SDHD c.281C>G, p.Ser94Cys

Reasoning

PM2 is met at supporting strength. The variant is present at extremely low frequency in the default all-comers population datasets: gnomAD v4.1 AF=3.7174e-06 from 6/1614032 alleles with 0 homozygotes, and gnomAD v2.1 AF=7.95292e-06 from 2/251480 alleles with 0 homozygotes. The non-cancer subsets are concordant: gnomAD v2.1 non-cancer exomes AF=8.44088e-06 from 2/236942 alleles with 0 homozygotes and gnomAD v3.1 non-cancer genomes AF=6.7605e-06 from 1/147918 alleles with 0 homozygotes. The maximum observed/default frequencies are below the supplied PM2 supporting threshold of <=0.0001.

Rule

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 all-comers: AF=3.7174e-06 from 6/1614032 alleles, homozygotes=0; grpmax FAF=5.53e-06.
• gnomAD v2.1 all-comers: AF=7.95292e-06 from 2/251480 alleles, homozygotes=0; non-cancer exomes: AF=8.44088e-06 from 2/236942 alleles, homozygotes=0.
• gnomAD v3.1 non-cancer genomes: AF=6.7605e-06 from 1/147918 alleles, homozygotes=0; v3.1 has no exome cohort.
• The supplied generic PM2 calibration threshold is <=0.0001 for supporting PM2, identified as the ClinGen SVI recommendation (PMID:25741868).

Sources

Reasoning

The variant is a missense substitution, NM_003002.4:c.281C>G (NP_002993.1:p.(Ser94Cys)), so the governing generic rule selects the REVEL path only; SpliceAI and BayesDel are not used for PP3 in this situation. The REVEL score is 0.8, meeting the calibrated moderate PP3 threshold of >= 0.773 from Pejaver et al. 2022 (PMID:36413997).

Rule

Missense variant -> REVEL only. Its SpliceAI score says nothing about whether the amino-acid substitution is tolerated, so 'no predicted splice impact' is never BP4 support for a missense variant. ... PP3 (moderate): >= 0.773 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• NM_003002.4:c.281C>G is a missense variant encoding NP_002993.1:p.(Ser94Cys), selecting the REVEL-only path; SpliceAI is not counted for a missense PP3 decision.
• Local REVEL predictor lookup reports a score of 0.8.
• The supplied ClinGen SVI REVEL calibration assigns PP3 moderate at >=0.773; this threshold is from Pejaver et al. 2022, Am J Hum Genet (PMID:36413997).

Sources

Reasoning

The variant is SDHD c.281C>G, p.Ser94Cys. No previously established pathogenic variant producing the same Ser94Cys amino-acid change through a different nucleotide change was identified in the reviewed evidence. PMID:17576205 reports a different exon 3 deletion affecting codons 91-94, not a pathogenic missense substitution at residue 94, and the ClinVar record for the exact variant is uncertain significance rather than pathogenic or likely pathogenic.

Rule

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

Evidence considered

• ClinVar variation 412506 lists SDHD NM_003002.4:c.281C>G (p.Ser94Cys) as uncertain significance with multiple submitters and no conflicts.
• Neumayer et al. 2007, PMID:17576205, Results/Patient-family 3 and Table 1: the reported exon 3 event is c.271_282del, a 12-bp deletion affecting codons 91-94, not the same amino-acid missense change.

Sources

Reasoning

BA1 is not met. The governing generic stand-alone threshold is >=0.05 (5%). The required filtering frequency is the gnomAD v4.1 grpmax FAF of 5.53e-06 (0.000553%), far below 0.05; the higher Admixed American popmax point estimate of 3.33311e-05 is not used for BA1, and its observed allele count is only 2/60004. The gnomAD v2.1 all-comers frequency was 2/251480 (7.95292e-06), and the non-cancer exome frequency was 2/236942 (8.44088e-06), also far below the threshold. No disease-associated pathogenic consensus is available that would create a conflict with a high-frequency benign call.

Rule

BA1: Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v4.1: total AF 3.7174e-06 from 6/1614032 alleles, homozygotes=0; filtering grpmax FAF=5.53e-06 (0.000553%), while the Admixed American popmax point estimate is 3.33311e-05 from 2/60004 alleles and is not used.
• gnomAD v2.1 all-comers: AF 7.95292e-06 from 2/251480 alleles, homozygotes=0; gnomAD v2.1 non-cancer exomes: AF 8.44088e-06 from 2/236942 alleles, homozygotes=0.
• The supplied generic BA1 calibration threshold is >=0.05, identified as the ACMG/AMP 2015 stand-alone benign allele-frequency threshold (PMID:25741868).

Sources

Reasoning

BS1 is not met. The generic default threshold supplied for BS1 is >=0.01, whereas the appropriate gnomAD v4.1 filtering frequency is grpmax FAF=5.53e-06 (0.000553%), not the Admixed American popmax point estimate of 3.33311e-05. This frequency is far below 1% and does not provide evidence that the allele frequency is greater than expected for SDHD-related disease. The available data do not show an ancestry-confined elevated frequency or a founder/reduced-penetrance scenario that would require a maximum-credible-frequency calculation before rejecting the default BS1 path.

Rule

BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168)

Evidence considered

• gnomAD v4.1 filtering frequency: grpmax FAF=5.53e-06; total AF=3.7174e-06 from 6/1614032 alleles, homozygotes=0. The Admixed American popmax point estimate of 3.33311e-05 from 2/60004 alleles is not used for BS1.
• gnomAD v2.1 all-comers: AF 7.95292e-06 from 2/251480 alleles; non-cancer exomes: AF 8.44088e-06 from 2/236942 alleles.
• The supplied generic BS1 default is >=0.01; maximum-credible-frequency assessment is preferred when prevalence, penetrance, or allelic heterogeneity make the default potentially inappropriate (Whiffin et al. 2017, PMID:28518168). The observed frequency is nevertheless orders of magnitude below that default.

Sources

Reasoning

The variant is a missense substitution, so BP4 must be judged using REVEL only; the SpliceAI score cannot provide BP4 support for this missense variant, and BayesDel has no generic ACMG-strength calibration. The REVEL score is 0.8, which exceeds the supplied BP4 supporting cutoff of <= 0.29, so BP4 is not met.

Rule

Missense variant -> REVEL only. Its SpliceAI score says nothing about whether the amino-acid substitution is tolerated, so 'no predicted splice impact' is never BP4 support for a missense variant. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)

Evidence considered

• NM_003002.4:c.281C>G is a missense variant encoding NP_002993.1:p.(Ser94Cys), selecting the REVEL-only path; SpliceAI is not counted for a missense BP4 decision.
• Local REVEL predictor lookup reports a score of 0.8.
• The supplied ClinGen SVI REVEL calibration assigns BP4 supporting at <=0.29; this threshold is from Pejaver et al. 2022, Am J Hum Genet (PMID:36413997).

Sources

Reasoning

No variant-specific proband report documents confirmed maternity and paternity, de novo occurrence, absence of family history, or phenotype details sufficient to evaluate PS2. The available PMID:17576205 report concerns a different SDHD deletion, c.271_282del, found in an affected father and daughter, and cannot be transferred to NM_003002.4:c.281C>G.

Rule

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

Evidence considered

• No case-specific parental testing or de novo observation for NM_003002.4:c.281C>G is present in the available evidence.
• Neumayer et al. (PMID:17576205) reported a different SDHD exon 3 deletion, c.271_282del, in an affected daughter and father; that observation is not evidence for this variant.

Still missing

• Variant-specific proband phenotype and disease diagnosis
• Confirmed maternity and paternity
• Parental genotypes establishing de novo status
• Documented family history

Sources

Reasoning

PS3 cannot be assessed because the available evidence contains no variant-specific in vitro or in vivo functional study for NM_003002.4:c.281C>G (NP_002993.1:p.(Ser94Cys)). PMID:17576205 evaluated a different exon 3 deletion, c.271_282del, and did not report this variant or a functional assay for it. The available ClinVar record and general ACMG/AMP references do not provide validated, reproducible assay results, assay controls, or a demonstrated damaging effect for this variant.

Rule

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

Evidence considered

• PMID:17576205, Results, Patient/family 3 and Table 1: the reported exon 3 variant was c.271_282del, not NM_003002.4:c.281C>G; no assay result for p.Ser94Cys was provided.
• The evidence record contains no validated, reproducible, variant-specific functional assay, assay-control result, or direct demonstration of a damaging effect for NM_003002.4:c.281C>G (NP_002993.1:p.(Ser94Cys)).

Still missing

• A variant-specific, biologically relevant in vitro or in vivo functional assay with appropriate controls and reproducible evidence of impaired SDHD function is unavailable.

Sources

Reasoning

The generic PS4 rule requires a significantly increased prevalence in affected individuals compared with controls; the supplied literature was checked, including the PS4-indexed prospective series (PMID:19454582), but no source reports this exact variant, affected-carrier and control counts, or an odds ratio and 95% confidence interval. The paper packet's ai_classified_papers list is empty. Therefore no case-control enrichment calculation can be performed and PS4 is not assessed.

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:19454582 abstract: a prospective study recruited 445 patients with head and neck and/or thoracic-abdominal or pelvic paragangliomas, but the available abstract does not identify SDHD c.281C>G or provide exact-variant case/control counts.
• PMID:17576205 full-text extraction: the study sequenced 70 patients with apparently sporadic pheochromocytoma and reported a different SDHD exon 3 deletion, c.271_282del, not c.281C>G.
• PMID:20664475 and PMID:24319509 full-text extractions discuss SDHD-associated disease generally but do not mention c.281C>G or provide variant-specific prevalence comparisons.
• No odds ratio, relative risk, or 95% confidence interval for NM_003002.4:c.281C>G is available; consequently no numerical inequality against the generic PS4 threshold can be written.

Still missing

• Exact-variant case and matched control counts, or a reported odds ratio/relative risk with 95% confidence interval, are needed.

Sources

Reasoning

The variant is at residue 94 of SDHD. No SDHD VCEP or authoritative domain table is available, and the reviewed case evidence does not establish that residue 94 lies in a mutational hotspot or a critical, well-established functional domain lacking benign variation. The cancer-hotspot search found no statistically significant hotspot, but that negative result does not resolve whether residue 94 is in a critical functional domain; domain and benign-variation evidence are missing.

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 search for SDHD S94 returned no result and reported that the variant does not lie in a statistically significant hotspot.
• vcep_materials.json contains no SDHD VCEP materials and its domain_tables object is empty.

Still missing

• Authoritative SDHD critical-domain boundaries and evidence of absent benign variation at the relevant domain are unavailable.

Sources

Reasoning

The variant is SDHD p.Ser94Cys, but the available comparator collection contains no same-residue candidate variants and the reviewed literature does not establish a different pathogenic missense change at residue 94. The reported exon 3 c.271_282 deletion spans codons 91-94 and is not a qualifying different 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

• The same-residue comparator collection reports zero candidates.
• Neumayer et al. 2007, PMID:17576205, Results/Patient-family 3 and Table 1: c.271_282del affects codons 91-94 but is a deletion rather than a different pathogenic missense substitution at residue 94.

Still missing

• A sufficiently curated set of SDHD residue-94 missense variants with established pathogenic classifications is unavailable.

Sources

Reasoning

No variant-specific evidence shows that NM_003002.4:c.281C>G is assumed de novo. There is no documented affected proband, parental genotype, or family-history assessment for this variant; the available family report concerns a different SDHD deletion.

Rule

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

Evidence considered

• The available evidence contains no report of NM_003002.4:c.281C>G as de novo or assumed de novo.
• PMID:17576205 describes familial transmission of a different c.271_282del variant and does not establish PM6 for c.281C>G.

Still missing

• Variant-specific de novo observation
• Parental genotypes or documented lack of parental testing
• Affected proband phenotype and family history

Sources

Reasoning

No variant-specific segregation data are available for NM_003002.4:c.281C>G, including affected relatives, unaffected relatives, informative meioses, or genotype-phenotype concordance. A published SDHD family with c.271_282del is a different variant and cannot support PP1 for c.281C>G.

Rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. ... May be used as stronger evidence with increasing segregation data.

Evidence considered

• No affected-family-member segregation data for NM_003002.4:c.281C>G are documented.
• PMID:17576205 reports cosegregation of a different SDHD deletion, c.271_282del, in one affected father-daughter pair; this cannot be counted for the subject variant.

Still missing

• Variant-specific family pedigree
• Genotypes and phenotypes of affected relatives
• Genotypes and phenotypes of informative unaffected relatives
• Informative meioses and segregation analysis

Sources

Reasoning

The variant is missense, but the reviewed evidence does not provide the two gene-level facts required for PP2: a low rate of benign missense variation in SDHD and evidence that missense variants are a common disease mechanism. General SDHD disease descriptions and a low population frequency for this individual variant do not establish either gene-level condition.

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.

Still missing

• Gene-level benign missense variation rate and evidence quantifying missense as a common SDHD disease mechanism are unavailable.

Reasoning

The generic PP4 rule requires a patient's phenotype or family history highly specific for a disease with a single genetic etiology. The case materials identify SDHD-related disease contexts in general, but provide no patient phenotype, family history, or exact-variant clinical presentation for this case. General disease descriptions in PMID:20664475 and PMID:24319509 cannot substitute for the patient's phenotype. PP4 is therefore not assessed.

Rule

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

Evidence considered

• PMID:20664475 describes familial paraganglioma/pheochromocytoma associated with SDHD generally, not the phenotype or family history of this case.
• PMID:24319509 describes hereditary paraganglioma/pheochromocytoma and renal-cell-cancer risk generally, but does not document this patient's phenotype or family history.
• No case-specific clinical phenotype or family-history description is available for NM_003002.4:c.281C>G.

Still missing

• Patient phenotype and relevant family history, including the diagnosed disease and specificity of its presentation, are needed.

Sources

Reasoning

PP5 requires a reputable source to recently report this exact variant as pathogenic when the evidence is unavailable for independent evaluation. Exact-variant ClinVar records show Uncertain significance with no expert-panel submissions, and the validated literature trail does not identify c.281C>G as pathogenic. The available papers either do not mention the exact variant or discuss SDHD disease generally. No qualifying PP5 source is present, so PP5 is not assessed.

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_003002.4(SDHD):c.281C>G (p.Ser94Cys) is classified Uncertain significance with criteria provided by multiple submitters and zero expert-panel submissions; ordinary laboratory submissions do not qualify for PP5.
• The validated ClinVar literature trail contains PMID:19454582 and PMID:17576205, but PMID:17576205 reports a different c.271_282del variant and PMID:19454582's available abstract does not identify c.281C>G as pathogenic.
• No exact-variant reputable pathogenic report was verified.

Still missing

• A recent exact-variant pathogenic classification from a reputable source, preferably with an expert-panel status, would be needed for PP5.

Sources

Reasoning

BS2 is not assessed. The available gnomAD population records show zero homozygotes, but they do not identify a confirmed healthy adult carrier or establish that a heterozygous carrier was phenotypically healthy after the relevant surveillance period. SDHD-associated paraganglioma-pheochromocytoma predisposition is an autosomal-dominant cancer susceptibility context with age-dependent or incomplete penetrance concerns, so generic gnomAD control status alone cannot satisfy the requirement for an unaffected adult when full penetrance at an early age is expected. A documented healthy adult heterozygote, together with disease-specific penetrance and age information, is required.

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 v4.1 records 0 homozygotes among 1614032 alleles; gnomAD v2.1 records 0 homozygotes among 251480 alleles; gnomAD v2.1 non-cancer exomes record 0 homozygotes among 236942 alleles; gnomAD v3.1 non-cancer genomes record 0 homozygotes among 147918 alleles.
• The extracted literature describes SDHD-related hereditary paraganglioma/pheochromocytoma as autosomal dominant but does not provide a confirmed healthy adult observation for this exact variant or establish full early-age penetrance. PMID:24319509 and PMID:20664475 were consulted for this disease-context limitation.

Still missing

• No documented healthy adult carrier observation for NM_003002.4:c.281C>G was found.
• No disease-specific evidence establishing full penetrance at an early age for SDHD-associated disease was found.

Sources

Reasoning

BS3 cannot be assessed because the available evidence contains no variant-specific in vitro or in vivo functional study showing that NM_003002.4:c.281C>G (NP_002993.1:p.(Ser94Cys)) has no damaging effect on protein function or splicing. PMID:17576205 evaluated a different exon 3 deletion, c.271_282del, and did not report this variant or a benign functional assay. No validated, reproducible assay with appropriate controls establishes preserved SDHD function or normal splicing for this variant.

Rule

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

Evidence considered

• PMID:17576205, Results, Patient/family 3 and Table 1: the reported exon 3 variant was c.271_282del, not NM_003002.4:c.281C>G; no assay result showing preserved function or normal splicing for p.Ser94Cys was provided.
• The evidence record contains no validated, reproducible, variant-specific functional assay, assay-control result, or direct demonstration of an absence of damaging effect for NM_003002.4:c.281C>G (NP_002993.1:p.(Ser94Cys)).

Still missing

• A variant-specific, biologically relevant in vitro or in vivo assay with appropriate controls demonstrating no damaging effect on SDHD protein function or splicing is unavailable.

Sources

Reasoning

No variant-specific family data identify affected relatives who lack NM_003002.4:c.281C>G, so lack of segregation cannot be evaluated. The available familial report concerns a different SDHD deletion and provides no non-segregation evidence for c.281C>G.

Rule

Lack of segregation in affected members of a family.

Evidence considered

• No affected relatives with documented absence of NM_003002.4:c.281C>G are reported.
• The family described in PMID:17576205 carried a different SDHD deletion and does not provide BS4 evidence for c.281C>G.

Still missing

• Affected-relative genotypes
• Family phenotype data
• Variant-specific non-segregation analysis
• Assessment for phenocopies or multiple pathogenic variants

Sources

Reasoning

The variant is missense, but the reviewed evidence does not establish that SDHD is a gene for which primarily truncating variants are known to cause disease. Evidence that SDH deficiency can involve loss of function is not a gene-wide comparison showing that truncating variants predominate among disease-causing SDHD variants.

Rule

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

Still missing

• A gene-level distribution of established SDHD disease-causing variant types is unavailable.

Reasoning

BP2 cannot be assessed from the available evidence. The disease-context literature describes SDHD-related hereditary paraganglioma/pheochromocytoma as generally autosomal dominant, but no report provides the required observation of NM_003002.4:c.281C>G in trans with a pathogenic variant or in cis with a pathogenic variant, and no parent- or offspring-tested phase data are available. The available sources do not establish the fully penetrant dominant condition required by the supplied BP2 rule.

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 North American Neuroendocrine Tumor Society consensus guideline states that familial paragangliomas and pheochromocytomas due to germ-line SDHB, SDHC, or SDHD mutations are generally inherited in an autosomal dominant pattern, but it provides no c.281C>G-specific phase or co-occurrence data.
• The Canadian hereditary renal cancer guideline describes hereditary paraganglioma/pheochromocytoma involving SDHB, SDHC, and SDHD as autosomal dominant, but it provides no c.281C>G-specific phase or co-occurrence data.
• The available case evidence contains no parent- or offspring-tested observation demonstrating NM_003002.4:c.281C>G in trans or in cis with a pathogenic variant.

Still missing

• Direct phase testing or an otherwise reliable cis/trans determination is needed.
• A qualifying pathogenic or likely pathogenic allele and its phase relative to NM_003002.4:c.281C>G are not documented.
• The available evidence does not establish full penetrance for the relevant SDHD dominant disorder.

Sources

Reasoning

The generic BP5 rule requires the variant to be found in a case with an alternate molecular basis for disease. The supplied evidence contains no case-specific report of NM_003002.4:c.281C>G in a patient with an independently established alternate molecular cause. General SDHD disease discussions and unrelated variants do not satisfy BP5. BP5 is therefore not assessed.

Rule

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

Evidence considered

• No case-specific alternate molecular diagnosis is documented for NM_003002.4:c.281C>G.
• The reviewed papers either do not mention the exact variant or report different variants and do not establish an alternate molecular basis for this case.

Still missing

• A documented case carrying this exact variant with an independently established alternate molecular basis for the phenotype is needed.

Sources

Reasoning

BP6 requires a reputable source to recently report this exact variant as benign when the evidence is unavailable for independent evaluation. Exact-variant ClinVar is Uncertain significance with zero expert-panel submissions, and no reviewed publication reports c.281C>G as benign. Ordinary laboratory submissions, aggregate labels, and non-expert assertions cannot trigger BP6. BP6 is therefore not assessed.

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_003002.4(SDHD):c.281C>G (p.Ser94Cys) is classified Uncertain significance with zero expert-panel submissions; ordinary laboratory submissions and the aggregate label do not qualify for BP6.
• The validated literature trail does not provide an exact-variant benign classification: PMID:17576205 reports a different SDHD deletion, and PMID:19454582's available abstract does not classify c.281C>G as benign.
• No exact-variant reputable benign report was verified.

Still missing

• A recent exact-variant benign classification from a reputable source, preferably with an expert-panel status, would be needed for BP6.

Sources