NM_012433.3:c.2098A>G

SF3B1 · NP_036565.2:p.(Lys700Glu) · NM_012433.3

GRCh37: chr2:198266834 T>C · GRCh38: chr2:197402110 T>C

Gene: SF3B1 Transcript: NM_012433.3

Final call

Likely Pathogenic

PS3 moderate PM1 moderate PM2 supporting PP3 supporting

Variant details

Gene

SF3B1

Transcript

NM_012433.3

Protein

NP_036565.2:p.(Lys700Glu)

gnomAD AF

4.4885262048887535e-05 (v4.1)

ClinVar

Uncertain significance

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

SF3B1 c.2098A>G (p.Lys700Glu) is a missense variant located in the HEAT repeat domain (H4-H8), a critical functional region essential for 3' splice site recognition during pre-mRNA splicing.

This variant is the most recurrent SF3B1 hotspot across hematologic malignancies and solid tumors, with 811 somatic occurrences in COSMIC and statistical significance at cancerhotspots.org.

Multiple independent functional studies demonstrate that K700E causes aberrant 3' splice site selection, cryptic branchpoint usage, and a conserved alternative splicing signature, confirmed in isogenic Nalm-6 cell lines and conditional Sf3b1 K700E/+ knock-in mice.

Mechanistically, K700E promotes MYC protein stabilization through aberrant splicing and nonsense-mediated decay of PPP2R5A, a regulatory subunit of the PP2A phosphatase complex, leading to oncogenic transformation.

The variant is present at very low frequency in population databases (gnomAD v2.1: 0.0083%, 23/276,636 alleles; gnomAD v4.1: 0.0045%, 72/1,604,090 alleles), meeting the PM2 threshold for rarity.

ClinVar reports conflicting classifications: Uncertain significance (2 laboratories), Likely pathogenic (2 laboratories), and Pathogenic (1 laboratory, somatic), with an aggregate 1-star review status (criteria provided, single submitter).

In silico predictions are mixed: REVEL (0.619) supports a deleterious effect, while BayesDel (0.234) is ambiguous and SpliceAI (0.03) predicts no splicing impact.

This variant meets PS3 (moderate), PM1 (moderate), PM2 (supporting), and PP3 (supporting). No benign criteria are met. The functional data strength is tempered by its derivation from somatic cancer models; correlation with germline disease phenotype requires clinical review.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Pathogenic classification based on the observed combination of pathogenic criteria.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Not met	NM_012433.3:c.2098A>G is a missense variant (p.Lys700Glu) and does not fall into any generic PVS1 null-variant category (nonsense, frameshift, or canonical ±1,2 splice site). The ClinGen SVI PVS1 framework (PMC6185798) does not apply to this variant class.	pvs1_generic_framework
PS1	Not met	No evidence that a different nucleotide change at codon 700 resulting in the same amino acid substitution (p.Lys700Glu) has been previously established as pathogenic in a germline context.
PS2	Not met	No de novo occurrence data available for this variant with confirmed maternity and paternity. While de novo SF3B1 germline missense variants have been reported in neurodevelopmental disorders (PMID:41577671), these are distinct variants from K700E and do not provide de novo evidence for this specific variant.
PS3	Met	SF3B1 K700E has been directly tested in multiple independent publications demonstrating unequivocal gain-of-function effects on RNA splicing. K700E expression causes aberrant 3' splice site selection and cryptic branchpoint usage (PMID:21909114, PMID:26565915), generates a conserved alternative splicing signature across cancer types (PMID:24434863, PMID:25424858), and promotes tumorigenesis through MYC stabilization via PPP2R5A mis-splicing, confirmed in isogenic Nalm-6 cell lines and conditional Sf3b1 K700E/+ knock-in mice (PMID:32188705). Functional effects are well-established; however, data derive from somatic cancer models and the relevance to germline disease is not fully resolved.	PMID:21909114 PMID:24434863 PMID:25424858 PMID:32188705 PMID:23160465
PS4	Not met	No case-control study demonstrating statistically significant enrichment of this variant in affected individuals versus controls in a germline context. The variant is frequent in somatic cancers (COSMIC n=811) but this does not satisfy PS4 for germline interpretation.
PS5	Not met	No evidence that a different missense change at codon 700 (e.g., K700R, K700N) has been established as pathogenic in a germline context. While other K700 variants exist somatically, no ClinVar germline pathogenic classification for a distinct K700 substitution was identified.
PM1	Met	Residue K700 lies within the HEAT repeat domain (H4-H8) of SF3B1, a structurally and functionally critical region essential for branchpoint recognition and 3' splice site selection during pre-mRNA splicing. This residue is a statistically significant mutational hotspot in cancer (cancerhotspots.org) and is the most frequently mutated codon in SF3B1 across hematologic malignancies and solid tumors (PMID:21909114, PMID:32188705).	PMID:21909114 PMID:32188705
PM2	Met	This variant is present at very low frequency in population databases. gnomAD v2.1 allele frequency is 8.31×10⁻⁵ (0.0083%, 23/276,636 alleles, 0 homozygotes); gnomAD v4.1 allele frequency is 4.49×10⁻⁵ (0.0045%, 72/1,604,090 alleles, 0 homozygotes). Both are below the 0.1% PM2 threshold for a rare variant absent from population controls.	gnomad_v2 gnomad_v4
PM5	Not met	No qualifying comparator variant at the same residue (K700) with a different amino acid change classified as pathogenic was identified. Automated ClinVar PM5 candidate harvesting returned no results.
PM6	Not met	No confirmed de novo occurrence of this variant with maternity and paternity testing has been reported.
PP1	Not met	No co-segregation data with disease in multiple affected family members is available for this variant.
PP2	Not assessed	Constraint metrics (e.g., gnomAD missense Z-score, LOEUF) were not directly reviewed for SF3B1. While SF3B1 is a known disease gene and de novo missense variants cause neurodevelopmental disorders (PMID:41577671), formal constraint analysis is needed to determine whether the gene has a low rate of benign missense variation meeting PP2 thresholds.
PP3	Met	REVEL score of 0.619 exceeds the commonly used 0.5 threshold, supporting a deleterious effect. BayesDel score of 0.234 is below most pathogenicity thresholds. SpliceAI max delta of 0.03 predicts no splicing impact. In silico evidence is mixed but REVEL provides supporting-level evidence for pathogenicity.	revel bayesdel spliceai
PP4	Not met	No patient-specific phenotypic information was available for review. PP4 requires a phenotype highly specific for a disease with a single genetic etiology; this cannot be evaluated without clinical data.
PP5	Not met	ClinVar aggregate classification is Uncertain significance (review status: criteria provided, single submitter; 1-star). Submissions are split: 2 VUS, 2 Likely pathogenic, 1 Pathogenic (somatic). No expert panel review is present. The 3-star expert panel requirement for PP5 at supporting is not met.	clinvar
BA1	Not met	gnomAD v2.1 allele frequency of 0.0083% is well below the 1% BA1 threshold for a benign stand-alone classification.	gnomad_v2
BS1	Not met	gnomAD v2.1 allele frequency of 0.0083% is below the 0.3% BS1 threshold for a benign strong classification. The variant is rare in population databases.	gnomad_v2
BS2	Not met	No evidence of observation in healthy adult individuals for a disorder with full penetrance expected at an early age. BS2 also requires the variant to be observed in trans with a pathogenic variant or in a homozygous state in an unaffected individual, none of which has been documented.
BS3	Not met	Functional studies uniformly demonstrate deleterious gain-of-function effects: K700E causes aberrant 3' splice site selection, cryptic branchpoint usage, MYC stabilization, and oncogenic transformation (PMID:21909114, PMID:25424858, PMID:32188705). No functional study supports a benign or neutral effect. BS3 is clearly contradicted by the available evidence.	PMID:21909114 PMID:32188705 PMID:25424858
BS4	Not met	No evidence of lack of segregation in affected family members. No segregation data is available for this variant.
BP1	Not met	This is a missense variant (p.Lys700Glu). BP1 applies only when a missense variant is found in a gene where primarily truncating variants cause disease. SF3B1 germline disease is associated with both truncating and missense variants (PMID:41577671), and K700E is a missense change in a known functional hotspot.
BP2	Not met	No evidence of observation in trans with a known pathogenic variant for a fully penetrant dominant disorder, nor in cis with a pathogenic variant in a recessive disorder.
BP4	Not met	In silico evidence is mixed and does not meet the requirement for multiple lines of computational evidence suggesting no impact. REVEL score of 0.619 supports a deleterious effect. BayesDel (0.234) is ambiguous. SpliceAI (0.03) predicts no splice impact. The overall computational evidence does not point uniformly toward benignity.	revel bayesdel spliceai
BP5	Not met	SF3B1 is a gene in which variants have been reported as pathogenic. BP5 requires the variant to be found in a case with an alternate molecular basis for disease. This information is not available for the present case.
BP6	Not met	ClinVar aggregate classification is Uncertain significance (1-star). No reputable source classifies this variant as Benign or Likely benign. BP6 requires a 3-star expert panel classification as benign; this is not met.	clinvar
BP7	Not met	This is a missense variant (c.2098A>G, p.Lys700Glu), not a synonymous or intronic variant. BP7 is only applicable to synonymous variants with no predicted splicing impact.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.