IL23A (Interleukin-23 subunit alpha) variants and mutations
IL23A (also known as Interleukin-23 subunit alpha) is a human protein-coding gene encoding an interleukin-23 subunit alpha protein. It combines with p40 to form IL-23, which sustains pathogenic and protective Th17-cell responses at barrier tissues. Excess IL-23 signaling is central to psoriasis and inflammatory bowel disease, making the pathway a major therapeutic target. This analysis covers 478 IL23A variants and mutations. Of these, 98% have computational variant effect predictions. Disease context includes psoriasis, psoriasis vulgaris, and Crohn disease. Example IL23A variants include L2P, L2V, and L2M.
Variant analysis overview
- Gene: IL23A
- Protein: Interleukin-23 subunit alpha
- UniProt accession: Q9NPF7
- Organism: Homo sapiens
- Variants analyzed: 478
- Variant scope: all variants
- Completed: 2026-08-19
Variant and mutation evidence
- Variant composition: 167 unspecified-consequence records; 178 missense variants; 95 synonymous variants; 21 frameshift variants; 4 in-frame deletions; 1 in-frame insertions; 10 stop-gained variants; 2 splice-region variants
- Prediction scores: 468 variants have prediction scores (98% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: psoriasis, psoriasis vulgaris, Crohn disease, ulcerative colitis, psoriatic arthritis, immune system disorder, pustular psoriasis, psoriasis-related juvenile idiopathic arthritis, palmoplantar pustulosis, generalized pustular psoriasis, intestinal obstruction, rheumatoid arthritis.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, MaveDB, LitVar.
Notable IL23A variants
Examples include L2P, L2V, L2M, L2L, L2R, G3E, G3R, G3W. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- L2P (p.Leu2Pro), ExAC rs745769997, TOPMed rs745769997, gnomAD rs745769997, REVEL 0.04, MetaLR 0.12
- L2V (p.Leu2Val), TOPMed rs1592456595, gnomAD rs1592456595, MetaLR 0.09, MetaSVM -0.98
- L2M (p.Leu2Met), gnomAD 12-56339048-C-A, REVEL 0.06, MetaLR 0.08
- L2L (p.Leu2Leu), gnomAD 12-56339048-C-T, CADD 7.64
- L2R (p.Leu2Arg), gnomAD 12-56339049-T-G, REVEL 0.35, MetaLR 0.08
- G3E (p.Gly3Glu), Ensembl rs1876393751, REVEL 0.08, MetaLR 0.12
- G3R (p.Gly3Arg), gnomAD 12-56339051-G-A, REVEL 0.05, MetaLR 0.12
- G3W (p.Gly3Trp), gnomAD 12-56339051-G-T, REVEL 0.07, MetaLR 0.10
- G3G (p.Gly3Gly), gnomAD 12-56339053-G-A, CADD 2.16
- S4A (p.Ser4Ala), gnomAD 12-56339049-TG-T, CADD 24.10
- S4G (p.Ser4Gly), gnomAD 12-56339054-A-G, REVEL 0.02, MetaLR 0.12
- S4N (p.Ser4Asn), gnomAD 12-56339055-G-A, REVEL 0.14, MetaLR 0.06
- S4R (p.Ser4Arg), gnomAD 12-56339056-C-A, REVEL 0.04, MetaLR 0.14
- S4S (p.Ser4Ser), gnomAD 12-56339056-C-T, CADD 8.66
- R5I (p.Arg5Ile), gnomAD 12-56339058-G-T, REVEL 0.08, MetaLR 0.09
- R5R (p.Arg5Arg), gnomAD 12-56339059-A-G, CADD 10.80
- A6V (p.Ala6Val), TOPMed rs1020985680, REVEL 0.10, MetaLR 0.09
- A6T (p.Ala6Thr), gnomAD 12-56339060-G-A, REVEL 0.10, MetaLR 0.09
- A6D (p.Ala6Asp), gnomAD 12-56339061-C-A, REVEL 0.20, MetaLR 0.15
- A6G (p.Ala6Gly), gnomAD 12-56339061-C-G, REVEL 0.06, MetaLR 0.09
- A6A (p.Ala6Ala), gnomAD 12-56339062-T-C, CADD 9.60
- V7I (p.Val7Ile), gnomAD 12-56339063-G-A, REVEL 0.09, MetaLR 0.08
- V7A (p.Val7Ala), gnomAD 12-56339064-T-C, REVEL 0.09, MetaLR 0.16
- V7V (p.Val7Val), rs1876393938, gnomAD 12-56339065-A-G, CADD 7.67
- M8I (p.Met8Ile), ExAC rs769687309, TOPMed rs769687309, gnomAD rs769687309, REVEL 0.06, MetaLR 0.08
- M8L (p.Met8Leu), gnomAD 12-56339066-A-C, REVEL 0.10, MetaLR 0.03
- L9L (p.Leu9Leu), rs375903516, gnomAD 12-56339069-C-T, CADD 11.00
- L9M (p.Leu9Met), gnomAD 12-56339069-C-A, REVEL 0.08, MetaLR 0.11
- L9P (p.Leu9Pro), gnomAD 12-56339070-T-C, REVEL 0.34, MetaLR 0.25
- L10C (p.Leu10Cys), gnomAD 12-56339070-TG-T, CADD 24.40
- L10L (p.Leu10Leu), gnomAD 12-56339072-C-T, CADD 11.20
- L10M (p.Leu10Met), gnomAD 12-56339072-C-A, REVEL 0.16, MetaLR 0.14
- L10P (p.Leu10Pro), gnomAD 12-56339073-T-C, REVEL 0.24, MetaLR 0.23
- L11L (p.Leu11Leu), gnomAD 12-56339075-T-C, CADD 7.40
- L11S (p.Leu11Ser), gnomAD 12-56339076-T-C, REVEL 0.09, MetaLR 0.09
- L11F (p.Leu11Phe), gnomAD 12-56339077-G-T, REVEL 0.09, MetaLR 0.10
- L12P (p.Leu12Pro), ExAC rs762696858, TOPMed rs762696858, gnomAD rs762696858, REVEL 0.36, MetaLR 0.40, Uncertain significance, not specified
- L12V (p.Leu12Val), TOPMed rs1196413532, gnomAD rs1196413532, REVEL 0.25, MetaLR 0.25
- L12L (p.Leu12Leu), gnomAD 12-56339078-C-T, CADD 9.28
- L12M (p.Leu12Met), gnomAD 12-56339078-C-A, REVEL 0.21, MetaLR 0.26
- L13del (p.Leu13del), gnomAD 12-56339066-ATGC-, CADD 17.00
- p.Leu13dup, gnomAD 12-56339075-T-TTG, CADD 15.70
- L13C (p.Leu13Cys), gnomAD 12-56339079-TG-T, CADD 23.30
- L13M (p.Leu13Met), gnomAD 12-56339081-C-A, REVEL 0.14, MetaLR 0.15
- L13L (p.Leu13Leu), rs199937376, gnomAD 12-56339081-C-T, CADD 9.04
- L13P (p.Leu13Pro), gnomAD 12-56339082-T-C, REVEL 0.31, MetaLR 0.31
- P14L (p.Pro14Leu), 1000Genomes rs145233794, ESP rs145233794, ExAC rs145233794, TOPMed rs145233794, REVEL 0.07, MetaLR 0.09
- P14T (p.Pro14Thr), ExAC rs774022773, gnomAD rs774022773, REVEL 0.05, MetaLR 0.08
- P14S (p.Pro14Ser), gnomAD 12-56339084-C-T, REVEL 0.04, MetaLR 0.07
- P14H (p.Pro14His), gnomAD 12-56339085-C-A, REVEL 0.08, MetaLR 0.09
- P14P (p.Pro14Pro), gnomAD 12-56339086-C-A, CADD 3.73
- W15G (p.Trp15Gly), gnomAD 12-56339083-GC-G, CADD 9.71
- W15R (p.Trp15Arg), gnomAD 12-56339087-T-C, REVEL 0.04, MetaLR 0.04
- W15* (p.Trp15Ter), gnomAD 12-56339088-G-A, CADD 29.10
- W15C (p.Trp15Cys), gnomAD 12-56339089-G-T, REVEL 0.10, MetaLR 0.06
- T16I (p.Thr16Ile), gnomAD rs1363398735, REVEL 0.04, MetaLR 0.07
- T16S (p.Thr16Ser), ExAC rs766907063, gnomAD rs766907063, REVEL 0.01, MetaLR 0.06
- T16A (p.Thr16Ala), gnomAD 12-56339090-A-G, REVEL 0.02, MetaLR 0.05
- T16K (p.Thr16Lys), gnomAD 12-56339091-C-A, REVEL 0.09, MetaLR 0.07
- T16T (p.Thr16Thr), rs754421582, gnomAD 12-56339092-A-G, CADD 0.11
- A17V (p.Ala17Val), TOPMed rs761463787, gnomAD rs761463787, REVEL 0.10, MetaLR 0.08
- A17T (p.Ala17Thr), gnomAD 12-56339093-G-A, REVEL 0.01, MetaLR 0.05
- A17S (p.Ala17Ser), gnomAD 12-56339093-G-T, REVEL 0.01, MetaLR 0.05
- A17D (p.Ala17Asp), gnomAD 12-56339094-C-A, REVEL 0.14, MetaLR 0.08
- A17A (p.Ala17Ala), gnomAD 12-56339095-T-C, CADD 3.54
- Q18A (p.Gln18Ala), gnomAD 12-56339090-ACAGC, CADD 26.60
- Q18K (p.Gln18Lys), gnomAD 12-56339096-C-A, REVEL 0.07, MetaLR 0.09
- Q18L (p.Gln18Leu), gnomAD 12-56339097-A-T, REVEL 0.12, MetaLR 0.08
- Q18R (p.Gln18Arg), gnomAD 12-56339097-A-G, REVEL 0.05, MetaLR 0.07
- Q18H (p.Gln18His), gnomAD 12-56339098-G-T, REVEL 0.06, MetaLR 0.07
- G19R (p.Gly19Arg), gnomAD 12-56339099-G-C, REVEL 0.05, MetaLR 0.07
- G19S (p.Gly19Ser), gnomAD 12-56339099-G-A, REVEL 0.03, MetaLR 0.07
- G19C (p.Gly19Cys), gnomAD 12-56339099-G-T, REVEL 0.05, MetaLR 0.07
- G19V (p.Gly19Val), gnomAD 12-56339100-G-T, REVEL 0.05, MetaLR 0.07
- G19D (p.Gly19Asp), gnomAD 12-56339100-G-A, REVEL 0.04, MetaLR 0.06
- G19A (p.Gly19Ala), gnomAD 12-56339100-G-C, REVEL 0.05, MetaLR 0.05
- G19G (p.Gly19Gly), gnomAD 12-56339101-C-A, CADD 6.54
- R20G (p.Arg20Gly), gnomAD 12-56339102-A-G, REVEL 0.14, MetaLR 0.06
- R20* (p.Arg20Ter), gnomAD 12-56339102-A-T, CADD 25.80
- R20K (p.Arg20Lys), gnomAD 12-56339103-G-A, REVEL 0.05, MetaLR 0.07
- R20R (p.Arg20Arg), gnomAD 12-56339104-A-G, CADD 7.37
- A21T (p.Ala21Thr), gnomAD 12-56339105-G-A, REVEL 0.10, MetaLR 0.08
- A21D (p.Ala21Asp), gnomAD 12-56339106-C-A, REVEL 0.17, MetaLR 0.08
- A21V (p.Ala21Val), gnomAD 12-56339106-C-T, REVEL 0.15, MetaLR 0.09
- A21A (p.Ala21Ala), rs2136024026, gnomAD 12-56339107-T-C, CADD 3.17
- V22M (p.Val22Met), gnomAD 12-56339108-G-A, REVEL 0.06, MetaLR 0.07
- V22L (p.Val22Leu), gnomAD 12-56339108-G-C, REVEL 0.06, MetaLR 0.07
- V22V (p.Val22Val), gnomAD 12-56339110-G-T, CADD 6.53
- P23S (p.Pro23Ser), TOPMed rs1305275384, gnomAD rs1305275384, REVEL 0.02, MetaLR 0.04
- P23C (p.Pro23Cys), rs779800802, gnomAD 12-56339106-C-CTG, CADD 22.50
- P23P (p.Pro23Pro), gnomAD 12-56339113-T-C, CADD 7.31
- G24R (p.Gly24Arg), TOPMed rs1490875264, gnomAD rs1490875264, REVEL 0.05, MetaLR 0.04
- G24W (p.Gly24Trp), gnomAD 12-56339114-G-T, REVEL 0.04, MetaLR 0.06
- G24G (p.Gly24Gly), gnomAD 12-56339116-G-A, CADD 9.45
- G25A (p.Gly25Ala), NCI-TCGA TCGA novel, MetaLR 0.07, MetaSVM -1.00, Variant assessed as somatic; high impact.
- G25D (p.Gly25Asp), TOPMed rs1876395700, REVEL 0.04, MetaLR 0.05
- G25S (p.Gly25Ser), gnomAD 12-56339117-G-A, REVEL 0.07, MetaLR 0.04
- G25C (p.Gly25Cys), gnomAD 12-56339117-G-T, REVEL 0.06, MetaLR 0.06
- G25V (p.Gly25Val), gnomAD 12-56339118-G-T, REVEL 0.04, MetaLR 0.07
- G25G (p.Gly25Gly), gnomAD 12-56339119-C-A, CADD 8.76
- S26Q (p.Ser26Gln), gnomAD 12-56339113-T-TG, CADD 22.00
- S26G (p.Ser26Gly), gnomAD 12-56339120-A-G, REVEL 0.01, MetaLR 0.05
- S26N (p.Ser26Asn), gnomAD 12-56339121-G-A, REVEL 0.06, MetaLR 0.07
- S26S (p.Ser26Ser), gnomAD 12-56339122-C-T, CADD 8.59
- S26R (p.Ser26Arg), gnomAD 12-56339122-C-A, REVEL 0.06, MetaLR 0.06
- S27G (p.Ser27Gly), ExAC rs202124814, gnomAD rs202124814, REVEL 0.03, MetaLR 0.06
- S27I (p.Ser27Ile), gnomAD 12-56339124-G-T, REVEL 0.09, MetaLR 0.07
- S27N (p.Ser27Asn), gnomAD 12-56339124-G-A, REVEL 0.01, MetaLR 0.05
- S27S (p.Ser27Ser), gnomAD 12-56339125-C-T, CADD 10.70
- S27R (p.Ser27Arg), gnomAD 12-56339125-C-A, REVEL 0.10, MetaLR 0.05
- P28L (p.Pro28Leu), gnomAD 12-56339127-C-T, REVEL 0.03, MetaLR 0.06
- P28P (p.Pro28Pro), gnomAD 12-56339128-T-C, CADD 10.40
- A29T (p.Ala29Thr), gnomAD 12-56339129-G-A, REVEL 0.03, MetaLR 0.08
- A29D (p.Ala29Asp), gnomAD 12-56339130-C-A, REVEL 0.05, MetaLR 0.06
- A29V (p.Ala29Val), gnomAD 12-56339130-C-T, REVEL 0.03, MetaLR 0.07
- A29A (p.Ala29Ala), rs765659551, gnomAD 12-56339131-C-T, CADD 12.40
- W30* (p.Trp30Ter), gnomAD rs1376230594, CADD 26.00
- W30R (p.Trp30Arg), gnomAD rs1299215777, REVEL 0.47, MetaLR 0.18
- W30G (p.Trp30Gly), gnomAD 12-56339132-T-G, REVEL 0.45, MetaLR 0.18
- W30L (p.Trp30Leu), gnomAD 12-56339133-G-T, REVEL 0.34, MetaLR 0.17
- T31A (p.Thr31Ala), gnomAD 12-56339135-A-G, REVEL 0.01, MetaLR 0.02
- T31I (p.Thr31Ile), gnomAD 12-56339136-C-T, REVEL 0.04, MetaLR 0.05
- T31N (p.Thr31Asn), gnomAD 12-56339136-C-A, REVEL 0.05, MetaLR 0.05
- Q32R (p.Gln32Arg), Ensembl rs1876396122, REVEL 0.02, MetaLR 0.04
- Q32K (p.Gln32Lys), gnomAD 12-56339138-C-A, REVEL 0.10, MetaLR 0.09
- Q32H (p.Gln32His), gnomAD 12-56339140-G-T, REVEL 0.02, MetaLR 0.08
- C33R (p.Cys33Arg), Ensembl rs200361320, REVEL 0.19, MetaLR 0.08
- C33S (p.Cys33Ser), gnomAD 12-56339141-T-A, REVEL 0.12, MetaLR 0.06
- C33Y (p.Cys33Tyr), gnomAD 12-56339142-G-A, REVEL 0.14, MetaLR 0.10
- C33C (p.Cys33Cys), rs61937689, gnomAD 12-56339143-C-T, CADD 11.10
- C33* (p.Cys33Ter), gnomAD 12-56339143-C-A, CADD 34.00
- Q34H (p.Gln34His), ExAC rs752995341, gnomAD rs752995341, REVEL 0.20, MetaLR 0.13
- Q34* (p.Gln34Ter), gnomAD 12-56339144-C-T, CADD 35.00
- Q34K (p.Gln34Lys), gnomAD 12-56339144-C-A, REVEL 0.15, MetaLR 0.08
- Q34L (p.Gln34Leu), gnomAD 12-56339145-A-T, REVEL 0.27, MetaLR 0.08
- Q34Q (p.Gln34Gln), gnomAD 12-56339146-G-A, CADD 7.32
- Q35* (p.Gln35Ter), gnomAD rs1305716320, CADD 34.00
- Q35R (p.Gln35Arg), ESP rs370833575, ExAC rs370833575, TOPMed rs370833575, gnomAD rs370833575, REVEL 0.14, MetaLR 0.09
- Q35E (p.Gln35Glu), gnomAD 12-56339147-C-G, REVEL 0.10, MetaLR 0.07
- Q35K (p.Gln35Lys), gnomAD 12-56339147-C-A, REVEL 0.14, MetaLR 0.08
- Q35H (p.Gln35His), gnomAD 12-56339149-G-T, REVEL 0.16, MetaLR 0.09
- Q35Q (p.Gln35Gln), rs774443373, gnomAD 12-56339149-G-A, CADD 9.32
- L36F (p.Leu36Phe), gnomAD rs1289222563, REVEL 0.35, MetaLR 0.33
- L36I (p.Leu36Ile), gnomAD 12-56339150-C-A, REVEL 0.33, MetaLR 0.33
- L36P (p.Leu36Pro), gnomAD 12-56339151-T-C, REVEL 0.55, MetaLR 0.32
- L36L (p.Leu36Leu), gnomAD 12-56339152-T-C, CADD 9.66
- S37L (p.Ser37Leu), ExAC rs751697693, gnomAD rs751697693, REVEL 0.25, MetaLR 0.19
- S37S (p.Ser37Ser), gnomAD 12-56339155-A-T, CADD 6.71
- Q38R (p.Gln38Arg), gnomAD rs1205666546, REVEL 0.05, MetaLR 0.06
- Q38K (p.Gln38Lys), gnomAD 12-56339156-C-A, REVEL 0.06, MetaLR 0.07
- Q38* (p.Gln38Ter), gnomAD 12-56339156-C-T, CADD 35.00
- Q38L (p.Gln38Leu), gnomAD 12-56339157-A-T, REVEL 0.10, MetaLR 0.07
- Q38Q (p.Gln38Gln), gnomAD 12-56339158-G-A, CADD 10.70
- Q38H (p.Gln38His), gnomAD 12-56339158-G-C, REVEL 0.12, MetaLR 0.08
- K39del (p.Lys39del), gnomAD 12-56339156-CAGA-, CADD 17.50
- K39R (p.Lys39Arg), gnomAD 12-56339160-A-G, REVEL 0.02, MetaLR 0.05
- K39M (p.Lys39Met), gnomAD 12-56339160-A-T, REVEL 0.04, MetaLR 0.06
- K39N (p.Lys39Asn), gnomAD 12-56339161-G-C, REVEL 0.07, MetaLR 0.04
- K39K (p.Lys39Lys), rs201143212, gnomAD 12-56339161-G-A, CADD 9.77
- L40I (p.Leu40Ile), gnomAD rs1479634872, REVEL 0.04, MetaLR 0.08
- L40P (p.Leu40Pro), gnomAD 12-56339162-CT-C, CADD 26.90
- L40F (p.Leu40Phe), gnomAD 12-56339162-C-T, REVEL 0.21, MetaLR 0.11
- L40L (p.Leu40Leu), gnomAD 12-56339164-C-A, CADD 10.30
- C41W (p.Cys41Trp), NCI-TCGA TCGA novel, MetaLR 0.18, MetaSVM -0.80, Variant assessed as somatic; moderate impact.
- C41L (p.Cys41Leu), gnomAD 12-56339164-C-CT, CADD 27.40
- C41R (p.Cys41Arg), gnomAD 12-56339165-T-C, REVEL 0.26, MetaLR 0.17
- C41Y (p.Cys41Tyr), gnomAD 12-56339166-G-A, REVEL 0.22, MetaLR 0.18
- C41S (p.Cys41Ser), gnomAD 12-56339166-G-C, REVEL 0.16, MetaLR 0.11
- C41F (p.Cys41Phe), gnomAD 12-56339166-G-T, REVEL 0.24, MetaLR 0.18
- C41* (p.Cys41Ter), gnomAD 12-56339167-C-A, CADD 34.00
- C41C (p.Cys41Cys), gnomAD 12-56339167-C-T, CADD 12.10
- T42A (p.Thr42Ala), gnomAD 12-56339168-A-G, REVEL 0.09, MetaLR 0.07
- T42I (p.Thr42Ile), gnomAD 12-56339169-C-T, REVEL 0.09, MetaLR 0.07
- T42K (p.Thr42Lys), gnomAD 12-56339169-C-A, REVEL 0.10, MetaLR 0.06
- T42T (p.Thr42Thr), rs781117953, gnomAD 12-56339170-A-C, CADD 1.20
- L43M (p.Leu43Met), gnomAD 12-56339171-C-A, REVEL 0.23, MetaLR 0.16
- L43L (p.Leu43Leu), gnomAD 12-56339171-C-T, CADD 10.80
- A44S (p.Ala44Ser), gnomAD 12-56339174-G-T, REVEL 0.13, MetaLR 0.15
- A44T (p.Ala44Thr), gnomAD 12-56339174-G-A, REVEL 0.12, MetaLR 0.10
- A44V (p.Ala44Val), gnomAD 12-56339175-C-T, REVEL 0.11, MetaLR 0.07
Public IL23A analysis runs
- IL23A analysis run — IL23A (478 variants) — completed 2026-08-19