ASXL1 encodes a chromatin-binding protein of the Polycomb group that helps regulate gene expression by recruiting repressive complexes (such as PRC2) to chromatin and modifying histone marks. Germline mutations in ASXL1 cause Bohring-Opitz syndrome, a developmental disorder with distinctive craniofacial abnormalities. Somatic loss-of-function mutations in ASXL1 are common in blood cancers, including myelodysplastic syndromes, chronic myelomonocytic leukemia, myelofibrosis, and acute myeloid leukemia, where the gene acts as a tumor suppressor. Loss of ASXL1 function disrupts normal repression of target genes, contributing to leukemogenesis.
This variant
ASXL1 truncating mutations are established drivers in myeloid malignancies, and germline loss-of-function variants cause Bohring-Opitz syndrome, giving this last-exon truncation a plausible disease mechanism. The VUS classification reflects that this specific allele lacks the functional, familial, or population evidence needed to confirm or refute pathogenicity.
Transcript
NM_015338.5
HGVS · transcript:coding
NM_015338.5:c.2148dup
GRCh38
chr20:32434859 C>CT
GRCh37
chr20:31022662 C>CT
BasisVUS: PVS1 (Moderate, last-exon NMD-escape truncation) plus PM2 and BP4 (Supporting, gnomAD absence and negative SpliceAI) match no pathogenic or benign ACMG/AMP 2015 rule.▾
VUS: PVS1 (Moderate, last-exon NMD-escape truncation) plus PM2 and BP4 (Supporting, gnomAD absence and negative SpliceAI) match no pathogenic or benign ACMG/AMP 2015 rule.
Classification rationale
PVS1PM2BP4VUS
ASXL1 c.2148dupnonsense · exon 13
PVS1 (Moderate): last-exon nonsense escapes nonsense-mediated decay but truncates ~54% of the protein, exceeding the >10% consequential-truncation threshold. PM2 (Supporting): variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0. BP4 (Supporting): SpliceAI max delta 0.018, below the 0.2 splice-altering threshold. Overall: VUS - met criteria (PVS1 Moderate, PM2 Supporting, BP4 Supporting) combine under no ACMG/AMP 2015 rule.
PVS1 + PM2 + BP4→VUS
Gene diagram
· NM_015338.5 · variants mapped to exon structure
ASXL1NM_015338.5
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in ASXL1—click a row to locate it on the plot · use the link column to open its page
Variant ↕
Protein
Location
Classification
Link
Applied criteria · 3 applied · 17 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 · 3
Strength Supporting Moderate Strong Very strong
✓
PVS1moderatereviewPathogenic
Met (Moderate): last-exon stop codon escapes nonsense-mediated decay but removes 54% of the protein, exceeding the >10% truncation threshold.
mutalyzer/VariantValidator normalization confirms NM_015338.5:c.2148dup produces NP_056153.2:p.(Arg717Ter), a nonsense/premature-termination-codon variant.VariantValidator variant_exonic_positions places the variant in exon 13 of 13 (start_exon=end_exon='13'), the final exon of the ASXL1 transcript, meaning NMD is not predicted to occur per the ClinGen SVI PVS1 decision tree (PMC6185798).Mutalyzer predicted protein data show the truncated protein length is 716 aa versus a full-length 1542 aa protein, a loss of approximately 54% of the protein, exceeding the 10% threshold used in the SVI framework's NMD-escape branch to justify at least PVS1_Moderate.
Met (Supporting): absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0.
gnomAD v2.1 queried 20-31022662-C-CT and reported the variant absent.gnomAD v4.1 queried chr20-32434859-C-CT and reported the variant absent.gnomAD-Canada v1.0 queried 20-32434859-C-CT and reported the variant absent.
Met (Supporting): SpliceAI max delta 0.018, far below the 0.2 splice-altering cutoff.
case_summary.json compact_evidence.spliceai: SpliceAI predicts no significant splice impact for this variant (max delta score = 0.018); scores DS_AG=0.001, DS_AL=0.0, DS_DG=0.0, DS_DL=0.018.SpliceAI delta scores well below the 0.2 threshold established in the original SpliceAI validation publication (Jaganathan KM et al., Cell 2019, PMID 30661751) support a benign/no-effect prediction for splicing, satisfying BP4 at supporting strength.
Triaged references · 5 PMIDs not cited in assessment
19388938 ↗Mutations of polycomb-associated gene ASXL1 in myelodysplastic syndromes and chronic myelomonocytic leukaemia.ONCOKB
21455215 ↗Concomitant analysis of EZH2 and ASXL1 mutations in myelofibrosis, chronic myelomonocytic leukemia and blast-phase myeloproliferative neoplasms.ONCOKB
22897849 ↗ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression.ONCOKB
24216483 ↗Myelodysplastic syndromes are induced by histone methylation–altering ASXL1 mutations.ONCOKB
26095772 ↗Cancer-associated ASXL1 mutations may act as gain-of-function mutations of the ASXL1-BAP1 complex.ONCOKB