SETD2 c.6631G>T, p.(Gly2211Ter)

Reasoning

Generic ClinGen SVI PVS1 recommendations (PMC6185798) apply because no SETD2-specific VCEP or CSPEC framework is available and the gene-level evidence supports germline loss of function as a disease mechanism. NM_014159.6:c.6631G>T is a nonsense variant, NM_014159.6 is the selected RefSeq transcript, and the variant is in exon 15 of 19, with four downstream exons. The predicted stop at NP_054878.5:p.(Gly2211Ter) occurs 354 amino acids before the 2565-amino-acid reference protein terminus and is therefore expected to be well upstream of the final exon-exon junction, making escape from nonsense-mediated decay unlikely. No evidence indicates a non-critical distal exon, repeat-region exception, or population loss-of-function enrichment. Because no named SVI or VCEP downgrade rule is triggered, PVS1 remains at full strength: very strong.

Rule

generic ClinGen SVI PVS1 framework (PMC6185798)

Evidence considered

• The case-specific assessment identifies NM_014159.6:c.6631G>T as a nonsense variant causing NP_054878.5:p.(Gly2211Ter).
• VariantValidator places the variant in exon 15, while the transcript structure contains four downstream exons; the predicted stop is 354 amino acids before the 2565-amino-acid reference protein terminus.
• The gene-level context supports SETD2 loss of function as a germline disease mechanism and marks the PVS1 gene gate eligible.
• The ClinGen SVI PVS1 recommendations (PMC6185798) support full-strength PVS1 for a disease-relevant nonsense variant expected to undergo nonsense-mediated decay when no downgrade rule applies.
• No direct RNA assay confirming nonsense-mediated decay, non-critical distal exon exception, repeat-region exception, or population loss-of-function enrichment was identified.

Still missing

• Direct RNA evidence confirming nonsense-mediated decay was not available.
• The selected transcript is NM_014159.6, for which a newer NM_014159.7 version is available; transcript equivalence should be confirmed if clinically material.

Sources

Reasoning

No applicable SETD2-specific VCEP or gene framework was available, so generic ACMG/AMP population rules were used. The variant is absent from gnomAD v2.1 and gnomAD v4.1, and the available non-cancer gnomAD v2.1 exome and v3.1 genome subsets also report absence. This supports PM2 at supporting strength as a rare variant in population databases, without assuming that absence alone establishes pathogenicity.

Rule

Generic ACMG/AMP PM2: the variant is absent or extremely rare in population databases appropriate for the disease context; apply at supporting strength here because no gene-specific calibration is available.

Evidence considered

• gnomAD v2.1 reports the variant as absent.
• gnomAD v4.1 reports the variant as absent.
• The case data additionally report absence from GNOMAD_V2_1_NON_CANCER exomes and GNOMAD_V3_1_NON_CANCER genomes; no disease-specific population threshold requiring a different source was available because no VCEP specification was found.
• The evidence supports rarity only; it does not by itself establish pathogenicity, penetrance, or disease mechanism.

Sources

Reasoning

PP5 is restricted here to an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic. ClinVar returned no exact match for NM_014159.6:c.6631G>T, with no variation ID, classification, review status, or expert-panel assertion; therefore PP5 is not met. OncoKB's Likely Oncogenic label is not a ClinVar expert-panel assertion and is not used for PP5.

Rule

PP5 applies only when an exact-variant ClinVar expert panel classifies the variant as Pathogenic or Likely pathogenic; ordinary submissions, aggregate labels, non-expert assertions, and other databases do not trigger PP5.

Evidence considered

• ClinVar exact-variant search reported no result for NM_014159.6:c.6631G>T; no expert-panel classification was available.
• The OncoKB Likely Oncogenic label is not an exact-variant ClinVar expert-panel classification and was excluded from PP5.

Sources

Reasoning

No applicable SETD2-specific VCEP or gene framework was available, so generic ACMG/AMP population rules were used. The variant is absent from gnomAD v2.1 and gnomAD v4.1, with no observed allele frequency approaching the BA1 threshold for a stand-alone benign call (typically >5% in a suitable population).

Rule

Generic ACMG/AMP BA1: allele frequency is sufficiently high in a population database to stand alone as benign evidence; absence or rarity does not meet BA1.

Evidence considered

• gnomAD v2.1 reports the variant as absent.
• gnomAD v4.1 reports the variant as absent.
• The case data also report absence from the available non-cancer gnomAD v2.1 exome and v3.1 genome subsets; no population-specific frequency is present to support BA1.

Sources

Reasoning

No applicable SETD2-specific VCEP or gene framework was available, so generic ACMG/AMP population rules were used. The variant is absent from gnomAD v2.1 and gnomAD v4.1; therefore, its frequency is not greater than expected for the relevant disease and penetrance model. No threshold artifact or ancestry-specific excess was identified.

Rule

Generic ACMG/AMP BS1: allele frequency is greater than expected for the disorder; an absent variant cannot satisfy this benign criterion.

Evidence considered

• gnomAD v2.1 reports the variant as absent.
• gnomAD v4.1 reports the variant as absent.
• The case data also report absence from the available non-cancer gnomAD v2.1 exome and v3.1 genome subsets, so there is no excess frequency in those subsets either.

Sources

Reasoning

BP6 is restricted here to an exact-variant ClinVar expert-panel classification of Benign or Likely benign. ClinVar returned no exact match for NM_014159.6:c.6631G>T, with no variation ID, classification, review status, or expert-panel assertion; therefore BP6 is not met. No ordinary laboratory submission, aggregate ClinVar label, non-expert assertion, or other database label was used as a substitute.

Rule

BP6 applies only when an exact-variant ClinVar expert panel classifies the variant as Benign or Likely benign; ordinary submissions, aggregate labels, non-expert assertions, and other databases do not trigger BP6.

Evidence considered

• ClinVar exact-variant search reported no result for NM_014159.6:c.6631G>T; no expert-panel classification was available.
• No non-expert or aggregate assertion was treated as sufficient for BP6.

Sources

Reasoning

No case-level evidence documents that NM_014159.6:c.6631G>T occurred de novo in an affected proband. The available materials contain no proband phenotype record, parental genotypes, maternity or paternity confirmation, or recurrence information. Therefore, confirmed de novo evidence required for PS2 cannot be assessed.

Rule

Generic ACMG/AMP PS2: apply only when the variant is confirmed de novo in the proband with confirmed maternity and paternity; otherwise do not apply.

Evidence considered

• The case materials provide variant normalization and population/database results but no family-based clinical observation, parental testing, or confirmed de novo report.
• No applicable SETD2-specific VCEP or CSPEC framework was available; generic ACMG/AMP interpretation is used as the fallback, but the required de novo evidence is absent.

Still missing

• Proband phenotype and clinical diagnosis
• Maternal and paternal variant testing results
• Maternity and paternity confirmation
• Independent de novo observations or relevant recurrence data

Reasoning

No validated functional assay directly testing SETD2 NM_014159.6:c.6631G>T (p.Gly2211Ter) was identified. The reviewed publications provide gene-level or truncating-mutation context, including reduced H3K36me3 in SETD2-mutant tumors, but none reports this exact variant or supplies variant-specific assay results with appropriate controls. Therefore, PS3 cannot be applied under the generic ACMG/AMP framework; the variant's predicted nonsense consequence is not itself functional assay evidence.

Rule

Generic ACMG/AMP PS3: well-established functional studies supportive of a damaging effect may support PS3; variant-specific, validated assay evidence is required, and gene-level or other-variant observations are insufficient.

Evidence considered

• PMID:23417712 did not mention c.6631G>T or p.Gly2211Ter; it studied pediatric high-grade gliomas and reported reduced H3K36me3 in SETD2-mutant tumors as a group.
• PMID:24509477 did not mention c.6631G>T or p.Gly2211Ter; it studied other truncating SETD2 mutations and leukemia models, including Setd2 knockdown experiments.
• PMID:25728682 did not mention c.6631G>T or p.Gly2211Ter; it studied other SETD2 loss-of-function contexts in renal cancer cell lines and reported reduced H3K36me3 and replication-stress phenotypes.
• None of the reviewed sources provides a controlled functional result for this exact variant, so PS3 is not applied.

Still missing

• A validated assay directly comparing p.Gly2211Ter with wild-type SETD2 and appropriate positive and negative controls is unavailable.
• No variant-specific readout of SETD2 function, such as H3K36me3 methyltransferase activity or validated cellular rescue, was identified.

Sources

Reasoning

No exact-variant case-control study, affected-case count, or statistically significant enrichment estimate was identified for NM_014159.6:c.6631G>T. PMID:23417712 reports enrichment of SETD2 truncating mutations as a group in high-grade glioma, but explicitly does not mention this variant and therefore cannot establish PS4 for it. No gene-specific VCEP framework was retrieved; generic ACMG/AMP fallback was used.

Rule

Generic PS4: statistically significant enrichment of the variant in affected individuals compared with controls; no exact-variant enrichment evidence was available.

Evidence considered

• The case materials contain no exact-variant PS4 case-control counts, odds ratio, likelihood ratio, or other enrichment estimate.
• PMID:23417712 reports significant enrichment of SETD2 truncating mutations in pediatric high-grade gliomas versus 543 controls, but the paper does not mention c.6631G>T or p.(G2211*), so the gene-level finding is not assigned to this variant.
• No SETD2-specific VCEP/CSPEC framework was retrieved; generic ACMG/AMP fallback was therefore used.

Still missing

• An exact-variant case-control dataset or validated affected-case enrichment estimate is needed.

Sources

Reasoning

No applicable SETD2-specific VCEP specification was identified, so generic ACMG/AMP interpretation applies. PM3 requires observations of the variant in trans with a pathogenic or likely pathogenic variant in affected individuals with a recessive disorder, with strength based on informative proband and phase observations. The available case evidence contains no affected-proband observations, second pathogenic variants, parental testing, or phase data for NM_014159.6:c.6631G>T. Therefore PM3 cannot be assessed.

Rule

Generic ACMG/AMP PM3: apply when the variant is observed in trans with a pathogenic or likely pathogenic variant in an affected individual with a recessive disorder; strength depends on the number and informativeness of observations.

Evidence considered

• The case evidence identifies SETD2 NM_014159.6:c.6631G>T (p.Gly2211Ter) but provides no affected-proband series, additional pathogenic allele, parental testing, or phase information.
• No SETD2-specific VCEP or gene-specific allelic rule was available; generic ACMG/AMP criteria were therefore used.
• The reviewed literature findings concern somatic SETD2 mutation spectra or functional loss-of-function effects and do not provide PM3-relevant germline in-trans observations for this variant.

Still missing

• Affected-proband observations are not available.
• No pathogenic or likely pathogenic variant in the same individual is documented.
• No parental testing or cis/trans phase information is available.
• The inheritance context needed for PM3 is not established in the available evidence.

Reasoning

No case-level or published observation documents an assumed de novo occurrence of NM_014159.6:c.6631G>T in an affected individual without confirmed maternity and paternity. The available materials contain no proband phenotype, parental testing, or family-history evidence. Therefore, PM6 cannot be assessed.

Rule

Generic ACMG/AMP PM6: apply only for an assumed de novo occurrence in an affected individual when maternity and paternity are not confirmed; no qualifying observation is available here.

Evidence considered

• The available case materials contain no affected-family-member report, parental genotype information, or assumed de novo observation for this variant.
• The reviewed literature extracts concern SETD2 somatic or gene-level loss-of-function findings and do not report this variant or a relevant de novo clinical observation.

Still missing

• Affected individual and phenotype documentation
• Parental testing results or family history
• Documentation supporting an assumed rather than confirmed de novo occurrence

Reasoning

No affected relatives, unaffected relatives, informative meioses, phenotype assessments, or variant genotypes are provided for this family or for published families carrying NM_014159.6:c.6631G>T. Consequently, cosegregation evidence and any strength escalation for PP1 cannot be evaluated.

Rule

Generic ACMG/AMP PP1: apply when a variant cosegregates with disease in affected family members; the amount of supporting evidence and any strength escalation require informative meioses and phenotype/genotype data.

Evidence considered

• No pedigree, relative-level phenotype, relative-level genotype, or meiosis count is present in the available case materials.
• The reviewed papers report population, tumor, or functional SETD2 findings rather than clinical family segregation for NM_014159.6:c.6631G>T.

Still missing

• Family pedigree and phenotype data
• Variant genotypes in affected and unaffected relatives
• Number of informative meioses
• Independent families or segregation studies

Reasoning

The case materials provide no patient phenotype, clinical feature list, or disease-specific phenotype match for the individual carrying NM_014159.6:c.6631G>T. The SETD2 literature retrieved here is not an exact-variant clinical case report and cannot establish a specific phenotype match for PP4. No gene-specific VCEP framework was retrieved.

Rule

Generic PP4: the patient's phenotype or family history is highly specific for a disease with a single-gene etiology; patient phenotype evidence was unavailable.

Evidence considered

• No patient-level phenotype or clinical presentation is present in the case materials.
• The reviewed SETD2 publications do not report this exact variant in a clinical case and therefore do not establish PP4.

Still missing

• Patient-level phenotype information and a defined disease-specific phenotype spectrum are needed.

Sources

Reasoning

No applicable SETD2-specific VCEP or gene framework was available, so generic ACMG/AMP rules were considered. The population resources report absence of the variant, but they do not provide evidence that an unaffected adult homozygote or multiple unaffected individuals carry it. Absence from a database is not evidence of observed unaffected homozygosity, so BS2 cannot be applied.

Rule

Generic ACMG/AMP BS2: observation of the variant in healthy adults, including unaffected homozygotes where applicable, can support benign evidence; absence of observations is not BS2 evidence.

Evidence considered

• gnomAD v2.1 and v4.1 report the variant as absent, which does not establish the presence of unaffected homozygotes.
• No homozygote count, unaffected-carrier series, disease-prevalence estimate, or penetrance-calibrated BS2 analysis is available in the case evidence.

Still missing

• No documented unaffected adult homozygote or suitable unaffected-carrier series is available for this variant.

Sources

Reasoning

No validated functional assay directly testing SETD2 NM_014159.6:c.6631G>T (p.Gly2211Ter) demonstrated a normal or preserved functional effect. The reviewed publications examine other SETD2 mutations, loss-of-function models, or tumor-level biology and do not provide a benign assay result for this exact variant. Consequently, BS3 cannot be applied under the generic ACMG/AMP framework.

Rule

Generic ACMG/AMP BS3: well-established functional studies showing no damaging effect may support BS3; a validated benign result for the evaluated variant with appropriate controls is required.

Evidence considered

• PMID:23417712 did not mention c.6631G>T or p.Gly2211Ter and did not provide a benign functional result for this variant.
• PMID:24509477 did not mention c.6631G>T or p.Gly2211Ter and did not provide a benign functional result for this variant.
• PMID:25728682 did not mention c.6631G>T or p.Gly2211Ter and did not provide a benign functional result for this variant.
• Because no exact-variant assay demonstrates preserved function, BS3 is not applied.

Still missing

• A validated assay directly testing p.Gly2211Ter for preserved SETD2 function is unavailable.
• No assay-specific controls or quantitative benign-effect threshold for this exact variant were identified.

Sources

Reasoning

No unaffected relatives with reliable phenotype assessment and confirmed absence of NM_014159.6:c.6631G>T are documented. Without informative non-segregation observations, BS4 cannot be distinguished from simply unavailable family data and is not applied.

Rule

Generic ACMG/AMP BS4: apply when a variant is observed not to segregate with disease in affected or appropriately informative family members; no qualifying non-segregation evidence is available here.

Evidence considered

• The available case materials contain no variant-negative relatives, phenotype assessments of unaffected relatives, or family-based non-segregation results.
• Population absence from gnomAD does not provide the family-based non-segregation evidence required for BS4.

Still missing

• Unaffected relatives with reliable phenotype assessment
• Confirmed variant-negative testing in those relatives
• Informative family structure and penetrance context

Reasoning

No applicable SETD2-specific VCEP specification was identified, so generic ACMG/AMP interpretation applies. BP2 requires the variant to be observed in trans with a pathogenic or likely pathogenic variant for a dominant disorder, or in cis with a pathogenic variant for a recessive disorder, with the relevant inheritance and phase established. The available case evidence contains no second pathogenic variant, affected-proband observation, parental testing, or cis/trans phase data for NM_014159.6:c.6631G>T. Therefore BP2 cannot be assessed.

Rule

Generic ACMG/AMP BP2: apply when the variant is observed in trans with a pathogenic or likely pathogenic variant for a dominant disorder, or in cis with a pathogenic variant for a recessive disorder, with phase and inheritance adequately established.

Evidence considered

• The case evidence provides no second pathogenic or likely pathogenic allele, family segregation data, parental testing, or phase determination for NM_014159.6:c.6631G>T.
• No SETD2-specific VCEP or gene-specific allelic rule was available; generic ACMG/AMP criteria were therefore used.
• The reviewed literature findings do not report this germline variant in a cis or trans allelic context and cannot establish BP2.

Still missing

• No pathogenic or likely pathogenic variant in the same individual is documented.
• No parental testing or cis/trans phase information is available.
• The inheritance context needed to select the BP2 configuration is not established.
• No affected-proband observation is available to support interpretation of the allelic relationship.

Reasoning

No clinical phenotype, molecular diagnosis, or independent disease-causing variant information was provided for this case that would demonstrate an alternative molecular explanation for the patient's phenotype. The available literature concerns SETD2 biology and does not establish an alternative cause for this individual; BP5 cannot be assessed.

Rule

Generic BP5: an alternate molecular basis explains the patient's phenotype; no patient-level alternate cause was available.

Evidence considered

• The case materials contain no patient phenotype, competing diagnosis, or alternate pathogenic variant for the individual.
• The reviewed literature does not provide patient-level evidence of an alternative cause for this case.

Still missing

• Patient-level phenotype and testing information identifying an alternative molecular cause are needed.