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NM_003000.3:c.744C>G
p.Asn248Lys · SDHB
0%
complete
Final classification
VUS
PM2PP3
SDHB
c.744C>G
p.Asn248Lys
missense · exon 7

SDHB encodes a subunit of the succinate dehydrogenase (SDH) complex, a mitochondrial enzyme that converts succinate to fumarate in the citric acid cycle and transfers electrons to the oxidative phosphorylation pathway. It functions as a tumor suppressor, and loss of its function stabilizes hypoxia-inducible factors, promoting tumor development. Inherited mutations in SDHB cause hereditary paraganglioma and pheochromocytoma, and SDH dysfunction is also linked to gastrointestinal stromal tumors, renal cell carcinoma, and pituitary adenomas. Mutations in this gene are additionally associated with mitochondrial complex II deficiency.

This variant

SDHB is a tumor suppressor whose loss of function drives hereditary paraganglioma and pheochromocytoma, and the c.744C>G (p.Asn248Lys) missense change was classified as a Variant of Uncertain Significance. Computational missense prediction supports a damaging effect and the variant is nearly absent from population databases, but this evidence does not reach the thresholds for a likely pathogenic call. Its contribution to SDHB-associated tumor risk therefore remains unresolved pending functional or segregation data.

Transcript
NM_003000.3
HGVS · transcript:coding
NM_003000.3:c.744C>G
GRCh38
chr1:17022629 G>C
GRCh37
chr1:17349124 G>C
With no explicit combination rules in the SDHB expert-panel specification, the generic ACMG/AMP 2015 framework applied: only PM2 (Supporting) and PP3 (Supporting) are met, insufficient for any other classification.
Classification rationale
PM2PP3 VUS
SDHB c.744C>G missense · exon 7

PM2 (Supporting): the variant is nearly absent from population databases, with a gnomAD v4.1 allele frequency of 6.2e-07 (1/1,613,934 alleles). PP3 (Supporting): the missense REVEL score of 0.866 exceeds the calibrated threshold of >0.750. Classification: VUS - only PM2 and PP3 are met, below the ACMG/AMP 2015 combination thresholds for a pathogenic or benign call.

PM2 + PP3 → VUS
LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
Gene diagram · NM_003000.3 · variants mapped to exon structure
SDHB NM_003000.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 22 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
Met (Supporting): the variant is nearly absent from population databases, with a gnomAD v4.1 allele frequency of 6.2e-07 (1/1,613,934 alleles).
gnomAD v2.1 and gnomAD-Canada v1.0 report no occurrence of the variant.gnomAD v4.1 reports only 1 alternate allele among 1,613,934 total alleles (AF 6.19604e-07), no homozygotes, and a maximum ancestry-specific AF of 8.47489e-07 in European (non-Finnish) individuals.Because the variant is observed once in gnomAD v4.1 rather than completely absent from all population datasets, the evidence supports rare-population occurrence at PM2 supporting strength rather than an unqualified absent-from-controls claim.
PP3 supporting Pathogenic
Met (Supporting): the missense REVEL score is 0.866, above the calibrated PP3 threshold of >0.750.
Variant normalization identifies NM_003000.3:c.744C>G as SDHB p.(Asn248Lys), a missense substitution.The SDHB Endocrine Tumor Predisposition CSPEC v1.0 was reviewed; its extracted criteria list and rule payload contain no PP3/BP4-specific instruction or pre-assigned lookup result for this variant.The local REVEL lookup reports 0.866 for this variant. Under the applicable generic missense calibration, REVEL >0.750 supports PP3 at supporting strength; the calibrated REVEL thresholds are from the ClinGen SVI computational-evidence calibration publication (PMID:36413997).
Assessed · not applied · 6 not met · 16 not assessed
Pathogenic
PS1 Not met: the reported p.N248K publication describes the same c.744C>G change, not a distinct nucleotide substitution producing the same amino acid.
PS2 Not assessed: no parental genotypes or maternity/paternity confirmation were available to establish de novo occurrence.
PS3 Not assessed: no functional assay tested p.Asn248Lys; the available publications provide only clinical screening or non-variant-specific context.
PS4 Not assessed: only one affected individual is reported, with no case-control comparison, cohort denominator, or statistical enrichment available.
PM1 Not assessed: the variant lies at residue 248, immediately outside the reported SDHB iron-sulfur domain boundary (B115-B247), with no approved hotspot designation.
PM3 Not assessed: the single reported case provides no second pathogenic SDHB variant, phase information, or recessive disease context.
PM5 Not assessed: no different pathogenic amino-acid substitution at residue 248 was identified, as the report concerns p.N248K itself.
PM6 Not assessed: no evidence states the variant was presumed de novo or provides a clinical basis for that presumption.
PP1 Not assessed: only one affected individual is documented, with no affected relatives, informative meioses, or cosegregation analysis.
PP2 Not assessed: SDHB loss of function is the established mechanism, and missense variation is not shown to be a common pathogenic mechanism for this gene.
PP4 Not assessed: the reported vagal head-and-neck paraganglioma does not establish phenotype specificity for SDHB-related disease, and no case phenotype data were provided.
PP5 Not met: the exact ClinVar record has three Likely pathogenic laboratory submissions but no expert-panel submission required for this criterion.
Benign
BA1 Not met: the highest ancestry-specific gnomAD v4.1 allele frequency is 8.5e-07, far below the >1% BA1 threshold.
BS1 Not met: the gnomAD v4.1 allele frequency is 6.2e-07, far below the >0.3% BS1 threshold in every population.
BS2 Not assessed: gnomAD reports one heterozygous allele and no homozygotes, with no evidence establishing unaffected adult carriers or penetrance.
BS3 Not assessed: no functional assay demonstrating preserved SDHB function for p.Asn248Lys was identified.
BS4 Not assessed: no unaffected relatives carrying the variant were reported, and no segregation or clinical data were provided.
BP1 Not assessed: no SDHB-specific evidence shows missense variation is a benign mechanism or that pathogenic missense variation is rare in this gene.
BP2 Not assessed: no evidence shows this variant in trans with a pathogenic variant, and phase data are insufficient to establish a benign configuration.
BP4 Not met: the missense REVEL score of 0.866 is well above the calibrated BP4 threshold of <0.250.
BP5 Not assessed: no alternative molecular diagnosis explaining the phenotype was identified in a carrier of this variant.
BP6 Not met: no expert-panel Benign or Likely benign classification for this exact variant is present in ClinVar.
N/A · 4 PVS1 · PM4 · BP3 · BP7
Research & evidence
Population frequency
v4.1
This variant is present in gnomAD v4.1 (AF= 6.19604e-07; MAF= 0.00006%, 1/1613934 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47489e-07; MAF= 0.00008%, 1/1179956 alleles, homozygotes = 0).
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
6.2e-05% · 1 / 1,613,934
0 hom
European (non-Finnish)
1 / 1,179,956
8.5e-05%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar
This variant has been reported in ClinVar as Likely pathogenic (3 clinical laboratories). (ClinVarID = 428929)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.866. BayesDel score = 0.10873.
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. SDHB, a subunit of succinate dehydrogenase, is infrequently altered in cancer.
OncoKB ↗
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 8 PMIDs not cited in assessment
15989954 ↗ Crystal structure of mitochondrial respiratory membrane protein complex II. CLINVAR
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
18551016 ↗ High prevalence of SDHB mutations in head and neck paraganglioma in Belgium. CLINVAR
23512077 ↗ Inherited mutations in pheochromocytoma and paraganglioma: why all patients should be offered genetic testing. CLINVAR
24493721 ↗ American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers. CLINVAR
24758379 ↗ Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. CLINVAR
25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
25720320 ↗ SDHB/SDHA immunohistochemistry in pheochromocytomas and paragangliomas: a multicenter interobserver variation analysis using virtual microscopy: a Multinational Study of the European Network for the Study of Adrenal Tumors (ENS@T). CLINVAR