ARID1B (Q8NFD5) variants and mutations
ARID1B (also known as Q8NFD5) is a human protein-coding gene encoding an AT-rich interactive domain-containing protein 1B protein. It helps SWI/SNF chromatin-remodeling complexes regulate access to developmental gene programs, especially in the nervous system. Haploinsufficiency is a major cause of Coffin-Siris syndrome and related neurodevelopmental disorders. This analysis covers 7,506 ARID1B variants and mutations. Of these, 37% have computational variant effect predictions. Disease context includes Coffin-Siris syndrome, Coffin-Siris syndrome 1, and hereditary disease. Example ARID1B variants include M1?, A2P, and A2T.
Variant analysis overview
- Gene: ARID1B
- Protein: Q8NFD5
- UniProt accession: Q8NFD5
- Organism: Homo sapiens
- Variants analyzed: 7506
- Variant scope: all variants
- Completed: 2026-08-10
Variant and mutation evidence
- Variant composition: 7,062 unspecified-consequence records; 230 missense variants; 48 frameshift variants; 115 synonymous variants; 30 in-frame deletions; 17 in-frame insertions; 4 stop-gained variants
- Prediction scores: 2,792 variants have prediction scores (37% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Coffin-Siris syndrome, Coffin-Siris syndrome 1, hereditary disease, arid1b-related disorder, Intellectual disability, Thin upper lip vermilion, Moderate intellectual disability, Blepharophimosis, Absent speech, Long eyelashes, Thick lower lip vermilion, Global developmental delay.
Protein structure and variant hotspots
- Protein features: 1 domains; 11 post-translational modification sites.
- Structural context: 420 variants have structural context.
- PTM context: 41 variants overlap post-translational modification sites.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, Interaction Network Analysis, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Notable ARID1B variants
Examples include M1?, A2P, A2T, A2G, A2V, A2D, A2A, A3T. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1?, cosmic curated COSV51649
- A2P (p.Ala2Pro), gnomAD 6-156777684-G-C, CADD 17.60, PolyPhen-2 0.00
- A2T (p.Ala2Thr), gnomAD 6-156777684-G-A, CADD 17.80, PolyPhen-2 0.00
- A2G (p.Ala2Gly), gnomAD 6-156777685-C-G, CADD 18.00, PolyPhen-2 0.00
- A2V (p.Ala2Val), gnomAD 6-156777685-C-T, CADD 18.30, PolyPhen-2 0.00
- A2D (p.Ala2Asp), gnomAD 6-156777685-C-A, CADD 17.90, PolyPhen-2 0.00
- A2A (p.Ala2Ala), gnomAD 6-156777686-C-A, CADD 17.80
- A3T (p.Ala3Thr), Ensembl rs1583021519, CADD 17.00, PolyPhen-2 0.00
- A3V (p.Ala3Val), Ensembl rs2114950777
- A3R (p.Ala3Arg), gnomAD 6-156777686-CG-C, CADD 16.10
- A3S (p.Ala3Ser), gnomAD 6-156777687-G-T, CADD 16.70, PolyPhen-2 0.00
- A3E (p.Ala3Glu), gnomAD 6-156777688-C-A, CADD 17.20, PolyPhen-2 0.00
- A3A (p.Ala3Ala), gnomAD 6-156777689-G-T, CADD 17.30
- R4W (p.Arg4Trp), gnomAD rs1401179920, CADD 17.50, PolyPhen-2 0.00
- R4A (p.Arg4Ala), gnomAD 6-156777686-CGCGC, CADD 16.90
- R4R (p.Arg4Arg), gnomAD 6-156777690-C-A, CADD 17.10
- R4L (p.Arg4Leu), gnomAD 6-156777691-G-T, CADD 16.60, PolyPhen-2 0.00
- R4P (p.Arg4Pro), gnomAD 6-156777691-G-C, CADD 16.70, PolyPhen-2 0.00
- R4Q (p.Arg4Gln), gnomAD 6-156777691-G-A, CADD 16.90, PolyPhen-2 0.00
- p.Arg4 Ala5insThr, gnomAD 6-156777692-G-GAC, CADD 17.90
- A5V (p.Ala5Val), gnomAD rs1778712629, CADD 18.10, PolyPhen-2 0.00
- A5Q (p.Ala5Gln), gnomAD 6-156777692-G-GCA, CADD 17.90
- A5T (p.Ala5Thr), gnomAD 6-156777693-G-A, CADD 18.40, PolyPhen-2 0.00
- A5E (p.Ala5Glu), gnomAD 6-156777694-C-A, CADD 17.70, PolyPhen-2 0.00
- A5A (p.Ala5Ala), rs547599734, gnomAD 6-156777695-A-G, CADD 18.10
- A6P (p.Ala6Pro), TOPMed rs1778713009
- p.Ala6 Ala20del, gnomAD 6-156777686-CGCGC, CADD 16.90
- A6T (p.Ala6Thr), gnomAD 6-156777696-G-A, CADD 18.10, PolyPhen-2 0.00
- A6V (p.Ala6Val), gnomAD 6-156777697-C-T, CADD 18.60, PolyPhen-2 0.00
- A6A (p.Ala6Ala), gnomAD 6-156777698-A-T, CADD 15.00
- p.Ala7 Ala8insGlyAlaAlaAla, rs1778711977, gnomAD 6-156777690-C-CGG, CADD 16.60
- A7P (p.Ala7Pro), gnomAD 6-156777699-G-C, CADD 16.90, SIFT 0.00
- A7T (p.Ala7Thr), gnomAD 6-156777699-G-A, CADD 17.10, PolyPhen-2 0.00
- A7V (p.Ala7Val), gnomAD 6-156777700-C-T, CADD 18.10, PolyPhen-2 0.00
- A7E (p.Ala7Glu), gnomAD 6-156777700-C-A, CADD 17.70, PolyPhen-2 0.00
- A7A (p.Ala7Ala), gnomAD 6-156777701-G-C, CADD 18.30
- A8G (p.Ala8Gly), TOPMed rs1160954100
- A8P (p.Ala8Pro), TOPMed rs1397938107, gnomAD rs1397938107, CADD 17.80, PolyPhen-2 0.00, Conflicting interpretations, Inborn genetic diseases; not provided
- A8T (p.Ala8Thr), TOPMed rs1397938107, gnomAD rs1397938107, CADD 18.10, PolyPhen-2 0.00
- A8Q (p.Ala8Gln), gnomAD 6-156777701-G-GCA, CADD 18.20
- A8V (p.Ala8Val), gnomAD 6-156777703-C-T, CADD 17.60, PolyPhen-2 0.00
- A8E (p.Ala8Glu), gnomAD 6-156777703-C-A, CADD 17.10, PolyPhen-2 0.00
- A8A (p.Ala8Ala), rs1269350951, gnomAD 6-156777704-G-A, CADD 17.10
- A9T (p.Ala9Thr), TOPMed rs1472215057, CADD 17.30, PolyPhen-2 0.00
- A9N (p.Ala9Asn), gnomAD 6-156777695-AGCAG, CADD 16.50
- p.Ala9 Ala10insValAlaAla, gnomAD 6-156777700-C-CGG, CADD 17.90
- A9R (p.Ala9Arg), gnomAD 6-156777703-CG-C, CADD 16.30
- A9S (p.Ala9Ser), gnomAD 6-156777705-G-T, CADD 16.90, PolyPhen-2 0.00
- A9P (p.Ala9Pro), gnomAD 6-156777705-G-C, CADD 17.00, PolyPhen-2 0.00
- A9V (p.Ala9Val), gnomAD 6-156777706-C-T, CADD 17.50, PolyPhen-2 0.00
- A9E (p.Ala9Glu), gnomAD 6-156777706-C-A, CADD 17.10, PolyPhen-2 0.00
- A9A (p.Ala9Ala), gnomAD 6-156777707-G-C, CADD 16.10
- p.Ala10 Ala11insGlyAlaAla, gnomAD 6-156777703-C-CGG, CADD 16.70
- A10S (p.Ala10Ser), gnomAD 6-156777708-G-T, CADD 16.60, PolyPhen-2 0.00
- A10T (p.Ala10Thr), gnomAD 6-156777708-G-A, CADD 16.90, PolyPhen-2 0.00
- A10E (p.Ala10Glu), gnomAD 6-156777709-C-A, CADD 16.20, PolyPhen-2 0.00
- A10V (p.Ala10Val), gnomAD 6-156777709-C-T, CADD 16.60, PolyPhen-2 0.00
- A10A (p.Ala10Ala), gnomAD 6-156777710-G-T, CADD 14.20
- A11S (p.Ala11Ser), TOPMed rs1778717491
- p.Ala11 Ala14del, gnomAD 6-156777691-GGGCA, CADD 17.50
- A11G (p.Ala11Gly), gnomAD 6-156777705-GCGGC, CADD 16.40
- A11R (p.Ala11Arg), gnomAD 6-156777709-CG-C, CADD 13.70
- A11T (p.Ala11Thr), gnomAD 6-156777711-G-A, CADD 14.60, PolyPhen-2 0.00
- A11P (p.Ala11Pro), gnomAD 6-156777711-G-C, CADD 14.30, PolyPhen-2 0.00
- A11E (p.Ala11Glu), gnomAD 6-156777712-C-A, CADD 17.00, PolyPhen-2 0.00
- A11V (p.Ala11Val), gnomAD 6-156777712-C-T, CADD 17.40, PolyPhen-2 0.00
- A11A (p.Ala11Ala), rs2114951628, gnomAD 6-156777713-G-A, CADD 16.90
- p.Ala12 Ala14del, rs576322233, gnomAD 6-156777695-AGCAG, CADD 17.40
- A12N (p.Ala12Asn), gnomAD 6-156777707-GGCGG, CADD 16.20
- p.Ala12 Ala13insValAlaAla, gnomAD 6-156777709-C-CGG, CADD 16.00
- A12T (p.Ala12Thr), gnomAD 6-156777714-G-A, CADD 16.40, PolyPhen-2 0.00
- A12S (p.Ala12Ser), gnomAD 6-156777714-G-T, CADD 16.10, PolyPhen-2 0.00
- A12V (p.Ala12Val), gnomAD 6-156777715-C-T, CADD 16.30, PolyPhen-2 0.00
- A12E (p.Ala12Glu), gnomAD 6-156777715-C-A, CADD 15.90, PolyPhen-2 0.00
- A12A (p.Ala12Ala), gnomAD 6-156777716-G-A, CADD 15.90
- A13G (p.Ala13Gly), gnomAD rs1002797837, CADD 15.60, PolyPhen-2 0.00
- A13P (p.Ala13Pro), gnomAD rs1211283818, CADD 15.80, PolyPhen-2 0.00
- A13T (p.Ala13Thr), gnomAD rs1211283818, CADD 16.10, PolyPhen-2 0.00
- p.Ala13 Ala14del, rs557453022, gnomAD 6-156777692-GGCAG, CADD 17.50
- A13R (p.Ala13Arg), gnomAD 6-156777715-CG-C, CADD 15.10
- A13S (p.Ala13Ser), gnomAD 6-156777717-G-T, CADD 15.80, PolyPhen-2 0.00
- A13E (p.Ala13Glu), gnomAD 6-156777718-C-A, CADD 15.50, PolyPhen-2 0.00
- A13V (p.Ala13Val), gnomAD 6-156777718-C-T, CADD 15.90, PolyPhen-2 0.00
- A13A (p.Ala13Ala), rs1031921484, gnomAD 6-156777719-G-T, CADD 15.00
- A14V (p.Ala14Val), Ensembl rs1583021632, CADD 14.60, PolyPhen-2 0.00
- A14del (p.Ala14del), rs557453022, gnomAD 6-156777692-GGCA-, CADD 17.50
- p.Ala14dup, gnomAD 6-156777692-G-GGC, CADD 17.90
- p.Ala14 Arg15insValAlaAla, gnomAD 6-156777715-C-CGG, CADD 15.50
- A14R (p.Ala14Arg), gnomAD 6-156777718-CG-C, CADD 14.50
- A14G (p.Ala14Gly), gnomAD 6-156777718-C-CG, CADD 15.30
- A14S (p.Ala14Ser), gnomAD 6-156777720-G-T, CADD 14.30, PolyPhen-2 0.00
- A14T (p.Ala14Thr), gnomAD 6-156777720-G-A, CADD 14.60, PolyPhen-2 0.00
- A14P (p.Ala14Pro), gnomAD 6-156777720-G-C, CADD 14.40, PolyPhen-2 0.00
- A14E (p.Ala14Glu), gnomAD 6-156777721-C-A, CADD 14.20, PolyPhen-2 0.00
- A14A (p.Ala14Ala), gnomAD 6-156777722-G-C, CADD 14.20
- R15G (p.Arg15Gly), gnomAD rs1270815175, CADD 13.40, PolyPhen-2 0.00, Likely benign, not provided
- R15P (p.Arg15Pro), gnomAD rs891652115, CADD 13.10, PolyPhen-2 0.00, Likely benign, not provided
- R15Q (p.Arg15Gln), gnomAD rs891652115, CADD 13.40, PolyPhen-2 0.00, Likely benign
- R15W (p.Arg15Trp), gnomAD rs1270815175, CADD 13.70, PolyPhen-2 0.00, Likely benign
- p.Arg15 Ala53del, rs1778716003, gnomAD 6-156777701-GGCGG, CADD 16.70
- R15A (p.Arg15Ala), gnomAD 6-156777721-C-CG, CADD 14.10
- R15S (p.Arg15Ser), gnomAD 6-156777722-G-GT, CADD 14.00
- R15R (p.Arg15Arg), gnomAD 6-156777723-C-A, CADD 13.20
- R15L (p.Arg15Leu), gnomAD 6-156777724-G-T, CADD 13.00, PolyPhen-2 0.00
- A16T (p.Ala16Thr), TOPMed rs1166594526, gnomAD rs1166594526, CADD 15.00, PolyPhen-2 0.00, Uncertain significance, not provided
- A16V (p.Ala16Val), Ensembl rs1455340163, CADD 13.40, PolyPhen-2 0.00
- A16R (p.Ala16Arg), rs1778718419, gnomAD 6-156777716-GGCGG, CADD 16.50
- A16G (p.Ala16Gly), gnomAD 6-156777724-G-GT, CADD 13.90
- A16P (p.Ala16Pro), gnomAD 6-156777726-G-C, CADD 14.80, PolyPhen-2 0.00
- A16S (p.Ala16Ser), gnomAD 6-156777726-G-T, CADD 14.70, PolyPhen-2 0.00
- A16E (p.Ala16Glu), gnomAD 6-156777727-C-A, CADD 12.80, PolyPhen-2 0.00
- A16A (p.Ala16Ala), gnomAD 6-156777728-G-A, CADD 11.80
- R17P (p.Arg17Pro), TOPMed rs1021302619, gnomAD rs1021302619, CADD 13.90, PolyPhen-2 0.00
- R17Q (p.Arg17Gln), TOPMed rs1021302619, gnomAD rs1021302619, CADD 14.20, PolyPhen-2 0.00
- p.Arg17 Ala20del, rs1157870200, gnomAD 6-156777718-CGGCG, CADD 15.10
- R17G (p.Arg17Gly), gnomAD 6-156777729-C-G, CADD 14.20, PolyPhen-2 0.00
- R17W (p.Arg17Trp), gnomAD 6-156777729-C-T, CADD 14.50, PolyPhen-2 0.00
- R17R (p.Arg17Arg), rs1411620677, gnomAD 6-156777729-C-A, CADD 14.10
- R17L (p.Arg17Leu), gnomAD 6-156777730-G-T, CADD 13.80, PolyPhen-2 0.00
- A18G (p.Ala18Gly), gnomAD rs964449228, CADD 15.10, PolyPhen-2 0.00
- A18P (p.Ala18Pro), TOPMed rs1245472872
- A18R (p.Ala18Arg), gnomAD 6-156777730-G-GGC, CADD 14.10
- A18T (p.Ala18Thr), gnomAD 6-156777732-G-A, CADD 15.60, PolyPhen-2 0.00
- A18S (p.Ala18Ser), gnomAD 6-156777732-G-T, CADD 15.30, PolyPhen-2 0.00
- A18V (p.Ala18Val), gnomAD 6-156777733-C-T, CADD 15.30, PolyPhen-2 0.00
- A18E (p.Ala18Glu), gnomAD 6-156777733-C-A, CADD 14.90, PolyPhen-2 0.00
- A18A (p.Ala18Ala), gnomAD 6-156777734-G-T, CADD 10.50
- R19Q (p.Arg19Gln), Ensembl rs1778722716, CADD 14.90, PolyPhen-2 0.00
- p.Arg19 Ala20del, rs1157870200, gnomAD 6-156777718-CGGCG, CADD 14.60
- R19W (p.Arg19Trp), gnomAD 6-156777735-C-T, CADD 14.90, PolyPhen-2 0.00
- R19R (p.Arg19Arg), gnomAD 6-156777735-C-A, CADD 14.50
- R19P (p.Arg19Pro), gnomAD 6-156777736-G-C, CADD 14.60, PolyPhen-2 0.00
- R19L (p.Arg19Leu), gnomAD 6-156777736-G-T, CADD 14.50, PolyPhen-2 0.00
- A20T (p.Ala20Thr), 1000Genomes rs868243197, gnomAD rs868243197, CADD 14.00, PolyPhen-2 0.00
- A20V (p.Ala20Val), Ensembl rs1778723173, CADD 14.50, PolyPhen-2 0.00
- A20R (p.Ala20Arg), gnomAD 6-156777733-CGCGG, CADD 16.10
- A20S (p.Ala20Ser), gnomAD 6-156777738-G-T, CADD 13.70, PolyPhen-2 0.00
- A20P (p.Ala20Pro), gnomAD 6-156777738-G-C, CADD 13.80, PolyPhen-2 0.00
- A20E (p.Ala20Glu), gnomAD 6-156777739-C-A, CADD 14.00, PolyPhen-2 0.00
- A20A (p.Ala20Ala), gnomAD 6-156777740-A-T, CADD 11.30
- G21A (p.Gly21Ala), cosmic curated COSV51657, Ensembl rs1057518648, Likely pathogenic
- G21D (p.Gly21Asp), 1000Genomes rs1029962198, TOPMed rs1029962198, CADD 11.10, PolyPhen-2 0.00
- G21R (p.Gly21Arg), TOPMed rs1583021699, gnomAD rs1583021699, CADD 14.10, PolyPhen-2 0.00
- G21S (p.Gly21Ser), TOPMed rs1583021699, gnomAD rs1583021699, CADD 14.30, PolyPhen-2 0.00
- G21V (p.Gly21Val), 1000Genomes rs1029962198, TOPMed rs1029962198, CADD 10.50, PolyPhen-2 0.00
- G21C (p.Gly21Cys), gnomAD 6-156777741-G-T, CADD 14.00, PolyPhen-2 0.00
- G21G (p.Gly21Gly), gnomAD 6-156777743-C-A, CADD 15.20
- S22I (p.Ser22Ile), TOPMed rs1473297502, gnomAD rs1473297502, CADD 15.30, PolyPhen-2 0.00
- S22Y (p.Ser22Tyr), cosmic curated COSV51673
- S22C (p.Ser22Cys), cosmic curated COSV51677
- S22F (p.Ser22Phe), rs995863053, ClinGen CA150802690, cosmic curated COSV10729, ClinVar RCV002967927, AlphaMissense 0.30, MetaLR 0.08, Likely benign, not provided
- S22G (p.Ser22Gly), gnomAD 6-156777744-A-G, CADD 17.30, PolyPhen-2 0.00
- S22R (p.Ser22Arg), gnomAD 6-156777744-A-C, CADD 17.10, PolyPhen-2 0.00
- S22S (p.Ser22Ser), rs1165226962, gnomAD 6-156777746-C-T, CADD 16.10
- G23C (p.Gly23Cys), gnomAD rs1392550528, CADD 15.60, PolyPhen-2 0.00
- G23S (p.Gly23Ser), gnomAD rs1392550528, CADD 15.90, PolyPhen-2 0.00
- G23D (p.Gly23Asp), gnomAD 6-156777748-G-A, CADD 15.80, PolyPhen-2 0.00
- G23G (p.Gly23Gly), gnomAD 6-156777749-C-A, CADD 15.50
- E24K (p.Glu24Lys), rs1212813613, ClinGen CA366381061, ClinVar RCV002922729, gnomAD rs1212813613, AlphaMissense 0.45, MetaLR 0.00, Benign, not provided
- E24G (p.Glu24Gly), Ensembl rs1778724568
- E24* (p.Glu24Ter), gnomAD 6-156777750-G-T, CADD 16.50
- E24A (p.Glu24Ala), gnomAD 6-156777751-A-C, CADD 17.70, PolyPhen-2 0.00
- E24D (p.Glu24Asp), gnomAD 6-156777752-A-C, CADD 15.30, PolyPhen-2 0.00
- R25L (p.Arg25Leu), gnomAD rs955120283, CADD 16.00, PolyPhen-2 0.00
- R25P (p.Arg25Pro), gnomAD rs955120283
- R25G (p.Arg25Gly), gnomAD 6-156777752-ACGGC, CADD 16.50
- R25W (p.Arg25Trp), gnomAD 6-156777753-C-T, CADD 17.00, PolyPhen-2 0.00
- R25R (p.Arg25Arg), gnomAD 6-156777753-C-A, CADD 16.60
- R25Q (p.Arg25Gln), gnomAD 6-156777754-G-A, CADD 16.30, PolyPhen-2 0.00
- R26L (p.Arg26Leu), TOPMed rs1272968421
- R26P (p.Arg26Pro), TOPMed rs1272968421
- R26Q (p.Arg26Gln), TOPMed rs1272968421, CADD 16.30, PolyPhen-2 0.00
- R26W (p.Arg26Trp), 1000Genomes rs2114952623, CADD 16.90, PolyPhen-2 0.00
- R26R (p.Arg26Arg), gnomAD 6-156777756-C-A, CADD 16.60
- A27P (p.Ala27Pro), NCI-TCGA TCGA novel, Ensembl rs2114958637, Variant assessed as somatic; moderate impact.
- A27V (p.Ala27Val), 1000Genomes rs1327350233, TOPMed rs1327350233, gnomAD rs1327350233, CADD 15.70, PolyPhen-2 0.00
- A27S (p.Ala27Ser), gnomAD 6-156777759-G-T, CADD 15.00, PolyPhen-2 0.00
- A27E (p.Ala27Glu), gnomAD 6-156777760-C-A, CADD 15.40, PolyPhen-2 0.00
- A27A (p.Ala27Ala), rs1432362092, gnomAD 6-156777761-G-A, CADD 16.30
- P28L (p.Pro28Leu), TOPMed rs1778726001, CADD 15.90, PolyPhen-2 0.00
Public ARID1B analysis runs
- ARID1B analysis run — ARID1B (7,506 variants) — completed 2026-08-10