TP53 c.1010G>A, p.Arg337His

Reasoning

The TP53 VCEP Functional Worksheet Supplementary Table S3 exact row for R337H (corresponding to NM_000546.6:c.1010G>A / p.Arg337His) records Kato as Partially functional, Giacomelli as noLOF, Kawaguchi as Monomer, and assigns the pre-assigned functional code No evidence. That governing pre-assignment outranks a threshold-based reassessment. The VCEP PS3_Moderate rule requires partially functional Kato data and LOF by the majority of other available assays, which is not established by this row; the PS3 Strong and Supporting paths likewise are not met.

VCEP rule

Partially functional on Kato et al. data **AND** loss of function (LOF) by the majority of other available assays

Evidence considered

• ClinGen TP53 VCEP Functional Worksheet, Supplementary Table S3, row R337H: Kato class Partially functional; Funk NA; Giacomelli class noLOF; Kotler NA; Kawaguchi class Monomer; preliminary functional code No evidence.
• ClinGen TP53 VCEP functional-code flowchart: for missense variants with Kato data, Partially functional (Kato) requires LOF by the majority of available assays for PS3_Moderate.
• The exact variant was searched as c.1010G>A, p.Arg337His, and p.R337H in both governing functional VCEP files; the Functional Worksheet matched p.R337H, while the flowchart contains no variant-specific row.

Sources

Reasoning

The TP53 VCEP PM1 codon route is limited to codons 175, 245, 248, 249, 273, and 282; p.Arg337His is at codon 337. The VCEP also permits a hotspot route only when the same amino-acid change has at least 10 cancerhotspots.org somatic occurrences. The case audit reports 4 cancerhotspots observations for Arg337His, below the required threshold. Therefore PM1 is not met.

VCEP rule

Missense variants within the following codons using transcript NM_00546.4: 175, 245, 248, 249, 273, 282. This code weight can also be used for germline missense variants seen in cancerhotspots.org with ≥ 10 somatic occurrences for the same amino acid change.

Evidence considered

• TP53 VCEP PM1 rule: the approved codon route lists 175, 245, 248, 249, 273, and 282; the variant is p.Arg337His at codon 337.
• ClinVar submission audit evidence reports cancerhotspots for Arg337His with 4 somatic observations, which is below the VCEP PM1 requirement of at least 10 somatic occurrences for the same amino-acid change.

Sources

Reasoning

The TP53 VCEP PM2 rule requires supporting-level allele frequency below 0.00003 and, when multiple alleles are present in a genetic-ancestry group, that group's allele frequency below 0.00004. gnomAD v4.1 total AF is 3.09817e-06, but Admixed American contains 3 variant alleles among 59,966 tested (AF 0.0000500283), exceeding the VCEP's 0.00004 multi-allele-group limit. The rule therefore is not met despite the low overall frequency; founder-effect groups are not used.

VCEP rule

This rule should be applied at supporting level. Variant should have an allele frequency of less than 0.00003 (0.003%) in gnomAD or another large sequenced population. If multiple alleles are present within any genetic ancestry group, allele frequency in that group must be \<0.00004 (0.004%).

Evidence considered

• ClinGen TP53 VCEP v2.4 PM2 rule: apply at supporting level when AF is <0.00003; if multiple alleles occur in an ancestry group, that group's AF must be <0.00004; founder-effect groups including Remaining are ignored.
• gnomAD v4.1: total AF 3.09817e-06 (5/1,613,858 alleles), with 0 homozygotes.
• gnomAD v4.1 Admixed American population: 3 variant alleles/59,966 tested, AF 5.00283494e-05; 0 homozygotes.

Sources

Reasoning

NM_000546.6:c.1010G>A is a missense variant, p.(Arg337His). The governing TP53 Supplementary Table S2 assigns this exact coding change the row c.1010G>A / p.Arg337His / Class C0 / BayesDel 0.177746 / No evidence. That pre-assigned VCEP result governs and does not support PP3. The independent SpliceAI result is max delta 0.001 (DS_AG 0.000, DS_AL 0.001, DS_DG 0.000, DS_DL 0.000), below the VCEP PP3 splice threshold of 0.2; therefore the splice path is not met either. The single-amino-acid-deletion spreadsheet has no entry for this missense variant.

VCEP rule

**Missense variants** _(See flowchart for application of PP3 and BP4 rules for missense variants)_ ... aGVGD class C25-C55 and BayesDel score ≥ 0.16 ... **Exonic (including silent variants and apparent “missense” variants or “single amino acid inframe deletions” for which there is a predicted splice effect) or Intronic Splice Variants (excluding ± 1,2 positions):** ... SpliceAI ≥ 0.2

Evidence considered

• ClinGen TP53 VCEP Supplementary Table S2 (PP3-BP4-codes.xlsx), matching row: c.1010G>A; p.Arg337His; BayesDel class C0; BayesDel score 0.177746; assigned code No evidence.
• ClinGen TP53 VCEP PP3 rule for missense variants: aGVGD class C25-C55 and BayesDel score ≥ 0.16; the VCEP lookup table's pre-assigned No evidence result governs this exact variant.
• SpliceAI Lookup for NM_000546.6:c.1010G>A: DS_AG 0.000, DS_AL 0.001, DS_DG 0.000, DS_DL 0.000, max delta score 0.001; this is below the VCEP PP3 splice threshold of 0.2.

Still missing

• No variant-specific entry for c.1010G>A, p.Arg337His, or p.R337H was found in Flowchart-for-application-of-PP3%2C-BP4%2C-and-BP7.pdf; the flowchart supplies the governing rule rather than a variant lookup.
• No entry for c.1010G>A, p.Arg337His, or p.R337H was found in TP53-single-amino-acid-deletions-BayesDel-scores-(1).xlsx; that file covers single amino acid in-frame deletions, not this missense variant.

Sources

Reasoning

The TP53 VCEP BA1 stand-alone threshold is a filtering allele frequency (FAF) of at least 0.001 in one eligible continental genetic-ancestry subpopulation, with at least 2,000 alleles tested and at least 2 variant alleles. gnomAD v4.1 reports a maximum joint FAF of 0.00001328, and the highest ordinary eligible subpopulation observation is Admixed American at 3/59,966 alleles (AF 0.0000500283); neither reaches 0.001. The higher-frequency Remaining-individuals group is expressly excluded by the VCEP rule.

VCEP rule

Filtering allele frequency (FAF) of ≥ 0.001 or 0.1% in gnomAD continental subpopulations of a single genetic ancestry group (excluding genetic ancestry groups influenced by founder effects, such as Ashkenazi Jewish, Finnish, Amish, Middle Eastern, and “Remaining”). Genetic ancestry group must have ≥2,000 alleles tested and a minimum of 2 alleles present. Caution should be exerted if the majority of alleles have a variant allele fraction ("allele balance" in gnomAD) below 0.35.

Evidence considered

• ClinGen TP53 VCEP v2.4 BA1 rule: eligible continental-subpopulation FAF must be ≥0.001, with ≥2,000 alleles tested and ≥2 variant alleles; founder-effect groups including Remaining are excluded.
• gnomAD v4.1: total AF 3.09817e-06 (5/1,613,858 alleles), maximum joint grpmax FAF 1.328e-05; highest ordinary subpopulation was Admixed American, 3/59,966 alleles, AF 5.00283494e-05.
• gnomAD v4.1: homozygotes = 0.

Sources

Reasoning

The TP53 VCEP BS1 strong threshold is a filtering allele frequency (FAF) of at least 0.0003 but less than 0.001 in one eligible continental genetic-ancestry subpopulation, with at least 2,000 alleles tested and at least 2 variant alleles. gnomAD v4.1 reports a maximum joint FAF of 0.00001328; the highest ordinary eligible subpopulation is Admixed American at AF 0.0000500283, below 0.0003. The Remaining-individuals group is excluded by the VCEP rule.

VCEP rule

Filtering allele frequency (FAF) of ≥ 0.0003 but \< 0.001 in gnomAD continental subpopulations of a single genetic ancestry group (excluding genetic ancestry groups influenced by founder effects, such as Ashkenazi Jewish, Finnish, Amish, Middle Eastern, and “Remaining”). Genetic ancestry group must have ≥2,000 alleles tested and a minimum of 2 alleles present. Caution should be exerted if the majority of alleles have a variant allele fraction ( “allele balance” in gnomAD) below 0.35.

Evidence considered

• ClinGen TP53 VCEP v2.4 BS1 rule: eligible continental-subpopulation FAF must be ≥0.0003 but <0.001, with ≥2,000 alleles tested and ≥2 variant alleles; founder-effect groups including Remaining are excluded.
• The VCEP rule states that its BS1 cutoff used prevalence 1 in 5,000, genetic and allelic heterogeneity of 100%, and penetrance of 30%.
• gnomAD v4.1: maximum joint grpmax FAF 1.328e-05; highest ordinary subpopulation was Admixed American, 3/59,966 alleles, AF 5.00283494e-05; homozygotes = 0.

Sources

Reasoning

The TP53 VCEP Functional Worksheet Supplementary Table S3 exact row for R337H (corresponding to NM_000546.6:c.1010G>A / p.Arg337His) assigns the pre-assigned functional code No evidence, despite recording Kato as Partially functional, Giacomelli as noLOF, and Kawaguchi as Monomer. That governing pre-assignment outranks a threshold-based reassessment. The VCEP BS3_Supporting rule requires partially functional Kato data and no evidence of LOF by all available assays; the worksheet's final pre-assigned result is No evidence, so BS3 is not applied.

VCEP rule

Partially functional on Kato et al. data **AND** no evidence of loss of function (LOF) by **all** available assays

Evidence considered

• ClinGen TP53 VCEP Functional Worksheet, Supplementary Table S3, row R337H: Kato class Partially functional; Funk NA; Giacomelli class noLOF; Kotler NA; Kawaguchi class Monomer; preliminary functional code No evidence.
• ClinGen TP53 VCEP functional-code flowchart: for missense variants with Kato data, Partially functional (Kato) requires noLOF by all available assays for BS3_Supporting.
• The exact variant was searched as c.1010G>A, p.Arg337His, and p.R337H in both governing functional VCEP files; the Functional Worksheet matched p.R337H, while the flowchart contains no variant-specific row.

Sources

Reasoning

NM_000546.6:c.1010G>A is a missense variant, p.(Arg337His), so the missense BP4 pathway requires both a qualifying BayesDel result and no predicted splicing. The governing TP53 Supplementary Table S2 assigns the exact row c.1010G>A / p.Arg337His / Class C0 / BayesDel 0.177746 / No evidence; because the BayesDel score is above the supporting BP4 upper bound of <0.16, BP4 is not met. SpliceAI max delta is 0.001, below the required <0.2 no-splicing condition, but that condition alone cannot establish BP4. The single-amino-acid-deletion spreadsheet has no entry for this missense variant.

VCEP rule

**Missense variants** _(See flowchart for application of PP3 and BP4 rules for missense variants):_ ... BayesDel < 0.16 and > -0.008 irrespective of aGVGD score (except C65, this case do not apply BP4) AND no predicted differences in splicing (SpliceAI < 0.2)

Evidence considered

• ClinGen TP53 VCEP Supplementary Table S2 (PP3-BP4-codes.xlsx), matching row: c.1010G>A; p.Arg337His; BayesDel class C0; BayesDel score 0.177746; assigned code No evidence.
• ClinGen TP53 VCEP BP4 missense rule: BayesDel < 0.16 and > -0.008, with no predicted differences in splicing (SpliceAI < 0.2); the VCEP lookup row's BayesDel 0.177746 and No evidence assignment fail this pathway.
• SpliceAI Lookup for NM_000546.6:c.1010G>A: max delta score 0.001, below the VCEP no-splicing cutoff of 0.2; this satisfies only the splice component, not the BayesDel component.

Still missing

• No variant-specific entry for c.1010G>A, p.Arg337His, or p.R337H was found in Flowchart-for-application-of-PP3%2C-BP4%2C-and-BP7.pdf; the flowchart supplies the governing rule rather than a variant lookup.
• No entry for c.1010G>A, p.Arg337His, or p.R337H was found in TP53-single-amino-acid-deletions-BayesDel-scores-(1).xlsx; that file covers single amino acid in-frame deletions, not this missense variant.

Sources

Reasoning

The TP53 VCEP permits PS1 only for a variant asserted as pathogenic or likely pathogenic under its specifications when compared with the same amino-acid change, with splicing excluded. The available evidence establishes TP53 p.Arg337His itself, but does not identify a distinct nucleotide change producing the same p.Arg337His substitution that has been established as pathogenic or likely pathogenic under the TP53 VCEP. SpliceAI is 0.001, below the VCEP's 0.2 exclusion threshold, but that does not supply the required comparator.

Evidence considered

• The TP53 VCEP PS1 instructions require comparison with variants asserted as pathogenic or likely pathogenic following the TP53 VCEP specifications and require no splicing difference; the available same-residue comparator search found 0 same-residue candidates.
• SpliceAI maximum delta score is 0.001 for NM_000546.6:c.1010G>A (p.Arg337His), so the VCEP splicing exclusion is satisfied.

Still missing

• A verified distinct nucleotide change producing p.Arg337His and established as pathogenic or likely pathogenic under the TP53 VCEP is required.

Sources

Reasoning

The TP53 VCEP assigns PS2 strength by de novo proband cancer points, with 1 point supporting, 2-3 points moderate, 4-7 points strong, and at least 8 points very strong. The reviewed variant-specific evidence includes inherited R337H families and explicitly reports no evidence of de novo mutation in the 30-kindred cohort, but provides no qualifying de novo proband with confirmed or assumed maternity and paternity for this variant. The governing Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf was searched under c.1010G>A, p.Arg337His, and p.R337H; no variant-specific pre-assigned PS2 entry was found.

VCEP rule

1 point

Evidence considered

• The TP53 VCEP PS2 rules specify Supporting at 1 point, Moderate at 2-3 points, Strong at 4-7 points, and Very Strong at >=8 points.
• PMID:16033918 examined 927 individuals from 30 southern Brazilian kindreds with germline R337H and reported no evidence of de novo mutation; the available finding does not document a qualifying de novo proband for PS2.
• The governing LFS cancer points table was searched for c.1010G>A, p.Arg337His, and p.R337H and contained no variant-specific entry.

Still missing

• No qualifying de novo proband with parental testing and an eligible LFS-associated cancer was identified for this variant.
• No entry for c.1010G>A, p.Arg337His, or p.R337H was found in Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf.

Sources

Reasoning

The governing TP53 VCEP PS4 table assigns points only for Revised Chompret criteria (0.5), Classic LFS criteria (1), or HER2-positive breast cancer diagnosed before age 40 (0.5), with Supporting at 1-1.5 points, Moderate at 2-3.5, Strong at 4-7.5, and Very Strong at >=8. PMID:19046423 reports the exact R337H variant in 3/123 breast-cancer cases and 0/223 matched controls; using a Haldane-Anscombe correction, the OR is 13.09 (95% CI 0.67-255.59), so the interval includes 1. The available extract does not establish the individual patients' Chompret or Classic-LFS status, HER2 status, or age, and the VCEP point table therefore cannot be applied to assign a PS4 strength. The case-control result was verified in the paper extract and is not sufficient by itself to map to the VCEP's required point-based strength thresholds.

VCEP rule

Clinical criteria | Revised Chompret | 0.5 Clinical criteria | Classic LFS criteria | 1 Tumor pathology | HER2+ breast cancer < 40 y [*] | 0.5 PS4 code strength based on total points: PS4_Supporting = 1-1.5 points PS4_Moderate = 2-3.5 points PS4 = 4-7.5 points PS4_Very Strong = >= 8 points

Evidence considered

• PS4-Points-Table.pdf, table row 'Clinical criteria | Revised Chompret | 0.5', row 'Clinical criteria | Classic LFS criteria | 1', row 'Tumor pathology | HER2+ breast cancer < 40 y | 0.5'; strength thresholds: Supporting 1-1.5, Moderate 2-3.5, PS4/Strong 4-7.5, Very Strong >=8 points.
• PMID:19046423, Association of the germline TP53 R337H mutation with breast cancer in southern Brazil: exact R337H was found in 3 of 123 breast-cancer patients and 0 of 223 age-matched controls; the paper reports p=0.0442. The case-control counts were treated as a case-control comparison and the odds ratio was computed with a Haldane-Anscombe correction: (3.5 x 223.5)/(119.5 x 0.5) = 13.09, 95% CI 0.67-255.59.
• PMID:16033918, R337H was observed in 40 of 40 tested children with adrenocortical tumour in a pedigree-based cohort, but the study reported 9.9% ACT penetrance and no clear increased predisposition to other typical TP53 cancers; it does not provide the VCEP PS4 proband categories needed for point assignment.
• PMID:16494995, R337H occurred in six of 13 Brazilian LFS/LFL families and all 53 cancer-free Brazilian controls tested were wild type at codon 337; individual point-category data required by the VCEP table are not provided in the extract.
• PMID:10864200, one R337H carrier family included a proband with adrenocortical carcinoma at age 4 and a paternal uncle with a brain tumour at age 33; the available report does not establish the VCEP PS4 point category for the proband cohort.

Still missing

• Patient-level Revised Chompret or Classic LFS criteria, HER2 status, and age are unavailable for the reported PS4 cohorts; PS4-Points-Table.pdf was searched and contains no variant-specific entry.

Sources

Reasoning

The VCEP PM5 rule requires a different missense variant at residue 337 that was previously determined pathogenic or likely pathogenic according to the TP53 VCEP, with the prior classification reached without PM5. The available TP53 functional worksheet lists R337C and R337G functional results, but does not establish either comparator as pathogenic or likely pathogenic under the VCEP; the comparator collection found no qualifying same-residue classification.

Evidence considered

• The TP53 VCEP PM5 rule requires one or more different missense variants at the same amino-acid residue previously determined pathogenic or likely pathogenic according to the TP53 VCEP, and the prior classification must be reached without PM5.
• TP53 Supplementary Table S3 lists R337C as non-functional/LOF with PS3 and R337G as non-functional/LOF with PS3, but these functional assignments are not qualifying VCEP pathogenic or likely pathogenic comparator classifications.
• The PM5 comparator collection reports 0 same-residue candidates and 0 expert-panel or non-expert-majority pathogenic/likely pathogenic candidates.

Still missing

• A distinct residue-337 missense comparator with a verified TP53 VCEP pathogenic or likely pathogenic classification reached without PM5 is required.

Sources

Reasoning

The TP53 VCEP requires cosegregation in 3-4 meioses for Supporting, 5-6 meioses for Moderate, or at least 7 meioses across more than one family for Strong. The literature documents inherited R337H in multiple families and family-member testing, including 30 Brazilian kindreds and 6 of 13 LFS/LFL families, but the available extractions do not provide a count of informative cosegregating meioses for c.1010G>A. The governing Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf was searched under c.1010G>A, p.Arg337His, and p.R337H; no variant-specific pre-assigned PP1 entry was found.

VCEP rule

Cosegregation must be observed in 3-4 meioses in/across 1 or more families ... Cosegregation must be observed in 5-6 meioses in/across 1 or more families ... Cosegregation must be observed in ≥ 7 meioses across > 1 family

Evidence considered

• The TP53 VCEP PP1 rules require cosegregation in 3-4 meioses for Supporting, 5-6 meioses for Moderate, and at least 7 meioses across more than one family for Strong.
• PMID:10864200 reports inherited Arg337His in family 108, with an adrenocortical carcinoma proband diagnosed at age 4 and a paternal uncle with a brain tumour at age 33, but does not provide an auditable meiosis count in the extracted finding.
• PMID:16033918 studied 30 southern Brazilian kindreds and reported 40 tested children with ACT carrying R337H and 240 of 695 tested individuals in carrier parental lines positive, but these totals do not establish the number of informative cosegregating meioses.
• PMID:16494995 reports R337H in 6 of 13 Brazilian LFS/LFL families and family-member segregation testing, but the extracted finding does not provide an informative meiosis count.
• The governing LFS cancer points table was searched for c.1010G>A, p.Arg337His, and p.R337H and contained no variant-specific entry.

Still missing

• An auditable count of informative cosegregating meioses for c.1010G>A is not available in the reviewed evidence.
• No entry for c.1010G>A, p.Arg337His, or p.R337H was found in Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf.

Sources

Reasoning

The TP53 VCEP defines PP4 here for low-VAF observations from multigene panel testing: Moderate requires at least two independent observations with VAF 5-25%, and Supporting requires an observation with VAF 5-35%. The available case evidence contains no qualifying patient VAF observations or confirmation that the variant was detected on multigene panel testing, so PP4 cannot be assessed.

VCEP rule

At least 2 independent observations of the variant with VAF 5-25%. ... Observation of the variant with VAF 5-35% (i.e., once or multiple times with VAF >25-35% and/or once with VAF 5-25%)

Evidence considered

• The available case materials provide published germline cohort and case-control observations but no qualifying low-VAF multigene-panel observations for PP4.

Still missing

• No patient-level VAF values, number of independent observations, or multigene-panel testing context are available.

Sources

Reasoning

The available case evidence does not provide a count of unrelated female TP53 carriers from one source who reached at least age 60 without cancer, nor does it provide the required exclusion details for late sarcoma or somatic VAF. Therefore the TP53 VCEP BS2 thresholds cannot be evaluated.

VCEP rule

Benign strong/moderate/supporting by count

Evidence considered

• No qualifying BS2 carrier-count dataset with age, sex, cancer status, source provenance, late-sarcoma status, and VAF is present in the reviewed case evidence.

Still missing

• A single-source count of unrelated female TP53 carriers who reached age 60 without cancer, with late-sarcoma and VAF exclusions, is missing.

Sources

Reasoning

The TP53 VCEP BS4 rule requires lack of segregation in affected family members diagnosed with LFS-associated cancers listed in the governing table. The reviewed R337H literature describes affected relatives and also unaffected carriers, but does not establish a documented lack of segregation in affected family members for this variant under the VCEP cancer definitions. Therefore BS4 cannot be applied.

VCEP rule

Lack of segregation in affected family members (i.e. family members diagnosed with LFS-associated cancers as described in Table of LFS Cancers and Points for PS2 and PP1 Code Application).

Evidence considered

• The TP53 VCEP BS4 rule is lack of segregation in affected family members diagnosed with LFS-associated cancers as described in the governing LFS cancer table.
• PMID:10864200 reports an affected proband with adrenocortical carcinoma and a paternal uncle with a brain tumour in family 108, but does not document lack of segregation.
• PMID:16494995 reports R337H families with breast cancer, brain tumors, sarcomas, and adrenocortical carcinoma, and four unaffected carriers in one family; this is not sufficient to establish the specific BS4 lack-of-segregation rule.
• The governing LFS cancer points table was searched for c.1010G>A, p.Arg337His, and p.R337H and contained no variant-specific entry.

Still missing

• No auditable affected-relative genotype/phenotype comparison demonstrating lack of segregation was available.
• No entry for c.1010G>A, p.Arg337His, or p.R337H was found in Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf.

Sources