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Variant interpretation report

U2AF1 c.470A>C, p.Gln157Pro

NM_006758.3:c.470A>C NP_006749.1:p.(Gln157Pro) Missense · exon 6 View identifiers
Classification
Uncertain significance

Variant description:

The U2AF1 NM_006758.3:c.470A>C (NP_006749.1:p.(Gln157Pro)) missense variant has previously been reported in somatic cancers (COSMIC; COSV52341120, n = 111 times), and lies in a statistically significant hotspot (cancerhotspots.org). Experimental evidence: Q157P altered splicing in K562 and 293T assays and increased ATR-inhibition-induced gamma-H2AX in HeLa cells versus wild-type controls. Based on available guidelines, this variant is considered to be a Variant of Uncertain Significance (VUS).

Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.

Uncertain.The recorded classification is uncertain significance.

In plain language

Gene-level background from the recorded interpretation.

About U2AF1

U2AF1 encodes a small subunit of the U2 auxiliary factor, a protein complex essential for recognizing pre-mRNA splice sites and removing introns to produce mature messenger RNA. Alterations in U2AF1 are associated with myelodysplastic syndromes, acute myeloid leukemia, and chronic myelomonocytic leukemia. U2AF1 functions as an oncogene in cancer, where recurrent alterations can disrupt RNA splicing and contribute to the development and progression of myeloid malignancies.

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.
01The reasoning

How it was classified

The recorded framework is Generic ACMG/AMP 2015 with ClinGen SVI recommendations. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 3 Benign evidence criteria: 0
Pathogenic criteria applied · 3
PS3Supporting
PS3 · supporting

Met at supporting strength: Q157P altered splicing in K562 and 293T assays and increased ATR-inhibition-induced gamma-H2AX in HeLa cells versus wild-type controls.

PM1Moderate
PM1 · moderate

Met: p.Gln157Pro lies at Q157, reported as a statistically significant Cancer Hotspots hotspot, although the extracted hotspot row requires human confirmation.

PM2Supporting
PM2 · supporting

Met at supporting strength: gnomAD v4.1 grpmax FAF is 3.085e-05, below the generic PM2 threshold of 0.0001, with zero homozygotes.

Benign criteria applied · 0

No benign criterion marked as applied in the recorded assessment.

Recorded classification: Uncertain significance

VUS: PS3 supporting, PM1 moderate, and PM2 supporting provide one moderate plus two supporting criteria, insufficient for a generic ACMG/AMP pathogenic or benign combination.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

gnomAD v4.1
gnomAD v2.1
Population frequency
18 / 506,060 alleles

gnomAD v4.1: 18 / 506,060 alleles. Recorded AF 3.55689e-05. Recorded homozygote count 0.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 2.38711e-05; MAF= 0.00239%, 6/251350 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.27872e-05; MAF= 0.00528%, 6/113664 alleles, homozygotes = 0); grpmax FAF= 2.294e-05.

gnomAD-Canada

Not available in gnomAD-Canada v1.0.

No screenshot for this evidence
REVEL score
0.555 recorded score

Recorded REVEL score: 0.555. Refer to the recorded PP3/BP4 rationale for interpretation.

No listed criterion applied
ClinVar submissions
1 reported laboratory submissions

1 Likely pathogenic. ClinVar API review status: criteria provided, single submitter.

Context only ClinVar ↗
Functional evidence
Statement recorded

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.

COSMIC
Cancer Hotspots
Somatic evidence
111 recorded samples

This variant has previously been reported in somatic cancers (COSMIC; COSV52341120, n = 111 times).

Cancer Hotspots

This variant lies in a statistically significant hotspot.

For specialists

Technical detail

ACMG/AMP criteria under Generic ACMG/AMP 2015 with ClinGen SVI recommendations, with the data and sources behind each one.

28 criteria with recorded statuses: 3 met · 9 not met · 12 not assessed · 4 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Met Not met Not assessed Not applicable

For generic ACMG/AMP review of U2AF1 p.Gln157Pro, PM1 is supported by the reported Q157 mutational hotspot; PS1 is not met, PM5 cannot be assessed without a qualifying pathogenic same-residue comparator, and PP2/BP1 lack required gene-level evidence.

No segregation, parental-testing, de novo, or non-segregation evidence sufficient to apply PS2, PM6, PP1, or BS4 was identified for NM_006758.3:c.470A>C (U2AF1 p.Gln157Pro).

No VCEP covers U2AF1 in this case; generic ACMG/AMP 2015 definitions govern.

PS4 was not assessed because the available Q157P case frequency lacked a matched control comparison sufficient to calculate the required OR and 95% CI.

The literature packet contained no ai_classified_papers; extracted Q157P papers were reviewed for phenotype, case-control, and alternate-basis evidence.

PP5 and BP6 were restricted to exact-variant expert-panel assertions; the ClinVar record is a single-submitter Likely pathogenic assertion.

Met · 3

PS3 SupportingACMG_2015Met at supporting strength: Q157P altered splicing in K562 and 293T assays and increased ATR-inhibition-induced gamma-H2AX in HeLa cells versus wild-type controls. Details ▾Hide ▴
Reasoning

PS3 is met at supporting strength for NM_006758.3:c.470A>C (p.Gln157Pro). Three variant-specific functional studies evaluated Q157P with appropriate wild-type comparators and assay readouts. In K562 cells expressing FLAG-tagged U2AF1 alongside endogenous protein, Q157P produced a distinct RNA-splicing program and altered 3-prime splice-site preference (PMID:25267526). In 293T minigene assays, Q157P reduced alternative splice-isoform expression relative to wild type (PMID:25311244). In stable HeLa cells expressing Q157P at similar levels to other mutants, ATR inhibition induced higher gamma-H2AX than in U2AF1-wild-type cells (PMID:30054334). These reproducible, biologically relevant cellular assays support an abnormal effect of the variant on U2AF1 function, but the evidence is from research models rather than a validated clinical diagnostic laboratory assay, so strong-level PS3 is not justified.

Rule
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
Evidence considered
  • PMID:25267526, Results, Figure 2: K562 erythroleukemic cells stably expressed FLAG-tagged U2AF1 WT, S34F, S34Y, Q157P, or Q157R alongside endogenous U2AF1; deep RNA sequencing showed Q157P-associated differential splicing and altered 3-prime splice-site preference.
  • PMID:25311244, Results, Specific effects of U2AF1 mutations in alternative splicing: transient 293T GH1 and FMR1 minigene assays showed reduced relative expression of alternative splice isoforms with Q157P compared with wild-type U2AF1.
  • PMID:30054334, Results, Figure 3D: stable HeLa cells expressing Q157P at similar levels to other U2AF1 mutants showed higher gamma-H2AX after ATR inhibition than U2AF1-wild-type-expressing cells.
  • The studies used cellular controls and variant-specific molecular readouts, but none was identified as a validated clinical diagnostic-laboratory assay; therefore PS3 is calibrated to supporting strength rather than strong.
Still missing
  • No validated and reproducible clinical diagnostic-laboratory assay was identified to justify PS3 at strong level.
Sources
PM1 ModerateACMG_2015Met: p.Gln157Pro lies at Q157, reported as a statistically significant Cancer Hotspots hotspot, although the extracted hotspot row requires human confirmation. Details ▾Hide ▴
Reasoning

The queried p.Gln157Pro variant is reported by Cancer Hotspots as lying in a statistically significant U2AF1 Q157 hotspot. Q157 is also recurrently represented in U2AF1 mutation literature, including Q157P and Q157R in MDS cohorts and functional studies. No VCEP governs U2AF1 and no domain-table restriction applies. The hotspot extraction is flagged as partially parsed and should receive human confirmation, but the available generic ACMG evidence supports PM1.

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 result for query U2AF1 Q157 states: This variant lies in a statistically significant hotspot; the result is flagged because the Q157 row was only partially parsed.
  • PMID:25267526 directly studied U2AF1 Q157P and Q157R in K562 cells and reported mutation-dependent splicing effects.
  • PMID:25311244 described Q157P and Q157R as recurrent U2AF1 mutations and demonstrated mutation-specific splicing effects in minigene assays.
  • PMID:33122737 detected Q157P in 7 of 234 patients with MDS and compared the Q157 mutation site with S34 sites.
Still missing
  • Confirm the complete Q157 Cancer Hotspots row from the captured screenshot because automated extraction was partial.
Sources
PM2 SupportingACMGMet at supporting strength: gnomAD v4.1 grpmax FAF is 3.085e-05, below the generic PM2 threshold of 0.0001, with zero homozygotes. Details ▾Hide ▴
Reasoning

PM2 is met at supporting strength. Under the generic rules, the all-comers gnomAD datasets are the default because no VCEP governs U2AF1. The variant is present at an extremely low frequency: gnomAD v2.1 exomes show AF 2.38711e-05 (6/251350 alleles; 0 homozygotes) with grpmax FAF=2.294e-05, and gnomAD v4.1 combined exomes and genomes show AF 3.55689e-05 (18/506060 alleles; 0 homozygotes) with grpmax FAF=3.085e-05. Both filtering allele-frequency values are below the supplied PM2 supporting threshold of 0.0001. The non-cancer subsets are concordant but are not required to replace the all-comers default in this generic interpretation.

Rule
Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium. ... PM2 (supporting): <= 0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868)
Evidence considered
  • gnomAD v2.1 all-comers exomes: AF=2.38711e-05, 6/251350 alleles, 0 homozygotes, grpmax FAF=2.294e-05.
  • gnomAD v4.1 all-comers combined exomes and genomes: AF=3.55689e-05, 18/506060 alleles, 0 homozygotes, grpmax FAF=3.085e-05.
  • Concordant non-cancer subset data are available: gnomAD v2.1 non-cancer exomes AF=1.26642e-05, 3/236888 alleles, grpmax FAF=7.76e-06; gnomAD v3.1 non-cancer genomes AF=7.55995e-05, 5/66138 alleles, grpmax FAF=3.869e-05.
  • Generic calibration threshold: PM2 <= 0.0001, supplied as the ClinGen SVI recommendation to downgrade PM2 to Supporting (PMID:25741868).
Sources

Not met · 9 · evaluated, threshold not reached

PS1 ACMG_2015Not met: no previously established pathogenic Gln157Pro substitution caused by a different nucleotide change was identified. Details ▾Hide ▴
Reasoning

The variant is NP_006749.1:p.(Gln157Pro) from NM_006758.3:c.470A>C. The available evidence identifies Q157P itself and the different substitution Q157R, but does not establish the same Gln-to-Pro amino-acid change caused by a different nucleotide change. Therefore PS1 is not met.

Rule
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.
Evidence considered
  • The queried variant is NM_006758.3:c.470A>C, NP_006749.1:p.(Gln157Pro).
  • The literature explicitly discusses Q157P and Q157R, which are substitutions at the same residue but Q157R is not the same amino-acid change as Q157P.
  • ClinVar contains the exact Q157P variant as a single-submitter Likely pathogenic record, not an independent nucleotide change producing the same amino-acid substitution.
Sources
PP3 ACMGNot met: missense REVEL 0.555 is below the >=0.644 PP3 supporting threshold. Details ▾Hide ▴
Reasoning

The variant is a missense substitution, p.(Gln157Pro), so the governing generic rule selects the REVEL path only; SpliceAI and BayesDel are not used for PP3. REVEL is 0.555, which is below the PP3 supporting threshold of >= 0.644 and therefore does not meet PP3.

Rule
Missense variant -> REVEL only. ... PP3 (supporting): >= 0.644 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
Evidence considered
  • Local REVEL predictor lookup: REVEL score 0.555 for NM_006758.3:c.470A>C (NP_006749.1:p.(Q157P)); this is below the supplied generic PP3 supporting cutoff of >= 0.644.
  • The supplied generic rule requires the single missense REVEL path; the available SpliceAI max delta 0.093 and BayesDel score 0.441524 were not counted for PP3.
  • The PP3 calibration threshold >= 0.644 is the supplied ClinGen SVI REVEL calibration from Pejaver et al. 2022, Am J Hum Genet (PMID:36413997).
Sources
revel
PP4 ACMG_2015Not met: available evidence documents somatic MDS mutation cohorts and assays, not a highly specific patient phenotype or family history for one genetic disease. Details ▾Hide ▴
Reasoning

The available literature concerns somatic U2AF1 Q157P in MDS cohorts and cellular assays, not a patient phenotype or family history highly specific for a disease with a single genetic etiology. ClinVar lists the condition as not provided, and no disease-specific germline phenotype is documented for this variant.

Rule
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
Evidence considered
  • PMID:33122737: retrospective cohort of 234 patients with de novo MDS evaluated U2AF1 mutation sites, including Q157P, but did not provide a highly specific individual phenotype or germline disease diagnosis.
  • ClinVar variation 376024: the submitted condition is listed as not provided.
  • PMID:25267526, PMID:25311244, and PMID:30054334 describe Q157P cellular splicing or ATR-inhibition experiments rather than a specific patient phenotype or family history.
Sources
PP5 ACMG_2015Not met: ClinVar has one exact-variant Likely pathogenic single-submitter record and zero expert-panel submissions, so PP5 is not triggered. Details ▾Hide ▴
Reasoning

ClinVar variation 376024 contains an exact-variant Likely pathogenic submission from one clinical laboratory with criteria provided and single-submitter status, but no expert-panel classification. Under the requested rule, this is not a qualifying reputable exact-variant expert-panel assertion for PP5.

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 variation 376024: exact variant NM_006758.3(U2AF1):c.470A>C (p.Gln157Pro) is Likely pathogenic with review status criteria provided, single submitter; one submission and zero expert-panel submissions.
  • The single-submitter classification is not treated as an expert-panel or equivalent qualifying assertion.
Sources
BA1 ACMGNot met: gnomAD grpmax FAF is 3.085e-05 at most, far below the 0.05 BA1 threshold in populations with over 2000 observed alleles. Details ▾Hide ▴
Reasoning

BA1 is not met. The applicable all-comers gnomAD datasets show grpmax FAF values of 2.294e-05 in gnomAD v2.1 exomes (6/251350 total alleles; 0 homozygotes) and 3.085e-05 in gnomAD v4.1 combined exomes and genomes (18/506060 total alleles; 0 homozygotes). These FILTERING allele-frequency values are far below the generic stand-alone threshold of 0.05, and the relevant populations have more than 2000 observed alleles. The highest point-estimate subpopulation frequencies are also far below 5% and are not used in place of grpmax FAF.

Rule
Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium. ... BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868)
Evidence considered
  • gnomAD v2.1 all-comers exomes: total AF 2.38711e-05, 6/251350 alleles, 0 homozygotes; grpmax FAF=2.294e-05.
  • gnomAD v4.1 all-comers combined exomes and genomes: total AF 3.55689e-05, 18/506060 alleles, 0 homozygotes; grpmax FAF=3.085e-05.
  • The gnomAD v4.1 highest observed subpopulation point estimate was 8.05607e-05 in Remaining individuals (2/24826 alleles), but BA1/BS1 assessment uses grpmax FAF rather than the popmax point estimate.
  • Generic calibration threshold: BA1 >= 0.05, identified in the supplied ACMG/AMP 2015 threshold block (PMID:25741868).
Sources
BS1 ACMGNot met: the highest applicable gnomAD grpmax FAF is 3.085e-05, far below the generic 0.01 BS1 threshold. Details ▾Hide ▴
Reasoning

BS1 is not met on the available population data. The applicable all-comers gnomAD v2.1 and v4.1 grpmax FAF values are 2.294e-05 and 3.085e-05, respectively, both far below the generic 0.01 default threshold. The observed frequencies do not require a maximum-credible-frequency exception analysis because they are not elevated; no ancestry-specific frequency signal approaches the threshold, and all relevant grpmax populations exceed 2000 observed alleles.

Rule
Allele frequency is greater than expected for the disorder. ... BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168)
Evidence considered
  • gnomAD v2.1 all-comers exomes: grpmax FAF=2.294e-05 from 6/251350 total alleles; highest observed point-estimate subpopulation AF=5.27872e-05 in European (non-Finnish).
  • gnomAD v4.1 all-comers combined exomes and genomes: grpmax FAF=3.085e-05 from 18/506060 total alleles; highest observed point-estimate subpopulation AF=8.05607e-05 in Remaining individuals (2/24826 alleles).
  • The relevant population sample sizes exceed 2000 observed alleles, so the grpmax FAF values are usable; small-isolate popmax artifacts do not drive this assessment.
  • Generic BS1 default threshold: >= 0.01; maximum-credible-frequency considerations are informed by Whiffin et al. 2017 (PMID:28518168), but no exception is needed at these frequencies.
Sources
BS3 ACMG_2015Not met: Q157P altered splicing and increased ATR-inhibition-induced gamma-H2AX versus wild-type controls, rather than showing no damaging effect on U2AF1 function. Details ▾Hide ▴
Reasoning

BS3 is not met. The available variant-specific functional studies do not show no damaging effect; instead, they show altered U2AF1-dependent splicing and a differential cellular response to ATR inhibition for Q157P relative to wild-type controls. The evidence therefore contradicts the benign-functional direction required for BS3.

Rule
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
Evidence considered
  • PMID:25267526: Q157P produced a distinct splicing program and altered 3-prime splice-site preference in controlled K562 cell assays.
  • PMID:25311244: Q157P reduced alternative splice-isoform expression in controlled 293T minigene assays relative to wild-type U2AF1.
  • PMID:30054334: Q157P-expressing HeLa cells showed higher gamma-H2AX after ATR inhibition than U2AF1-wild-type-expressing cells.
  • Because the studies demonstrate altered molecular or cellular function rather than absence of a damaging effect, they do not support BS3.
Sources
BP4 ACMGNot met: missense REVEL 0.555 exceeds the <=0.29 BP4 supporting threshold and is indeterminate. Details ▾Hide ▴
Reasoning

The variant is a missense substitution, p.(Gln157Pro), so the governing generic rule selects the REVEL path only; SpliceAI and BayesDel are not used for BP4. REVEL is 0.555, which is above the BP4 supporting threshold of <= 0.29 and lies in the indeterminate gray zone, so BP4 is not met.

Rule
Missense variant -> REVEL only. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
Evidence considered
  • Local REVEL predictor lookup: REVEL score 0.555 for NM_006758.3:c.470A>C (NP_006749.1:p.(Q157P)); this exceeds the supplied generic BP4 supporting cutoff of <= 0.29.
  • Because the applicable missense REVEL result is indeterminate, the available SpliceAI max delta 0.093 was not substituted as BP4 evidence; BayesDel was also not used because no generic ACMG-strength calibration is established.
  • The BP4 calibration threshold <= 0.29 is the supplied ClinGen SVI REVEL calibration from Pejaver et al. 2022, Am J Hum Genet (PMID:36413997).
Sources
revel
BP6 ACMG_2015Not met: ClinVar has no exact-variant Benign or Likely benign expert-panel assertion and instead contains one Likely pathogenic single-submitter record. Details ▾Hide ▴
Reasoning

ClinVar variation 376024 has no exact-variant Benign or Likely benign expert-panel classification. Its only submission is Likely pathogenic from a single clinical laboratory, so it cannot trigger BP6 under the requested exact-variant expert-panel rule.

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 variation 376024: one exact-variant submission is Likely pathogenic with criteria provided, single submitter; expert-panel submissions are absent.
  • No exact-variant Benign or Likely benign expert-panel classification was identified.
Sources

Not assessed · 12 · no assessment recorded

PS2 ACMG_2015Not assessed: no case-level evidence documents confirmed maternity, confirmed paternity, and absence of family history for this variant. Details ▾Hide ▴
Reasoning

PS2 cannot be assessed because the available evidence does not document a patient with the disease carrying this variant together with confirmed maternity, confirmed paternity, and no family history. The variant-specific literature concerns somatic U2AF1 Q157P in MDS cell lines or retrospective MDS cohorts and provides no parental testing or case-level de novo documentation for NM_006758.3:c.470A>C.

Rule
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.
Evidence considered
  • PMID:25267526 studied U2AF1 Q157P in engineered K562 erythroleukemic cell lines and did not report a patient pedigree, parental testing, or de novo status for the queried variant.
  • PMID:25311244 evaluated Q157P in cell-based splicing assays and referenced prior de novo MDS mutation data, but did not document confirmed maternity, confirmed paternity, or no family history for this variant.
  • PMID:30054334 evaluated Q157P in stable HeLa cell lines and explicitly provided no patient case, segregation, or population-frequency data for c.470A>C/p.Q157P.
  • PMID:33122737 reported Q157P in a retrospective cohort of 234 MDS patients, including seven Q157P cases, without parental testing, pedigree-level de novo evidence, or family-history documentation for c.470A>C.
Still missing
  • A disease-affected proband carrying NM_006758.3:c.470A>C with documented phenotype is not identified.
  • Maternity and paternity are not documented as confirmed.
  • Family history and parental variant testing are not documented.
Sources
PS4 ACMG_2015Not assessed: Q157P occurred in 7/234 MDS patients, but no matched control counts support the required OR >5.0 and confidence interval excluding 1.0. Details ▾Hide ▴
Reasoning

PMID:33122737 reports U2AF1 p.Q157P in 7 of 234 patients with MDS (2.99%), but it provides no unaffected or population-control carrier counts for that cohort. gnomAD v4 reports 18/506060 alleles (AF 3.56e-05), but the available evidence does not establish matched ancestry or compatible carrier-level counts, so a valid case-control OR and 95% CI cannot be calculated. The governing PS4 threshold is OR >5.0 with a confidence interval excluding 1.0; no such verified estimate is available. The literature packet's ai_classified_papers list is empty, and the extracted Q157P papers were checked for case-control evidence without finding an eligible comparison.

Rule
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... 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:33122737, Results/Table 1: Q157P was detected in 7 of 234 MDS patients, reported as 13.7% in the paper's site comparison; no unaffected control cohort or control carrier count was reported.
  • gnomAD v4.1: 18/506060 alleles, AF 3.55689e-05, with zero homozygotes; this is a population frequency but not a demonstrated matched-ancestry case-control carrier dataset.
  • No OR or 95% CI was calculated because the available case and population data are not shown to be ancestry-matched and are not reported in compatible carrier-count form.
Still missing
  • A matched-ancestry unaffected or population-control cohort with compatible carrier counts and uncertainty estimates is needed to calculate OR and 95% CI.
Sources
PM3 ACMG_2015Not assessed: no affected-proband observation, pathogenic allele, or parental/offspring phase testing demonstrates this variant in trans. Details ▾Hide ▴
Reasoning

PM3 cannot be assessed because the available evidence does not establish that U2AF1-related disease is recessive, does not identify an affected proband carrying this variant with a pathogenic allele, and provides no parental or offspring testing to demonstrate that NM_006758.3:c.470A>C (p.Gln157Pro) is in trans with a pathogenic variant. The ClinVar submission records germline origin but supplies no phase or affected-proband details. The reviewed Q157P literature describes functional studies and an MDS cohort, but does not report parental phase, a pathogenic variant in trans, or cis configuration for this variant.

Rule
PM3: For recessive disorders, detected in trans with a pathogenic variant ... Note: This requires testing of parents (or offspring) to determine phase.
Evidence considered
  • ClinVar exact-match submission SCV004026006 records germline origin and a single-submitter Likely pathogenic classification, but contains no parental testing, phase information, affected-proband description, or second pathogenic allele.
  • U2AF1 Q157P functional/cohort literature was reviewed; PMID:25311244 reports Q157P splicing effects and PMID:33122737 reports seven Q157P cases in a 234-patient MDS cohort, but neither reports a pathogenic allele in trans or phase testing for the queried variant.
Still missing
  • Disease inheritance mode for the relevant U2AF1 condition is not established in the available case evidence.
  • No affected-proband report identifies a second pathogenic variant and demonstrates trans phase by parental or offspring testing.
Sources
PM5 ACMG_2015Not assessed: Q157R is reported at residue 157, but a qualifying prior determination that Q157R is pathogenic is not supplied. Details ▾Hide ▴
Reasoning

Q157R is a different missense change at the same residue and is described in functional and MDS literature, but the supplied evidence does not establish Q157R as a previously determined pathogenic variant under the generic PM5 rule. The exact comparator pathogenicity record is therefore missing.

Rule
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.
Evidence considered
  • PMID:25267526, PMID:25311244, and PMID:33122737 report or study U2AF1 Q157R/Q157P, establishing same-residue missense observations but not a qualifying pathogenic determination for Q157R.
  • The PM5 candidate artifact contains zero harvested same-residue candidates and explicitly states that classic PM5 semantics could not be confirmed safely; it is not itself evidence of pathogenicity.
Still missing
  • Obtain a reliable pathogenic classification or adequately established pathogenic determination for a different missense variant at residue 157, such as Q157R.
Sources
PM6 ACMG_2015Not assessed: no disease-affected proband is documented with an assumed de novo variant and unconfirmed parental origin. Details ▾Hide ▴
Reasoning

PM6 cannot be assessed because no case-level evidence establishes that NM_006758.3:c.470A>C is assumed de novo in a disease-affected patient. The available Q157P publications are somatic functional or cohort studies and do not provide a proband pedigree, parental testing status, or de novo observation for this variant.

Rule
Assumed de novo, but without confirmation of paternity and maternity.
Evidence considered
  • PMID:25267526 and PMID:30054334 describe experimental Q157P models rather than a disease-affected proband with parental-origin assessment.
  • PMID:25311244 and PMID:33122737 discuss Q157P in MDS research cohorts but do not report an assumed de novo c.470A>C event or the parental testing status of a specific proband.
Still missing
  • A disease-affected proband carrying NM_006758.3:c.470A>C is not identified in the available evidence.
  • An assumed de novo event is not reported.
  • Parental testing status is not reported.
Sources
PP1 ACMG_2015Not assessed: no family-level segregation data show this variant co-segregating with disease in multiple affected relatives. Details ▾Hide ▴
Reasoning

PP1 cannot be assessed because no family with multiple affected members carrying and transmitting NM_006758.3:c.470A>C is documented. The available literature reports Q157P in experimental systems or unrelated MDS cohorts and contains no family segregation, affected-relative count, or meiosis data for this variant.

Rule
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.
Evidence considered
  • PMID:25267526 and PMID:30054334 provide cell-based Q157P experiments, not familial segregation data.
  • PMID:25311244 reports Q157P in splicing assays and an MDS research context, without a pedigree or affected-relative segregation analysis.
  • PMID:33122737 reports seven Q157P cases in a retrospective cohort of 234 MDS patients, but does not provide family-level co-segregation or informative meioses.
Still missing
  • No pedigree with multiple affected family members is documented.
  • No genotype and phenotype data for affected relatives are documented.
  • No informative meioses or segregation count is available.
Sources
PP2 ACMG_2015Not assessed: gene-level evidence for both low benign missense variation and a common missense disease mechanism is not supplied. Details ▾Hide ▴
Reasoning

The supplied evidence documents recurrent U2AF1 missense mutations and functional effects of Q157P, but it does not provide the gene-level evidence required to establish both a low rate of benign missense variation and missense variants as a common disease mechanism. PP2 cannot be assessed from the available data.

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.
Evidence considered
  • The reviewed papers show recurrent somatic U2AF1 missense mutations and functional effects, but do not quantify the gene's benign missense variation rate or establish the generic PP2 gene-level conditions.
Still missing
  • Provide gene-level benign missense constraint and disease-mechanism evidence sufficient to establish both PP2 conditions.
Sources
BS2 Not assessed: zero gnomAD homozygotes does not establish a healthy-adult observation or the full-penetrance inheritance context required for BS2. Details ▾Hide ▴
Reasoning

BS2 cannot be assessed from the available evidence. gnomAD reports zero homozygotes for this variant in the all-comers and available non-cancer datasets, but that is not an observation of the variant in a healthy adult individual and does not establish the required inheritance model, expected penetrance, or early-age full penetrance. The ClinVar record provides no disease condition and no healthy-adult observation suitable for BS2.

Rule
BS2
Evidence considered
  • gnomAD v2.1 all-comers exomes: 0 homozygotes among 251350 alleles.
  • gnomAD v4.1 all-comers combined exomes and genomes: 0 homozygotes among 506060 alleles.
  • The ClinVar record is a single-submitter Likely pathogenic entry with condition listed as not provided; it does not document a healthy adult carrier or establish the penetrance and inheritance requirements for BS2.
Still missing
  • A documented healthy adult carrying the variant in the relevant zygosity state.
  • Confirmed disease inheritance model and evidence that full penetrance is expected at an early age.
Sources
BS4 ACMG_2015Not assessed: no affected relatives with documented negative variant testing establish lack of segregation. Details ▾Hide ▴
Reasoning

BS4 cannot be assessed because no affected family members tested for NM_006758.3:c.470A>C are documented as lacking the variant. The available evidence contains no pedigree, affected-relative genotypes, phenotype adjudication, or non-segregation analysis; therefore lack of segregation cannot be distinguished from absent family data or phenocopy.

Rule
Lack of segregation in affected members of a family.
Evidence considered
  • The reviewed Q157P publications (PMID:25267526, PMID:25311244, PMID:30054334, and PMID:33122737) do not report affected-family-member testing or variant-negative affected relatives.
  • Because no family segregation dataset is available, there is no evidence establishing lack of segregation and no basis to evaluate phenocopy or multiple pathogenic-variant explanations.
Still missing
  • No affected relatives with reliable phenotype assessment are documented.
  • No negative variant results in affected relatives are documented.
  • No pedigree-based non-segregation analysis is available.
Sources
BP1 ACMG_2015Not assessed: the supplied evidence does not establish whether U2AF1 disease is primarily caused by truncating variants. Details ▾Hide ▴
Reasoning

The available evidence does not establish that U2AF1 disease is caused primarily by truncating variants. Instead, the supplied literature focuses on recurrent Q157 and S34 missense mutations and functional gain-of-function context, but this is insufficient to formally exclude a truncating-predominant disease mechanism under BP1.

Rule
Missense variant in a gene for which primarily truncating variants are known to cause disease.
Evidence considered
  • The reviewed U2AF1 papers focus on recurrent missense mutations at S34 and Q157 and their functional effects; they do not provide a comprehensive disease-variant spectrum demonstrating truncating predominance.
Still missing
  • Provide a gene-level disease-variant spectrum showing whether truncating variants are the primary known cause of disease.
Sources
BP2 ACMG_2015Not assessed: no phase-resolved observation shows this variant in trans or cis with a pathogenic variant in an affected individual. Details ▾Hide ▴
Reasoning

BP2 cannot be assessed because the available evidence does not establish a fully penetrant dominant U2AF1 disorder for this interpretation and provides no phase-resolved observation showing NM_006758.3:c.470A>C (p.Gln157Pro) in trans with a pathogenic variant or in cis with a pathogenic variant. The ClinVar submission records germline origin but supplies no phase or affected-proband details. The reviewed Q157P literature describes functional studies and an MDS cohort, but does not report cis/trans configuration with a pathogenic variant.

Rule
BP2: 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
  • ClinVar exact-match submission SCV004026006 records germline origin and a single-submitter Likely pathogenic classification, but contains no parental testing, phase information, affected-proband description, or pathogenic allele in cis or trans.
  • PMID:25311244 and PMID:33122737 were reviewed for Q157P case/cohort observations; they report functional findings and MDS cohort counts but no phase-resolved cis/trans observation with a pathogenic variant.
Still missing
  • Inheritance and penetrance of the relevant U2AF1 condition are not established in the available case evidence.
  • No family or molecular phasing data demonstrate cis or trans status with a pathogenic variant.
Sources
BP5 ACMG_2015Not assessed: one MDS patient had Q157P and S34F, but the evidence does not establish S34F as the alternate molecular basis of disease. Details ▾Hide ▴
Reasoning

PMID:33122737 reports that one MDS patient had both Q157P and S34F, but the available extraction does not establish that the co-occurring alteration was an alternate molecular basis for that patient's disease rather than a somatic co-mutation. No sufficiently documented individual case demonstrates that the disease was explained by an alternate molecular basis, so BP5 cannot be adjudicated reliably.

Rule
Variant found in a case with an alternate molecular basis for disease.
Evidence considered
  • PMID:33122737: the extracted finding reports one patient with both Q157P and S34F in a retrospective MDS cohort, but the paper context available here does not establish alternate-basis causation for that individual.
  • A co-mutation alone was not treated as proof that the alternate alteration explains the disease.
Still missing
  • A documented individual case must establish that an alternate molecular diagnosis, rather than Q157P, explains the phenotype or disease.
Sources
Not applicable · 4· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANot applicable: PVS1 requires a null variant (nonsense, frameshift, canonical splice, start-loss or stop-loss), and this is a missense variant. Details ▾Hide ▴
Reasoning

PVS1 (ClinGen SVI PVS1 recommendations, PMC6185798, pvs1_generic_framework) applies only to null variant classes — nonsense, frameshift, canonical ±1/2 splice-consensus, translation-initiation-codon loss, and stop-loss variants — each expected to trigger nonsense-mediated decay or otherwise abolish normal protein function. NM_006758.3:c.470A>C in U2AF1 is a missense substitution predicted to produce NP_006749.1:p.(Gln157Pro). As a result, no null-variant mechanism (nonsense-mediated decay, truncation, or canonical splice disruption) is triggered by this variant class, so PVS1's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PVS1 for U2AF1, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.

Rule
deterministic_prefilter: requires_null_variant_class
Evidence considered
  • Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
  • VCEP criterion policy: absent
Sources
pvs1_generic_framework ↗generic_acmg_combination_rules
PM4 N/ANot applicable: PM4 requires a protein-length change, and this is a missense variant. Details ▾Hide ▴
Reasoning

PM4 (Richards et al. 2015, PMID:25741868) applies to protein length changes: in-frame insertions/deletions in a non-repetitive region, or stop-loss variants that extend the protein past the reference stop codon. NM_006758.3:c.470A>C in U2AF1 is a missense substitution predicted to produce NP_006749.1:p.(Gln157Pro). As a result, no change in protein length occurs, so there is nothing for this criterion to evaluate, so PM4's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PM4 for U2AF1, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.

Rule
deterministic_prefilter: requires_stop_loss_or_nonrepeat_indel
Evidence considered
  • Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
  • VCEP criterion policy: absent
Sources
pvs1_generic_framework ↗generic_acmg_combination_rules
BP3 N/ANot applicable: BP3 requires an in-frame indel in a repeat region, and this is a missense variant. Details ▾Hide ▴
Reasoning

BP3 (Richards et al. 2015, PMID:25741868) applies to in-frame insertions/deletions located in a repetitive region without a known function. NM_006758.3:c.470A>C in U2AF1 is a missense substitution predicted to produce NP_006749.1:p.(Gln157Pro). As a result, the variant does not alter protein length within a repeat region, so there is nothing for this criterion to evaluate, so BP3's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP3 for U2AF1, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.

Rule
deterministic_prefilter: requires_repeat_region_indel
Evidence considered
  • Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
  • VCEP criterion policy: absent
Sources
pvs1_generic_framework ↗generic_acmg_combination_rules
BP7 N/ANot applicable: BP7 requires a synonymous variant, and this is a missense variant. Details ▾Hide ▴
Reasoning

BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_006758.3:c.470A>C in U2AF1 is a missense substitution predicted to produce NP_006749.1:p.(Gln157Pro). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for U2AF1, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.

Rule
deterministic_prefilter: requires_synonymous
Evidence considered
  • Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
  • VCEP criterion policy: absent
Sources
generic_acmg_combination_rules

Identifiers

Gene
U2AF1
Transcript
NM_006758.3
Coding (HGVS c.)
NM_006758.3:c.470A>C
Protein (HGVS p.)
NP_006749.1:p.(Gln157Pro)
GRCh38
chr21:43094667 T>G
GRCh37
chr21:44514777 T>G
Location and type
Exon 6 · missense
ClinVar
376024
COSMIC
COSV52341120

Gene diagram

Every interpreted variant in U2AF1, mapped onto the exon structure of NM_006758.3. Select a row to find it on the plot.

U2AF1NM_006758.3
Fetching transcript structure from UCSC…
gnomAD v4.1 18 / 506,060 alleles AF 3.56e-05 · 0 homozygotes · FAF 3.08e-05
gnomAD v2.1 6 / 251,350 alleles AF 2.39e-05 · 0 homozygotes · FAF 2.29e-05
gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 3.6e-05 · 18 / 506,060 alleles · 0 hom · FAF 3.1e-05
Remaining individuals2 / 24,826 8.1e-05
European (non-Finnish)15 / 291,644 5.1e-05
African/African American1 / 22,634 4.4e-05
0 alternate alleles recorded in 7 other groups: Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish.

gnomAD v2.1

AF 2.4e-05 · 6 / 251,350 alleles · 0 hom · FAF 2.3e-05
European (non-Finnish)6 / 113,664 5.3e-05
0 alternate alleles recorded in 7 other groups: African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian.

Statements

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 3.55689e-05; MAF= 0.00356%, 18/506060 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 8.05607e-05; MAF= 0.00806%, 2/24826 alleles, homozygotes = 0); grpmax FAF= 3.085e-05.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 2.38711e-05; MAF= 0.00239%, 6/251350 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.27872e-05; MAF= 0.00528%, 6/113664 alleles, homozygotes = 0); grpmax FAF= 2.294e-05.

gnomAD-Canada

Not available in gnomAD-Canada v1.0.

SpliceAI and Pangolin

SpliceAI acceptor lossat -76 bp
0.004
SpliceAI acceptor gainat -106 bp
0.007
SpliceAI donor lossat +0 bp
0.093
SpliceAI donor gainat -16 bp
0.001
Pangolin splice lossmagnitude shown
-0.021
Pangolin splice gain
0.001

Other predictors

REVEL
0.555
BayesDel
0.442

How the predictions were used

PP3 ACMGNot met: missense REVEL 0.555 is below the >=0.644 PP3 supporting threshold. Details ▾Hide ▴
Reasoning

The variant is a missense substitution, p.(Gln157Pro), so the governing generic rule selects the REVEL path only; SpliceAI and BayesDel are not used for PP3. REVEL is 0.555, which is below the PP3 supporting threshold of >= 0.644 and therefore does not meet PP3.

Rule
Missense variant -> REVEL only. ... PP3 (supporting): >= 0.644 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
Evidence considered
  • Local REVEL predictor lookup: REVEL score 0.555 for NM_006758.3:c.470A>C (NP_006749.1:p.(Q157P)); this is below the supplied generic PP3 supporting cutoff of >= 0.644.
  • The supplied generic rule requires the single missense REVEL path; the available SpliceAI max delta 0.093 and BayesDel score 0.441524 were not counted for PP3.
  • The PP3 calibration threshold >= 0.644 is the supplied ClinGen SVI REVEL calibration from Pejaver et al. 2022, Am J Hum Genet (PMID:36413997).
Sources
revel
BP4 ACMGNot met: missense REVEL 0.555 exceeds the <=0.29 BP4 supporting threshold and is indeterminate. Details ▾Hide ▴
Reasoning

The variant is a missense substitution, p.(Gln157Pro), so the governing generic rule selects the REVEL path only; SpliceAI and BayesDel are not used for BP4. REVEL is 0.555, which is above the BP4 supporting threshold of <= 0.29 and lies in the indeterminate gray zone, so BP4 is not met.

Rule
Missense variant -> REVEL only. ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
Evidence considered
  • Local REVEL predictor lookup: REVEL score 0.555 for NM_006758.3:c.470A>C (NP_006749.1:p.(Q157P)); this exceeds the supplied generic BP4 supporting cutoff of <= 0.29.
  • Because the applicable missense REVEL result is indeterminate, the available SpliceAI max delta 0.093 was not substituted as BP4 evidence; BayesDel was also not used because no generic ACMG-strength calibration is established.
  • The BP4 calibration threshold <= 0.29 is the supplied ClinGen SVI REVEL calibration from Pejaver et al. 2022, Am J Hum Genet (PMID:36413997).
Sources
revel
BP7 N/ANot applicable: BP7 requires a synonymous variant, and this is a missense variant. Details ▾Hide ▴
Reasoning

BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_006758.3:c.470A>C in U2AF1 is a missense substitution predicted to produce NP_006749.1:p.(Gln157Pro). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for U2AF1, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.

Rule
deterministic_prefilter: requires_synonymous
Evidence considered
  • Deterministic consequence classification: missense (prefetch.json normalized protein consequence)
  • VCEP criterion policy: absent
Sources
generic_acmg_combination_rules

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.09). REVEL score = 0.555. BayesDel score = 0.441524.

5 paper records listed. 4 cited in the classification.

Cited in the classification

  • U2AF1 mutations alter splice site recognition in hematological malignancies.
    The paper explicitly studied U2AF1 Q157P and Q157R in K562 erythroleukemic cells. Both Q157 substitutions produced mutation-dependent splicing changes and altered 3-prime splice-site preferences, supporting recurrent functional importance of the Q157 hotspot but not a formal pathogenic classification for Q157R.
    → PS3 · supporting → PM1 · moderate Names this variant
    PMID 25267526 ↗
    Source detail
    We generated K562 erythroleukemic cell lines that stably expressed transgenic FLAG-tagged U2AF1 protein (WT, S34F, S34Y, Q157P, or Q157R mutations) at modest levels in the presence of the endogenous protein.

    Location Results, “U2AF1 mutations alter RNA splicing in blood cells,” paragraph 1; Figure 2

    Context K562 erythroleukemic cell lines stably expressing FLAG-tagged WT, S34F, S34Y, Q157P, or Q157R U2AF1 alongside endogenous U2AF1; deep RNA sequencing and splice-site preference analysis.

  • U2AF1 mutations alter sequence specificity of pre-mRNA binding and splicing.
    The paper describes U2AF1 Q157P and Q157R and demonstrates mutation-specific splicing effects in 293T minigene assays. Q157P reduced alternative isoform expression relative to wild type, supporting functional relevance of residue 157 but not a qualifying pathogenic classification for Q157R.
    → PS3 · supporting → PM1 · moderate Names this variant
    PMID 25311244 ↗
    Source detail
    Conversely, there was a reduction in relative expression of the alternative isoforms for both minigenes in cells expressing mutant Q157R and Q157P.

    Location Results, “Specific effects of U2AF1 mutations in alternative splicing”; Discussion, final paragraph

    Context Transient co-transfection of GH1 or FMR1 minigene reporters with WT or mutant U2AF1 constructs in 293T cells, followed by RT-PCR and isoform quantification.

  • Spliceosome Mutations Induce R Loop-Associated Sensitivity to ATR Inhibition in Myelodysplastic Syndromes.
    The paper evaluated U2AF1 Q157P in stable HeLa cell lines and found increased gamma-H2AX after ATR inhibition compared with wild-type U2AF1, providing functional evidence for Q157P but not evidence that a different same-residue variant is pathogenic.
    → PS3 · supporting Names this variant
    PMID 30054334 ↗
    Source detail
    To examine the effects of other MDS-associated U2AF1 mutations on the ATRi response, we generated HeLa cell lines that stably express the S34Y, Q157P, or Q157R mutant alleles at similar levels (Fig. 3D). In all the cell lines expressing these U2AF1 mutants, ATRi induced higher levels of γH2AX than in U2AF1WT-expressing cells (Fig. 3D).

    Location Results, “U2AF1S34F and other MDS-associated spliceosome mutants sensitize cells to ATRi,” paragraph 4; Fig. 3D

    Context Stable HeLa cell lines expressing U2AF1 wild type, S34Y, Q157P, or Q157R; ATR-inhibitor treatment with gamma-H2AX DNA-damage assessment.

  • Differential U2AF1 mutation sites, burden and co-mutation genes can predict prognosis in patients with myelodysplastic syndrome.
    In a retrospective cohort of 234 patients with de novo MDS, Q157P was detected in 7 cases, demonstrating recurrent occurrence of the Q157P substitution and supporting the biological relevance of residue 157; the study does not establish Q157R as pathogenic or define the full U2AF1 disease mechanism.
    → PM1 · moderate Names this variant
    PMID 33122737 ↗
    Source detail
    13.7% (7 cases) had the 157th glutamate was substituted by proline (Q157P).

    Location Results, “Mutant gene detection”; Results, “Clinical characteristics and prognostic significance of different U2AF1 mutation sites”; Table 1

    Context Retrospective cohort of 234 patients with de novo MDS diagnosed from January 2016 to January 2020; targeted next-generation sequencing of a 22-gene panel.

Other recorded publications

  • 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.
    Richards S et al. · 2015
    No paper-specific finding is recorded.
    PMID 25741868 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 3.55689e-05; MAF= 0.00356%, 18/506060 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 8.05607e-05; MAF= 0.00806%, 2/24826 alleles, homozygotes = 0); grpmax FAF= 3.085e-05.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 2.38711e-05; MAF= 0.00239%, 6/251350 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.27872e-05; MAF= 0.00528%, 6/113664 alleles, homozygotes = 0); grpmax FAF= 2.294e-05.

gnomAD-Canada

Not available in gnomAD-Canada v1.0.

ClinVar

This variant has been reported in ClinVar as Likely pathogenic (1 clinical laboratory). (ClinVarID = 376024)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.09). REVEL score = 0.555. BayesDel score = 0.441524.

Functional

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.

Somatic

This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV52341120, n = 111 times).

Cancer Hotspots

This variant lies in a statistically significant hotspot.