID:24121147 as PS4 leads, but none has a source_registry entry, paper_extracts entry, or fetched full text in this case. The reviewed PMID:22325359 reports that FGFR3 c.1138G>A is a predominant achondroplasia-causing allele and gives an estimated birth prevalence, but it does not provide affected-case and unaffected/population-control counts for this exact variant. Therefore no case-control OR or 95% CI can be computed and the generic PS4 threshold cannot be evaluated.

Rule

PS4: 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:22325359 reports that FGFR3 c.1138G>A is the predominant achondroplasia-causing allele and quotes an estimated new-mutation birth prevalence of approximately 1 in 30,000, but it supplies no affected-versus-control comparison for this exact variant.
• The literature_pass.json PS4 index identified PMID:11186939, PMID:20301650, and PMID:24121147, but those papers were not available in source_registry, paper_extracts, or the fetched publication set, so their PS4 leads were not independently verifiable.

Still missing

• Verify PMID:11186939, PMID:20301650, and PMID:24121147 against their abstracts or full texts.
• Obtain exact-variant affected-case and unaffected/population-control counts, or a reported OR/RR with 95% CI, to evaluate OR >5.0 and CI excluding 1.0.

Sources

Reasoning

No adequately documented segregation series for the exact FGFR3 c.1138G>A variant is available in the reviewed evidence. PMID:17256796 describes an affected mother and daughter, but their familial variant is a different FGFR3 double mutation encoding Gly380Lys, not c.1138G>A (p.Gly380Arg), so it cannot establish segregation of this variant. The available PMID:11186940 title suggests two affected siblings and an unaffected father, but the underlying report was not available for direct verification and no source-registry entry supports citation of it here.

Rule

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

Evidence considered

• PMID:17256796, reported mother–daughter family: the familial variant was 1138_1139GG>AA encoding Gly380Lys, not the assessed c.1138G>A (p.Gly380Arg), so this is not segregation evidence for the assessed variant.
• The reviewed evidence does not provide a directly verifiable affected-relative segregation count or meiosis count for c.1138G>A.

Still missing

• Directly verified genotype and phenotype data for multiple affected relatives carrying c.1138G>A are needed.

Sources

Reasoning

The available evidence supports that disease-associated FGFR3 missense variants can act through gain of function, but it does not provide a gene-level estimate demonstrating a low rate of benign missense variation. The two required PP2 components therefore cannot both be established from the supplied evidence.

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

• Clinical hypochondroplasia in a family caused by a heterozygous double mutation in FGFR3: the disease-associated p.Gly380Arg substitution is described with constitutive FGFR3 activation and the alternate codon-380 missense p.Gly380Lys.
• OncoKB FGFR3 G380R record: biological-effect context is gain of function.

Still missing

• A gene-level benign missense constraint or equivalent validated evidence for FGFR3 is required.

Sources

Reasoning

The case evidence bundle identifies the variant as FGFR3 c.1138G>A, p.Gly380Arg, but does not provide the patient's phenotype or family history. Literature reports of achondroplasia in other individuals cannot substitute for the phenotype of this case. The highly specific phenotype required for PP4 therefore cannot be assessed.

Rule

PP4: Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.

Evidence considered

• The case summary establishes FGFR3 c.1138G>A, p.Gly380Arg, but contains no patient phenotype or family-history description.

Still missing

• Provide the patient's clinical phenotype and relevant family history, including whether findings are highly specific for a single-genetic-etiology disease.

Reasoning

BS2 is not assessed. gnomAD reports zero homozygotes in v2.1 and v4.1, but the available population records do not document that any observed heterozygous carrier was a healthy adult with phenotype and age information. For this autosomal-dominant, early-onset disorder, a population allele count alone cannot establish the required observation of a healthy adult heterozygote.

Rule

BS2: 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: 0 homozygotes among 0 variant alleles and 250,348 total alleles.
• gnomAD v4.1: 0 homozygotes among 7 variant alleles and 1,613,160 total alleles; the record provides allele counts but no individual-level healthy-adult phenotype or age ascertainment.

Still missing

• Individual-level phenotype and age documentation for an observed heterozygous carrier is unavailable.

Sources

Reasoning

The evidence does not document an affected family member who lacks FGFR3 c.1138G>A, nor does it provide a family genotype/phenotype table demonstrating non-segregation. The unaffected parents in PMID:16411219 are not affected members, so their absence of the variant supports de novo assessment but does not satisfy the BS4 definition. The family report in PMID:17256796 concerns a different FGFR3 variant and cannot establish lack of segregation for c.1138G>A.

Rule

Lack of segregation in affected members of a family.

Evidence considered

• PMID:16411219: both clinically unaffected parents lacked the variant; this is parental non-transmission, not lack of segregation in an affected family member.
• PMID:17256796: the reported family involved a different Gly380Lys FGFR3 variant, not c.1138G>A.
• No verified affected relative with a discordant genotype was identified.

Still missing

• A verified affected-family-member genotype showing absence of c.1138G>A is needed to assess BS4.

Sources

Reasoning

The phase-resolved report documents FGFR3 p.Gly380Arg in cis with p.Leu377Arg in one affected child, with parental testing showing both variants were de novo. However, that report does not establish p.Leu377Arg as pathogenic; it describes the second variant as novel and cannot determine its additional effect. Because BP2 requires the other variant to be pathogenic, the criterion cannot be assessed from the available evidence.

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

• PMID:16411219, Results/Mutational Analysis and Discussion: allele-specific PCR showed p.Gly380Arg and p.Leu377Arg on the same allele (cis); both were absent from the clinically unaffected parents and considered de novo.
• PMID:16411219, Discussion: the authors could not establish the additional effect of p.Leu377Arg and noted that the severe phenotype could reflect variability associated with p.Gly380Arg alone.

Still missing

• A reliable pathogenic classification or independent pathogenicity evidence for the cis p.Leu377Arg variant is required.
• The available report does not resolve whether p.Leu377Arg contributed to the phenotype beyond p.Gly380Arg.

Sources