NM_012433.3:c.1874G>T

SF3B1 · NP_036565.2:p.(Arg625Leu) · NM_012433.3

GRCh37: chr2:198267483 C>A · GRCh38: chr2:197402759 C>A

Gene: SF3B1 Transcript: NM_012433.3

Final call

VUS

PS3 supporting PM1 moderate PM2 supporting PP3 supporting

Variant details

Gene

SF3B1

Transcript

NM_012433.3

Protein

NP_036565.2:p.(Arg625Leu)

gnomAD AF

0.0 (v4.1)

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

One moderate pathogenic criterion (PM1) and three supporting pathogenic criteria (PM2, PS3, PP3) are met.

Under generic ACMG/AMP 2015 combination rules (PMID:25741868), the combination of 1 moderate and 3 supporting pathogenic criteria is insufficient to reach Likely Pathogenic (requires ≥1 Moderate + ≥4 Supporting, ≥2 Moderate + ≥2 Supporting, or other qualifying combinations).

No benign criteria are met.

Final classification: Variant of Uncertain Significance (VUS).

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

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	N/A	This is a missense variant (p.Arg625Leu). PVS1 under the generic ClinGen SVI framework (PMC6185798) applies only to null variants (nonsense, frameshift, canonical ±1,2 splice consensus variants). The variant does not fall into any PVS1 null-variant bucket.	pvs1_variant_assessment pvs1_generic_framework
PS1	Not met	No alternative nucleotide change at position c.1874 resulting in the same amino acid substitution (p.Arg625Leu) has been identified.
PS2	Not met	No de novo observation of NM_012433.3:c.1874G>T has been reported. De novo SF3B1 variants described in neurodevelopmental disorders (PMID:41577671) are largely distinct from cancer-associated hotspot variants such as R625L.
PS3	Met	The variant p.Arg625Leu was detected in uveal melanoma and MDS tumors and is associated with aberrant alternative splicing. The SF3B1 R625 codon is a recurrent hotspot where mutations induce neomorphic cryptic 3' splice site selection. The variant was explicitly identified in patient tumors exhibiting the alternative splicing signature (PMID:23861464, PMID:24434863). Mechanistic studies (PMID:26565915) experimentally demonstrated that hotspot mutations in the HEAT domain (residues 622-781) cause aberrant splicing through altered branch point usage, and the authors concluded that functional consequences are similar across hotspot mutations. However, R625L was not directly tested in a controlled experimental system (minigene assay, overexpression, or knockdown rescue), limiting the strength to supporting.	PMID:23861464 PMID:24434863 PMID:26565915
PS4	Not met	No germline case-control data are available to demonstrate statistically significant enrichment of this variant in affected individuals. The variant has been observed in somatic cancers (COSMIC n=40, one uveal melanoma in PMID:23861464) but this does not satisfy PS4 which requires germline disease association.
PS5	Not met	No alternative pathogenic variant at the same nucleotide position (c.1874) with functional data has been identified in ClinVar or the literature.
PM1	Met	The variant alters Arg625, located within the HEAT domain (H4-H8 repeats, residues 622-781) of SF3B1. This is a well-characterized critical functional domain required for branch point sequence recognition and pre-mRNA splicing. Residue R625 is a statistically significant hotspot in cancer (CancerHotspots.org) and is the most frequently mutated codon in uveal melanoma (PMID:23861464). Mutations in this domain have been experimentally shown to induce neomorphic aberrant splicing activity (PMID:26565915).	PMID:23861464 PMID:26565915
PM2	Met	The variant is absent from gnomAD v2.1 (exomes) and v4.1 (0/1,614,004 alleles, AF=0.0%), meeting the PM2 threshold of <0.1% allele frequency in population databases for a gene without a CSPEC framework.	gnomad_v2 gnomad_v4
PM5	Not met	No pathogenic missense variant at the same amino acid position (Arg625) has been identified in ClinVar for PM5 comparator analysis. The automated PM5 candidate search returned no candidates.	pm5_candidates
PM6	Not met	No de novo observation of this variant has been reported. De novo SF3B1 variants reported in neurodevelopmental disorders (PMID:41577671) are distinct from cancer-associated hotspot mutations.
PP1	Not met	No segregation data are available for this variant in affected families.
PP2	Not met	SF3B1 germline disease mechanisms are still emerging. While missense variants are a known mechanism in somatic cancer (neomorphic gain-of-function), the germline disease spectrum includes both predicted loss-of-function and missense variants with distinct functional consequences (PMID:41577671). A low rate of benign missense variation has not been specifically established for germline SF3B1.
PP3	Met	REVEL score of 0.865 predicts a deleterious effect on protein function. BayesDel score of 0.3522 is inconclusive. SpliceAI predicts no significant splice impact (max delta score 0.17). While only one of three in silico tools strongly supports pathogenicity, the high REVEL score in a well-conserved functional domain supports a deleterious effect.	revel bayesdel spliceai
PP4	Not met	No specific patient phenotype information is available for germline assessment of this variant. The variant has been observed in somatic cancer contexts (uveal melanoma, MDS) but no germline phenotype data are provided.
PP5	Not met	No reputable germline source has classified this variant as pathogenic. It is absent from ClinVar. OncoKB classifies it as 'Likely Oncogenic' in a somatic context, which does not satisfy PP5 for germline assessment.
BA1	Not met	The variant is absent from gnomAD v4.1 (0/1,614,004 alleles, AF=0.0%), far below the BA1 threshold of >1%.	gnomad_v4
BS1	Not met	The variant is absent from gnomAD (AF=0.0%), far below the BS1 threshold of >0.3% allele frequency.	gnomad_v4
BS2	Not met	The variant is absent from gnomAD. No observation in healthy adults has been documented to support a benign role.
BS3	Not met	Functional studies demonstrate that SF3B1 hotspot mutations in the HEAT domain, including at codon R625, induce neomorphic gain-of-function activity (aberrant cryptic 3' splice site selection, altered branch point usage) rather than having no deleterious effect. These findings are not consistent with a benign functional impact.	PMID:23861464 PMID:26565915
BS4	Not met	No segregation data are available to demonstrate lack of cosegregation with disease.
BP1	Not met	SF3B1-related disease is not caused primarily by truncating variants. Both predicted loss-of-function and missense variants are reported in the germline neurodevelopmental disorder spectrum (PMID:41577671), and missense variants in the HEAT domain are the predominant pathogenic mechanism in somatic disease.
BP2	Not met	No observation of this variant in trans with a known pathogenic variant has been reported.
BP4	Not met	Computational evidence does not support a benign impact. REVEL score of 0.865 predicts a deleterious effect, and the variant is located in a highly constrained functional domain.	revel spliceai
BP5	Not met	No alternative molecular basis for disease has been identified in a case harboring this variant.
BP6	Not met	No reputable source has classified this variant as benign. The variant is absent from ClinVar.
BP7	N/A	BP7 applies only to synonymous (silent) variants. NM_012433.3:c.1874G>T is a missense variant (p.Arg625Leu).

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