Variant classification summary

NM_006758.2:c.101C>T

U2AF1 · NP_006749.1:p.(Ser34Phe) · NM_006758.2

GRCh37: chr21:44524456 G>A · GRCh38: chr21:43104346 G>A

Gene: U2AF1 Transcript: NM_006758.2

Final call

Likely Pathogenic

PS3 strong PM1 moderate PM2 supporting PP2 supporting PP3 supporting

Variant details

Gene

U2AF1

Transcript

NM_006758.2

Protein

NP_006749.1:p.(Ser34Phe)

gnomAD AF

0.0 (v4.1)

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_006758.2:c.101C>T (p.Ser34Phe) in U2AF1 is classified as Likely Pathogenic using generic ACMG/AMP 2015 criteria (PMID:25741868) with 1 strong, 1 moderate, and 3 supporting pathogenic criteria.

2

Well-established functional studies demonstrate that the U2AF1 S34F substitution has a damaging gain-of-function effect: it alters 3′ splice site recognition, changes sequence specificity of pre-mRNA binding, promotes aberrant exon skipping, induces R-loop accumulation and ATR checkpoint activation, and produces altered hematopoiesis in transgenic mouse models (PS3_Strong).

3

The variant is located at codon 34 in the first CCCH zinc finger domain, a well-established mutational hotspot where recurrent somatic missense mutations (S34F, S34Y) are observed in myelodysplastic syndromes and acute myeloid leukemia (PM1_Moderate).

4

The variant is extremely rare in population databases: gnomAD v2.1 reports 1 allele in 281,256 (AF=3.56×10⁻⁶) and gnomAD v4.1 reports 0 alleles in 18,936, both well below the PM2 threshold of 0.1% (PM2_Supporting).

5

U2AF1 has a low rate of benign missense variation and missense variants at the zinc finger domains are the established disease mechanism, supporting PP2 at a supporting level (PP2_Supporting).

6

Multiple in silico predictors support a deleterious effect: REVEL score of 0.7 is above the pathogenic threshold; BayesDel (0.415) is borderline (PP3_Supporting).

7

No benign criteria were met. The variant is not a common polymorphism (BA1/BS1 not met), functional studies show a damaging effect (BS3 not met), and computational evidence does not support a benign interpretation (BP4 not met).

8

Limitations: all functional evidence is derived from somatic disease contexts (MDS/AML cell lines and patient samples); no germline-specific functional data, de novo reports, cosegregation data, or germline case-control data are available. PVS1, PS1, PS2, PS4, PS5, PM5, PM6, PP1, PP4, PP5, and most benign criteria were not assessed due to absent or insufficient evidence.

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	N/A	PVS1 is not applicable. This is a missense substitution (p.Ser34Phe), not a null variant (nonsense, frameshift, or canonical ±1,2 splice site). The generic PVS1 framework confirms the variant does not fall into any default null-variant bucket.	pvs1_generic_framework
PS1	Not assessed	No evidence of an alternate nucleotide change producing the same amino acid substitution (p.Ser34Phe) was identified.
PS2	Not assessed	No de novo case report confirming this variant as a confirmed de novo occurrence in a patient with disease was identified.
PS3	Met	Well-established functional evidence demonstrates that U2AF1 S34F has a damaging gain-of-function effect: it alters 3′ splice site recognition, changes sequence specificity of pre-mRNA binding, causes aberrant exon skipping and alternative splicing of hundreds of genes, induces R-loop accumulation and ATR checkpoint activation, and produces altered hematopoiesis with leukopenia and progenitor expansion in transgenic mouse models.	PMID:25267526 PMID:22158538 PMID:25311244 PMID:25965570 PMID:30054334
PS4	Not assessed	The variant is recurrently observed in somatic cancers (COSMIC n=340) but no germline case-control data demonstrating significantly increased prevalence in affected individuals versus controls is available.
PS5	Not assessed	No data available to assess this criterion.
PM1	Met	The variant is located at codon 34 in the first CCCH zinc finger domain (ZnF1) of U2AF1, a well-established mutational hotspot. Codon S34 is recurrently mutated (S34F, S34Y) in MDS and AML. The hotspot analysis confirms the residue is statistically significant. This domain is critical for RNA binding and 3′ splice site recognition.	PMID:25267526 PMID:22158538 PMID:25311244 PMID:25965570 PMID:30054334
PM2	Met	The variant is extremely rare in population databases. gnomAD v2.1 reports an allele frequency of 3.56×10⁻⁶ (1/281,256 alleles, no homozygotes), and gnomAD v4.1 reports 0/18,936 alleles. The highest subpopulation frequency is 4.01×10⁻⁵ in African/African American. This is well below the 0.1% PM2 threshold.	gnomad_v2 gnomad_v4
PM5	Not assessed	A different pathogenic missense change (p.Ser34Tyr, S34Y) is established at the same residue, but the automated PM5 candidate pipeline could not confirm classic same-residue comparator semantics from ClinVar. Manual review of the literature confirms S34Y is recurrently reported as pathogenic alongside S34F; however, per pipeline guidance PM5 should not be applied from this artifact alone.	PMID:25267526 PMID:22158538 PMID:25311244
PM6	Not assessed	No de novo occurrence of this variant confirmed in a patient with disease and no family history was identified.
PP1	Not assessed	No cosegregation data from affected families is available.
PP2	Met	U2AF1 has a low rate of benign missense variation in population databases and missense variants are a well-established disease mechanism. Pathogenic U2AF1 variants cluster in the zinc finger domains at specific residues (S34, Q157), and the gene shows constraint against missense variation.	gnomad_v2 gnomad_v4
PP3	Met	In silico predictors support a deleterious effect. REVEL score is 0.7 (above the 0.5 threshold for pathogenic prediction). SpliceAI predicts no splice impact (max delta 0.0), consistent with a missense effect rather than splicing defect. BayesDel score is 0.415 (borderline). Overall, REVEL provides supporting evidence for pathogenicity.	revel bayesdel spliceai
PP4	Not assessed	Insufficient patient phenotype data available to assess whether the variant is observed in a phenotype highly specific for U2AF1-related disease.
PP5	Not assessed	No reputable source (expert panel, clinical diagnostic laboratory) has classified this variant as pathogenic for a germline disorder. OncoKB classifies as Likely Oncogenic (somatic context). ClinVar has no expert panel classification.	clinvar oncokb
BA1	Not met	The variant allele frequency (3.56×10⁻⁶ in gnomAD v2.1, 0 in gnomAD v4.1) is far below the 1% BA1 threshold. Not a common benign polymorphism.	gnomad_v2 gnomad_v4
BS1	Not met	The variant allele frequency is far below the 0.3% BS1 threshold. Not a common benign variant.	gnomad_v2 gnomad_v4
BS2	Not assessed	No data available on observation of this variant in healthy adult individuals with full penetrance expected at an early age.
BS3	Not met	Well-established functional studies consistently show a damaging gain-of-function effect, not a benign effect. U2AF1 S34F alters splicing, causes R-loop accumulation, and produces hematopoietic abnormalities across multiple independent studies. BS3 requires evidence of no damaging effect.	PMID:25267526 PMID:22158538 PMID:25965570
BS4	Not assessed	No cosegregation data showing lack of segregation with disease is available.
BP1	N/A	BP1 applies to genes where primarily truncating variants cause disease. U2AF1-related disease is caused by specific missense variants (S34F/Y, Q157P/R) in zinc finger domains, not truncating variants.
BP2	Not assessed	No data available on observation of this variant in trans with a known pathogenic variant or in cis with a pathogenic variant in U2AF1.
BP4	Not met	Multiple lines of computational evidence do not suggest a benign impact. REVEL score of 0.7 supports a deleterious effect, and BayesDel score of 0.415 is borderline. SpliceAI predicts no splicing impact (delta 0.0), but REVEL outweighs toward deleterious. BP4 requires consensus evidence of no impact.	revel bayesdel
BP5	Not assessed	No data available on this variant found in a case with an alternate molecular basis for disease.
BP6	Not assessed	No reputable source has classified this variant as benign.
BP7	N/A	BP7 applies to synonymous variants with no predicted splice impact. This is a missense variant (p.Ser34Phe), not a synonymous variant.
BP3	N/A	BP3 applies to in-frame insertions/deletions in a repetitive region. This is a missense substitution.
PM3	N/A	PM3 applies to variants detected in trans with a pathogenic variant in recessive disorders. U2AF1-related disease is not recessively inherited; no biallelic disease association is established.
PM4	N/A	PM4 applies to protein length changes from in-frame insertions/deletions or stop-loss variants. This is a missense substitution.

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