ASXL3 (Q9C0F0) variants and mutations
ASXL3 (also known as Q9C0F0) is a human protein-coding gene encoding a putative Polycomb group protein. A chromatin regulator that helps maintain transcriptional programs during development. Pathogenic variants cause Bainbridge-Ropers syndrome. This analysis covers 2,726 ASXL3 variants and mutations. Of these, 91% have computational variant effect predictions. Disease context includes severe feeding difficulties-failure to thrive-microcephaly due to ASXL3 deficien, hereditary disease, and Intellectual disability. Example ASXL3 variants include K2E, K2*, and K2R.
Variant analysis overview
- Gene: ASXL3
- Protein: Q9C0F0
- UniProt accession: Q9C0F0
- Organism: Homo sapiens
- Variants analyzed: 2726
- Variant scope: all variants
- Completed: 2026-10-09
Variant and mutation evidence
- Variant composition: 2,941 unspecified-consequence records; 15 frameshift variants; 128 missense variants; 14 stop-gained variants; 34 synonymous variants; 1 in-frame insertions; 2 in-frame deletions; 3 splice-region variants
- Prediction scores: 2,483 variants have prediction scores (91% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: severe feeding difficulties-failure to thrive-microcephaly due to ASXL3 deficien, hereditary disease, Intellectual disability, autism spectrum disorder, neurodevelopmental disorder, syndromic intellectual disability, Abnormality of the skeletal system, mathematical ability, Global developmental delay, heart failure, hypertensive disorder, essential hypertension.
Protein structure and variant hotspots
- Protein features: 2 domains.
- Structural context: 272 variants have structural context.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Diseases linked to ASXL3
Notable ASXL3 variants
Examples include K2E, K2*, K2R, K2I, K2K, K2N, D3T, D3Y. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- K2E (p.Lys2Glu), gnomAD 18-33578635-A-G, REVEL 0.11, ESM-1b 0.00
- K2* (p.Lys2Ter), gnomAD 18-33578635-A-T, CADD 37.00
- K2R (p.Lys2Arg), gnomAD 18-33578636-A-G, REVEL 0.12, ESM-1b 0.00
- K2I (p.Lys2Ile), gnomAD 18-33578636-A-T, REVEL 0.12, ESM-1b 0.00
- K2K (p.Lys2Lys), gnomAD 18-33578637-A-G, CADD 14.20
- K2N (p.Lys2Asn), gnomAD 18-33578637-A-T, REVEL 0.06, ESM-1b 0.00
- D3T (p.Asp3Thr), gnomAD 18-33578634-GA-G, CADD 24.50
- D3Y (p.Asp3Tyr), gnomAD 18-33578638-G-T, REVEL 0.13, ESM-1b 0.00
- D3H (p.Asp3His), gnomAD 18-33578638-G-C, REVEL 0.08, ESM-1b 0.00
- D3N (p.Asp3Asn), gnomAD 18-33578638-G-A, REVEL 0.06, ESM-1b 0.00
- D3V (p.Asp3Val), gnomAD 18-33578639-A-T, REVEL 0.15, ESM-1b 0.00
- D3G (p.Asp3Gly), gnomAD 18-33578639-A-G, REVEL 0.11, ESM-1b 0.00
- D3E (p.Asp3Glu), gnomAD 18-33578640-C-A, REVEL 0.07, ESM-1b 0.00
- D3D (p.Asp3Asp), gnomAD 18-33578640-C-T, CADD 14.80
- K4R (p.Lys4Arg), TOPMed rs1484690727, gnomAD rs1484690727, REVEL 0.08, ESM-1b 0.00
- K4E (p.Lys4Glu), rs1599364162, gnomAD 18-33578640-CAA-C, CADD 24.70
- K4* (p.Lys4Ter), gnomAD 18-33578641-A-T, CADD 36.00
- K4T (p.Lys4Thr), gnomAD 18-33578642-A-C, REVEL 0.09, ESM-1b 0.00
- K4M (p.Lys4Met), gnomAD 18-33578642-A-T, REVEL 0.11, ESM-1b 0.00
- K4K (p.Lys4Lys), rs774853403, gnomAD 18-33578643-G-A, CADD 14.00
- K4N (p.Lys4Asn), gnomAD 18-33578643-G-T, REVEL 0.06, ESM-1b 0.00
- R5K (p.Arg5Lys), Ensembl rs1555715142, REVEL 0.05, ESM-1b 0.00
- p.Arg5dup, gnomAD 18-33578642-A-AGA, CADD 18.40
- R5del (p.Arg5del), gnomAD 18-33578642-AGAG-, CADD 18.00
- R5W (p.Arg5Trp), gnomAD 18-33578644-A-T, REVEL 0.09, ESM-1b 0.89
- R5G (p.Arg5Gly), gnomAD 18-33578644-A-G, REVEL 0.05, ESM-1b 0.00
- R5M (p.Arg5Met), gnomAD 18-33578645-G-T, REVEL 0.10, ESM-1b 0.00
- R5T (p.Arg5Thr), gnomAD 18-33578645-G-C, REVEL 0.07, ESM-1b 0.00
- R5S (p.Arg5Ser), gnomAD 18-33578646-G-C, REVEL 0.05, ESM-1b 0.00
- R5R (p.Arg5Arg), rs748441065, gnomAD 18-33578646-G-A, CADD 15.30
- K6R (p.Lys6Arg), gnomAD 18-33578644-AG-A, CADD 24.90
- K6* (p.Lys6Ter), gnomAD 18-33578647-A-T, CADD 39.00
- K6E (p.Lys6Glu), gnomAD 18-33578647-A-G, REVEL 0.09, ESM-1b 0.00
- K6N (p.Lys6Asn), gnomAD 18-33578649-G-T, REVEL 0.07, ESM-1b 0.00
- K6K (p.Lys6Lys), rs1257846317, gnomAD 18-33578649-G-A, CADD 15.10
- K7R (p.Lys7Arg), gnomAD 18-33578649-GA-G, CADD 26.90
- K7E (p.Lys7Glu), gnomAD 18-33578650-A-G, REVEL 0.11, ESM-1b 0.00
- K7* (p.Lys7Ter), gnomAD 18-33578650-A-T, CADD 38.00
- K7T (p.Lys7Thr), gnomAD 18-33578651-A-C, REVEL 0.12, ESM-1b 0.00
- K7K (p.Lys7Lys), gnomAD 18-33578652-G-A, CADD 14.80
- K7N (p.Lys7Asn), gnomAD 18-33578652-G-C, REVEL 0.10, ESM-1b 0.00
- K8del (p.Lys8del), rs773896616, gnomAD 18-33578645-GGAA-, CADD 19.80
- K8E (p.Lys8Glu), gnomAD 18-33578649-G-GA, CADD 27.40
- K8R (p.Lys8Arg), gnomAD 18-33578652-GA-G, CADD 24.90
- K8* (p.Lys8Ter), gnomAD 18-33578653-A-T, CADD 38.00
- K8T (p.Lys8Thr), gnomAD 18-33578654-A-C, REVEL 0.10, ESM-1b 0.36
- K8M (p.Lys8Met), gnomAD 18-33578654-A-T, REVEL 0.12, ESM-1b 0.91
- K8N (p.Lys8Asn), gnomAD 18-33578655-G-T, REVEL 0.08, ESM-1b 0.68
- K8K (p.Lys8Lys), gnomAD 18-33578655-G-A, CADD 13.60
- D9E (p.Asp9Glu), Ensembl rs2064966367, REVEL 0.04, ESM-1b 0.00
- D9H (p.Asp9His), gnomAD 18-33578656-G-C, REVEL 0.08, ESM-1b 0.00
- D9N (p.Asp9Asn), gnomAD 18-33578656-G-A, REVEL 0.08, ESM-1b 0.00
- D9Y (p.Asp9Tyr), gnomAD 18-33578656-G-T, REVEL 0.13, ESM-1b 0.00
- D9G (p.Asp9Gly), gnomAD 18-33578657-A-G, REVEL 0.06, ESM-1b 0.00
- D9V (p.Asp9Val), gnomAD 18-33578657-A-T, REVEL 0.11, ESM-1b 0.00
- D9D (p.Asp9Asp), rs2064966367, gnomAD 18-33578658-C-T, CADD 13.30
- R10C (p.Arg10Cys), ExAC rs772436861, TOPMed rs772436861, gnomAD rs772436861, REVEL 0.17, ESM-1b 0.00, Likely benign, not specified
- R10H (p.Arg10His), rs773417248, ClinGen CA8933435, ClinVar RCV002742305, ExAC rs773417248, REVEL 0.12, ESM-1b 0.00, Uncertain significance, Inborn genetic diseases
- R10L (p.Arg10Leu), ExAC rs773417248, TOPMed rs773417248, gnomAD rs773417248, REVEL 0.17, ESM-1b 0.00, Uncertain significance
- R10G (p.Arg10Gly), gnomAD 18-33578659-C-G, REVEL 0.15, ESM-1b 1.00
- R10S (p.Arg10Ser), gnomAD 18-33578659-C-A, REVEL 0.15, ESM-1b 0.33
- R10P (p.Arg10Pro), gnomAD 18-33578660-G-C, REVEL 0.19, ESM-1b 0.73
- R10R (p.Arg10Arg), gnomAD 18-33578661-C-A, CADD 14.30
- T11P (p.Thr11Pro), gnomAD 18-33578660-GC-G, CADD 24.60
- T11A (p.Thr11Ala), gnomAD 18-33578662-A-G, REVEL 0.13, ESM-1b 1.00
- T11I (p.Thr11Ile), gnomAD 18-33578663-C-T, REVEL 0.15, ESM-1b 1.00
- T11S (p.Thr11Ser), gnomAD 18-33578663-C-G, REVEL 0.12, ESM-1b 0.00
- T11N (p.Thr11Asn), gnomAD 18-33578663-C-A, REVEL 0.10, ESM-1b 1.00
- T11T (p.Thr11Thr), gnomAD 18-33578664-C-G, CADD 14.20
- W12* (p.Trp12Ter), rs2511301336, ClinGen CA402269292, ClinVar RCV003130454, CADD 38.00, Pathogenic
- W12G (p.Trp12Gly), gnomAD 18-33578662-AC-A, CADD 24.60
- W12R (p.Trp12Arg), gnomAD 18-33578665-T-A, REVEL 0.20, ESM-1b 1.00
- W12L (p.Trp12Leu), gnomAD 18-33578666-G-T, REVEL 0.18, ESM-1b 1.00
- W12C (p.Trp12Cys), gnomAD 18-33578667-G-T, REVEL 0.28, ESM-1b 1.00
- A13S (p.Ala13Ser), Ensembl rs2064966446, REVEL 0.06, ESM-1b 0.00
- A13P (p.Ala13Pro), gnomAD 18-33578665-TG-T, CADD 27.40
- A13T (p.Ala13Thr), gnomAD 18-33578668-G-A, REVEL 0.11, ESM-1b 0.23
- A13V (p.Ala13Val), gnomAD 18-33578669-C-T, REVEL 0.10, ESM-1b 1.00
- A13G (p.Ala13Gly), gnomAD 18-33578669-C-G, REVEL 0.08, ESM-1b 1.00
- A13D (p.Ala13Asp), gnomAD 18-33578669-C-A, REVEL 0.18, ESM-1b 1.00
- A13A (p.Ala13Ala), rs917031264, gnomAD 18-33578670-C-T, CADD 15.70
- E14K (p.Glu14Lys), gnomAD rs1343564632, REVEL 0.17, ESM-1b 1.00
- E14R (p.Glu14Arg), gnomAD 18-33578668-GC-G, CADD 28.10
- E14* (p.Glu14Ter), gnomAD 18-33578671-G-T, CADD 38.00
- E14Q (p.Glu14Gln), gnomAD 18-33578671-G-C, REVEL 0.16, ESM-1b 0.07
- E14G (p.Glu14Gly), gnomAD 18-33578672-A-G, REVEL 0.17, ESM-1b 1.00
- E14V (p.Glu14Val), gnomAD 18-33578672-A-T, REVEL 0.21, ESM-1b 1.00
- E14D (p.Glu14Asp), gnomAD 18-33578673-G-T, REVEL 0.12, ESM-1b 0.04
- E14E (p.Glu14Glu), rs760699200, gnomAD 18-33578673-G-A, CADD 13.70
- A15S (p.Ala15Ser), gnomAD 18-33578674-G-T, REVEL 0.07, ESM-1b 1.00
- A15P (p.Ala15Pro), gnomAD 18-33578674-G-C, REVEL 0.18, ESM-1b 1.00
- A15T (p.Ala15Thr), gnomAD 18-33578674-G-A, REVEL 0.11, ESM-1b 1.00
- A15G (p.Ala15Gly), gnomAD 18-33578675-C-G, REVEL 0.07, ESM-1b 1.00
- A15V (p.Ala15Val), gnomAD 18-33578675-C-T, REVEL 0.10, ESM-1b 1.00
- A15D (p.Ala15Asp), gnomAD 18-33578675-C-A, REVEL 0.16, ESM-1b 1.00
- A15A (p.Ala15Ala), gnomAD 18-33578676-T-C, CADD 16.00
- A16T (p.Ala16Thr), Ensembl rs2145082927, REVEL 0.17, ESM-1b 1.00
- A16G (p.Ala16Gly), NCI-TCGA Cosmic COSV5247, Variant assessed as somatic; moderate impact.
- A16S (p.Ala16Ser), gnomAD 18-33578677-G-T, REVEL 0.09, ESM-1b 1.00
- A16V (p.Ala16Val), gnomAD 18-33578678-C-T, REVEL 0.16, ESM-1b 1.00
- A16D (p.Ala16Asp), gnomAD 18-33578678-C-A, REVEL 0.24, ESM-1b 1.00
- A16A (p.Ala16Ala), gnomAD 18-33578679-C-G, CADD 14.70
- R17L (p.Arg17Leu), Ensembl rs1568260351, REVEL 0.15, ESM-1b 1.00
- R17S (p.Arg17Ser), ExAC rs766432387, gnomAD rs766432387, REVEL 0.17, ESM-1b 1.00
- R17P (p.Arg17Pro), gnomAD 18-33578677-GCC-G, CADD 25.40
- R17A (p.Arg17Ala), gnomAD 18-33578677-GC-G, CADD 25.50
- R17G (p.Arg17Gly), gnomAD 18-33578680-C-G, REVEL 0.16, ESM-1b 1.00
- R17C (p.Arg17Cys), gnomAD 18-33578680-C-T, REVEL 0.14, ESM-1b 1.00
- R17H (p.Arg17His), gnomAD 18-33578681-G-A, REVEL 0.14, ESM-1b 1.00
- R17R (p.Arg17Arg), gnomAD 18-33578682-C-T, CADD 15.80
- L18M (p.Leu18Met), gnomAD 18-33578683-C-A, REVEL 0.03, ESM-1b 0.00
- L18L (p.Leu18Leu), rs1428970437, gnomAD 18-33578683-C-T, CADD 18.80
- L18Q (p.Leu18Gln), gnomAD 18-33578684-T-A, REVEL 0.11, ESM-1b 1.00
- L18P (p.Leu18Pro), gnomAD 18-33578684-T-C, REVEL 0.12, ESM-1b 1.00
- A19S (p.Ala19Ser), gnomAD 18-33607594-G-T, REVEL 0.17, ESM-1b 0.41
- A19T (p.Ala19Thr), gnomAD 18-33607594-G-A, REVEL 0.25, ESM-1b 0.00
- A19V (p.Ala19Val), gnomAD 18-33607595-C-T, REVEL 0.31, ESM-1b 0.00
- A19E (p.Ala19Glu), gnomAD 18-33607595-C-A, REVEL 0.30, ESM-1b 1.00
- A19A (p.Ala19Ala), gnomAD 18-33607596-A-G, CADD 16.90
- L20R (p.Leu20Arg), gnomAD 18-33607594-GCA-G, CADD 26.60
- L20I (p.Leu20Ile), gnomAD 18-33607597-C-A, REVEL 0.11, ESM-1b 0.00
- L20P (p.Leu20Pro), gnomAD 18-33607598-T-C, REVEL 0.55, ESM-1b 1.00
- L20L (p.Leu20Leu), gnomAD 18-33607599-A-G, CADD 10.40
- E21G (p.Glu21Gly), ExAC rs202002253, TOPMed rs202002253, gnomAD rs202002253, REVEL 0.32, ESM-1b 1.00
- E21K (p.Glu21Lys), rs1403183821, ClinGen CA402269359, ClinVar RCV001931004, gnomAD rs1403183821, REVEL 0.28, ESM-1b 0.14, Uncertain significance, not provided
- E21* (p.Glu21Ter), gnomAD 18-33607600-G-T, CADD 37.00
- E21E (p.Glu21Glu), gnomAD 18-33607602-A-G, CADD 9.22
- K22E (p.Lys22Glu), gnomAD rs1366806112, ESM-1b 0.00, AlphaMissense 0.95
- K22N (p.Lys22Asn), gnomAD 18-33607600-GA-G, CADD 27.60
- H23Q (p.His23Gln), gnomAD rs1303101039, REVEL 0.14, ESM-1b 0.00
- H23Y (p.His23Tyr), rs555478574, ClinGen CA8933458, ClinVar RCV004526479, 1000Genomes rs555478574, REVEL 0.07, ESM-1b 0.00, Uncertain significance, not specified
- H23N (p.His23Asn), gnomAD 18-33607606-C-A, REVEL 0.11, ESM-1b 0.00
- H23H (p.His23His), gnomAD 18-33607608-C-T, CADD 5.76
- P24T (p.Pro24Thr), rs866252239, gnomAD 18-33607609-C-A, REVEL 0.23, ESM-1b 1.00
- P24R (p.Pro24Arg), gnomAD 18-33607610-C-G, REVEL 0.25, ESM-1b 1.00
- P24L (p.Pro24Leu), gnomAD 18-33607610-C-T, REVEL 0.24, ESM-1b 1.00
- P24H (p.Pro24His), gnomAD 18-33607610-C-A, REVEL 0.25, ESM-1b 1.00
- P24P (p.Pro24Pro), rs2145123853, gnomAD 18-33607611-C-T, CADD 11.40
- N25S (p.Asn25Ser), TOPMed rs1333815571, gnomAD rs1333815571, REVEL 0.13, ESM-1b 0.89, Uncertain significance, Inborn genetic diseases
- N25D (p.Asn25Asp), gnomAD 18-33607612-A-G, REVEL 0.19, ESM-1b 0.94
- N25I (p.Asn25Ile), gnomAD 18-33607613-A-T, REVEL 0.25, ESM-1b 1.00
- N25K (p.Asn25Lys), gnomAD 18-33607614-C-A, REVEL 0.07, ESM-1b 1.00
- N25N (p.Asn25Asn), gnomAD 18-33607614-C-T, CADD 8.95
- S26T (p.Ser26Thr), gnomAD 18-33607615-T-A, REVEL 0.22, ESM-1b 0.00
- S26P (p.Ser26Pro), gnomAD 18-33607615-T-C, REVEL 0.19, ESM-1b 1.00
- S26L (p.Ser26Leu), gnomAD 18-33607616-C-T, REVEL 0.24, ESM-1b 1.00
- S26* (p.Ser26Ter), gnomAD 18-33607616-C-A, CADD 36.00
- S26S (p.Ser26Ser), gnomAD 18-33607617-A-G, CADD 10.60
- P27T (p.Pro27Thr), gnomAD 18-33607618-C-A, REVEL 0.21, ESM-1b 1.00
- P27A (p.Pro27Ala), gnomAD 18-33607618-C-G, REVEL 0.19, ESM-1b 1.00
- P27S (p.Pro27Ser), gnomAD 18-33607618-C-T, REVEL 0.17, ESM-1b 1.00
- P27R (p.Pro27Arg), gnomAD 18-33607619-C-G, REVEL 0.19, ESM-1b 1.00
- P27Q (p.Pro27Gln), gnomAD 18-33607619-C-A, REVEL 0.14, ESM-1b 0.80
- P27L (p.Pro27Leu), gnomAD 18-33607619-C-T, REVEL 0.20, ESM-1b 1.00
- P27P (p.Pro27Pro), rs2065269503, gnomAD 18-33607620-A-C, CADD 13.20
- M28V (p.Met28Val), gnomAD 18-33607621-A-G, REVEL 0.29, ESM-1b 1.00
- M28T (p.Met28Thr), gnomAD 18-33607622-T-C, REVEL 0.23, ESM-1b 1.00
- M28I (p.Met28Ile), gnomAD 18-33607623-G-C, REVEL 0.24, ESM-1b 1.00
- T29A (p.Thr29Ala), TOPMed rs1454030713, REVEL 0.26, ESM-1b 1.00
- T29S (p.Thr29Ser), gnomAD 18-33607624-A-T, REVEL 0.23, ESM-1b 0.00
- T29I (p.Thr29Ile), gnomAD 18-33607625-C-T, REVEL 0.26, ESM-1b 1.00
- T29K (p.Thr29Lys), gnomAD 18-33607625-C-A, REVEL 0.26, ESM-1b 1.00
- T29T (p.Thr29Thr), gnomAD 18-33607626-A-G, CADD 11.80
- A30E (p.Ala30Glu), Ensembl rs868535897, REVEL 0.23, ESM-1b 0.00
- A30T (p.Ala30Thr), ExAC rs774236876, REVEL 0.15, ESM-1b 0.00
- A30P (p.Ala30Pro), gnomAD 18-33607627-G-C, REVEL 0.27, ESM-1b 0.00
- A30S (p.Ala30Ser), gnomAD 18-33607627-G-T, REVEL 0.23, ESM-1b 0.00
- A30V (p.Ala30Val), gnomAD 18-33607628-C-T, REVEL 0.15, ESM-1b 0.00
- A30A (p.Ala30Ala), gnomAD 18-33607629-A-G, CADD 11.30
- K31* (p.Lys31Ter), gnomAD 18-33607630-A-T, CADD 36.00
- K31T (p.Lys31Thr), gnomAD 18-33607631-A-C, REVEL 0.29, ESM-1b 1.00
- K31N (p.Lys31Asn), gnomAD 18-33607632-G-T, REVEL 0.14, ESM-1b 1.00
- K31K (p.Lys31Lys), rs761622426, gnomAD 18-33607632-G-A, CADD 9.93
- Q32* (p.Gln32Ter), gnomAD 18-33607633-C-T, CADD 36.00
- Q32K (p.Gln32Lys), gnomAD 18-33607633-C-A, REVEL 0.20, ESM-1b 1.00
- Q32R (p.Gln32Arg), gnomAD 18-33607634-A-G, REVEL 0.25, ESM-1b 1.00
- Q32H (p.Gln32His), gnomAD 18-33607635-G-T, REVEL 0.14, ESM-1b 0.00
- I33M (p.Ile33Met), gnomAD rs1286328186, REVEL 0.24, ESM-1b 1.00, Uncertain significance, not provided
- I33T (p.Ile33Thr), Ensembl rs1376712292, ESM-1b 1.00, AlphaMissense 1.00
- I33L (p.Ile33Leu), gnomAD 18-33607636-A-T, REVEL 0.20, ESM-1b 1.00
Public ASXL3 analysis runs
- ASXL3 analysis run — ASXL3 (2,726 variants) — completed 2026-10-09