SMARCA4 (P51532) variants and mutations
SMARCA4 (also known as P51532) is a human protein-coding gene encoding a SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 protein. Its ATPase activity drives nucleosome remodeling in BAF-family complexes and thereby controls access to regulatory DNA. Germline pathogenic variants cause Coffin-Siris syndrome or rhabdoid-tumor predisposition, while somatic loss defines several aggressive cancers. This analysis covers 7,890 SMARCA4 variants and mutations. Of these, 37% have computational variant effect predictions. Disease context includes intellectual disability, autosomal dominant 16, rhabdoid tumor predisposition syndrome 2, and familial rhabdoid tumor. Example SMARCA4 variants include M1I, S2C, and S2F.
Variant analysis overview
- Gene: SMARCA4
- Protein: P51532
- UniProt accession: P51532
- Organism: Homo sapiens
- Variants analyzed: 7890
- Variant scope: all variants
- Completed: 2026-08-18
Variant and mutation evidence
- Variant composition: 7,714 unspecified-consequence records; 125 synonymous variants; 38 missense variants; 6 frameshift variants; 6 in-frame deletions; 1 substitution
- Prediction scores: 2,882 variants have prediction scores (37% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: intellectual disability, autosomal dominant 16, rhabdoid tumor predisposition syndrome 2, familial rhabdoid tumor, rhabdoid tumor, medulloblastoma, Inherited cancer-predisposing syndrome, hereditary neoplastic syndrome, Coffin-Siris syndrome, lung adenocarcinoma, non-small cell lung carcinoma, neurodegenerative disease, Burkitt lymphoma.
Protein structure and variant hotspots
- Protein features: 5 domains; 1 binding sites; 17 post-translational modification sites.
- Structural context: 2,553 variants have structural context.
- PTM context: 71 variants overlap post-translational modification sites.
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, ClinGen, MaveDB, LitVar.
Notable SMARCA4 variants
Examples include M1I, S2C, S2F, S2P, S2T, S2Y, T3A, T3I. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1I (p.Met1Ile), rs2145720045, ClinGen CA404053838, ClinVar RCV001780029, ClinVar RCV001885146, MetaLR 0.67, MetaSVM 0.45, Uncertain significance, Neurodevelopmental disorder; Hereditary cancer-predisposing syndrome; Rhabdoid t
- S2C (p.Ser2Cys), Ensembl rs2145720092
- S2F (p.Ser2Phe), Ensembl rs2145720092
- S2P (p.Ser2Pro), cosmic curated COSV60810, Uncertain significance, Hereditary cancer-predisposing syndrome
- S2T (p.Ser2Thr), Ensembl rs2085800590
- S2Y (p.Ser2Tyr), Ensembl rs2145720092
- T3A (p.Thr3Ala), rs1599927930, ClinGen CA404053848, ClinVar RCV003040930, AlphaMissense 0.26, MetaLR 0.53, Uncertain significance, Rhabdoid tumor predisposition syndrome 2
- T3I (p.Thr3Ile), rs1339941779, ClinGen CA404053852, ClinVar RCV002016026, ClinVar RCV002370690, REVEL 0.54, CADD 23.40, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- T3N (p.Thr3Asn), rs1339941779, ClinGen CA404053850, ClinVar RCV002303740, ClinVar RCV002373090, REVEL 0.44, CADD 22.10, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- T3P (p.Thr3Pro), rs1599927930, ClinGen CA404053847, ClinVar RCV000818578, ClinVar RCV001027039, AlphaMissense 0.26, MetaLR 0.53, Uncertain significance, Rhabdoid tumor predisposition syndrome 2; Hereditary cancer-predisposing syndrom
- T3S (p.Thr3Ser), TOPMed rs1599927930, Uncertain significance
- T3T (p.Thr3Thr), rs764639389, gnomAD 19-10984160-T-C, CADD 9.71
- P4A (p.Pro4Ala), rs2085801503, ClinGen CA404053854, cosmic curated COSV10967, ClinVar RCV001324299, REVEL 0.58, CADD 22.30, Uncertain significance, Rhabdoid tumor predisposition syndrome 2; Hereditary cancer-predisposing syndrom
- P4L (p.Pro4Leu), Ensembl rs2145720277
- P4Q (p.Pro4Gln), rs2145720277, ClinGen CA404053856, ClinVar RCV002346985, AlphaMissense 0.59, MetaLR 0.78, Uncertain significance, Hereditary cancer-predisposing syndrome
- P4R (p.Pro4Arg), Ensembl rs2145720277
- P4S (p.Pro4Ser), rs2085801503, ClinGen CA404053855, ClinVar RCV001054974, ClinVar RCV002462293, REVEL 0.60, CADD 22.60, Uncertain significance, Rhabdoid tumor predisposition syndrome 2; Hereditary cancer-predisposing syndrom
- P4T (p.Pro4Thr), Ensembl rs2085801503, REVEL 0.64, CADD 22.70, Uncertain significance
- D5E (p.Asp5Glu), gnomAD rs1309825975, REVEL 0.42, CADD 24.10, Likely benign
- D5H (p.Asp5His), rs2145720331, ClinGen CA404053860, ClinVar RCV002389248, Ensembl rs2145720331, AlphaMissense 0.79, MetaLR 0.71, Uncertain significance, Hereditary cancer-predisposing syndrome
- D5Y (p.Asp5Tyr), Ensembl rs2145720331, Uncertain significance
- D5D (p.Asp5Asp), rs1309825975, gnomAD 19-10984166-C-T, CADD 11.30
- P6L (p.Pro6Leu), ExAC rs750113056, gnomAD rs750113056, Uncertain significance, Hereditary cancer-predisposing syndrome
- P6Q (p.Pro6Gln), rs750113056, ClinGen CA404053876, ClinVar RCV001234785, ExAC rs750113056, AlphaMissense 0.20, MetaLR 0.47, Uncertain significance, Rhabdoid tumor predisposition syndrome 2
- P6S (p.Pro6Ser), Ensembl rs2145720388, REVEL 0.49, CADD 23.40, Uncertain significance, Hereditary cancer-predisposing syndrome
- P6T (p.Pro6Thr), Ensembl rs2145720388
- P6R (p.Pro6Arg), gnomAD 19-10984168-C-G, REVEL 0.58, CADD 23.90
- P7A (p.Pro7Ala), rs762625346, ClinGen CA404053882, ClinVar RCV003617498, AlphaMissense 0.10, MetaLR 0.54, Uncertain significance, Rhabdoid tumor predisposition syndrome 2
- P7H (p.Pro7His), rs1568416569, ClinGen CA404053888, ClinVar RCV000694817, ClinVar RCV001014433, AlphaMissense 0.24, MetaLR 0.66, Uncertain significance, Rhabdoid tumor predisposition syndrome 2; Hereditary cancer-predisposing syndrom
- P7L (p.Pro7Leu), cosmic curated COSV10524, Ensembl rs1568416569, Uncertain significance
- P7R (p.Pro7Arg), rs1568416569, ClinGen CA404053889, ClinVar RCV001365427, ClinVar RCV002420804, AlphaMissense 0.24, MetaLR 0.66, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- P7S (p.Pro7Ser), ExAC rs762625346, gnomAD rs762625346, Uncertain significance
- P7T (p.Pro7Thr), rs762625346, ClinGen CA9203382, ClinVar RCV001977167, ClinVar RCV004042211, REVEL 0.48, AlphaMissense 0.10, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- P7P (p.Pro7Pro), gnomAD 19-10984172-C-A, CADD 5.55
- L8M (p.Leu8Met), rs1555750596, ClinGen CA404053890, ClinVar RCV002446300, ClinVar RCV003101209, AlphaMissense 0.08, MetaLR 0.30, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- L8V (p.Leu8Val), Ensembl rs1555750596, Uncertain significance, Hereditary cancer-predisposing syndrome
- L8R (p.Leu8Arg), rs2085803076, gnomAD 19-10984173-CT-C, CADD 27.80
- G9A (p.Gly9Ala), Ensembl rs2145720650, Uncertain significance
- G9C (p.Gly9Cys), Ensembl rs1568416609, Uncertain significance
- G9D (p.Gly9Asp), rs2145720650, ClinGen CA404053902, ClinVar RCV001915684, ClinVar RCV002441013, AlphaMissense 0.18, MetaLR 0.68, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- G9R (p.Gly9Arg), Ensembl rs1568416609, Uncertain significance
- G9S (p.Gly9Ser), rs1568416609, ClinGen CA404053896, ClinVar RCV002314498, Ensembl rs1568416609, REVEL 0.53, CADD 29.80, Uncertain significance, Hereditary cancer-predisposing syndrome
- G9G (p.Gly9Gly), rs372102929, gnomAD 19-10984178-C-T, CADD 2.01
- G10* (p.Gly10Ter), ESP rs140176945, ExAC rs140176945, gnomAD rs140176945, Uncertain significance
- G10A (p.Gly10Ala), Ensembl rs2145720766
- G10E (p.Gly10Glu), cosmic curated COSV60798, Ensembl rs2145720766
- G10R (p.Gly10Arg), rs140176945, ClinGen CA9203384, cosmic curated COSV10887, ClinVar RCV000824464, REVEL 0.54, CADD 27.80, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- G10G (p.Gly10Gly), rs2085803986, gnomAD 19-10984181-A-G, CADD 7.22
- T11A (p.Thr11Ala), rs1060502067, ClinGen CA16615864, ClinVar RCV000475362, ClinVar RCV001019147, AlphaMissense 0.13, MetaLR 0.68, Uncertain significance
- T11I (p.Thr11Ile), rs1568416665, ClinGen CA404053926, ClinVar RCV000697198, ClinVar RCV002325398, AlphaMissense 0.15, MetaLR 0.67, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- T11P (p.Thr11Pro), TOPMed rs1060502067, Uncertain significance
- T11S (p.Thr11Ser), TOPMed rs1060502067, Uncertain significance, Rhabdoid tumor predisposition syndrome 2
- T11N (p.Thr11Asn), gnomAD 19-10984183-C-A, REVEL 0.39, CADD 24.10
- P12A (p.Pro12Ala), cosmic curated COSV60793
- P12H (p.Pro12His), rs1201812441, ClinGen CA404053935, ClinVar RCV003507098, TOPMed rs1201812441, AlphaMissense 0.40, MetaLR 0.75, Uncertain significance, Rhabdoid tumor predisposition syndrome 2
- P12L (p.Pro12Leu), rs1201812441, ClinGen CA404053937, NCI-TCGA Cosmic COSV6080, cosmic curated COSV60801, REVEL 0.50, AlphaMissense 0.40, Uncertain significance, Hereditary cancer-predisposing syndrome; Intellectual disability, autosomal domi
- P12S (p.Pro12Ser), rs2145720953, ClinGen CA404053932, NCI-TCGA Cosmic COSV6079, NCI-TCGA Cosmic COSV6080, AlphaMissense 0.16, MetaLR 0.68, Uncertain significance, Hereditary cancer-predisposing syndrome
- R13G (p.Arg13Gly), Ensembl rs1568416700, Likely benign
- R13L (p.Arg13Leu), rs143950084, ClinGen CA404053947, ClinVar RCV002647057, ClinVar RCV003167587, AlphaMissense 0.15, MetaLR 0.45, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- R13P (p.Arg13Pro), rs143950084, ClinGen CA404053946, ClinVar RCV002357461, ESP rs143950084, AlphaMissense 0.15, MetaLR 0.45, Uncertain significance, Hereditary cancer-predisposing syndrome
- R13Q (p.Arg13Gln), rs143950084, ClinGen CA9203385, ClinVar RCV000559549, ClinVar RCV000573192, REVEL 0.40, AlphaMissense 0.15, Conflicting interpretations, not provided; Intellectual disability, autosomal dominant 16; Hereditary cancer
- R13W (p.Arg13Trp), rs1568416700, ClinGen CA404053942, NCI-TCGA Cosmic COSV6079, cosmic curated COSV60794, REVEL 0.60, CADD 26.50, Uncertain significance, not provided; Rhabdoid tumor predisposition syndrome 2; Hereditary cancer-predis
- p.Arg13 Pro14del, gnomAD 19-10984184-TCCTC, CADD 21.00
- P14A (p.Pro14Ala), ExAC rs754291337, gnomAD rs754291337, Uncertain significance
- P14E (p.Pro14Glu), rs2145721177, ClinGen CA2499225261, ClinVar RCV001369571, Ensembl rs2145721177, Uncertain significance, Rhabdoid tumor predisposition syndrome 2
- P14L (p.Pro14Leu), NCI-TCGA Cosmic COSV1007, cosmic curated COSV10075, Ensembl rs2145721195, Variant assessed as somatic; moderate impact.
- P14Q (p.Pro14Gln), Ensembl rs2145721195
- P14R (p.Pro14Arg), Ensembl rs2145721195
- P14S (p.Pro14Ser), cosmic curated COSV60812, ExAC rs754291337, gnomAD rs754291337, Uncertain significance
- P14T (p.Pro14Thr), rs754291337, ClinGen CA9203387, ClinVar RCV000686109, ClinVar RCV002325357, REVEL 0.41, CADD 25.30, Uncertain significance, Rhabdoid tumor predisposition syndrome 2; Hereditary cancer-predisposing syndrom
- P14P (p.Pro14Pro), rs1599928429, gnomAD 19-10984193-A-G, CADD 1.64
- G15A (p.Gly15Ala), rs1060502077, ClinGen CA404053967, ClinVar RCV001022593, ClinVar RCV003617883, REVEL 0.38, AlphaMissense 0.85, Conflicting interpretations, Rhabdoid tumor predisposition syndrome 2; Hereditary cancer-predisposing syndrom
- G15D (p.Gly15Asp), rs1060502077, ClinGen CA404053970, ClinVar RCV002328689, ClinVar RCV003094730, AlphaMissense 0.85, MetaLR 0.61, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- G15R (p.Gly15Arg), Ensembl rs2145721270, Uncertain significance
- G15S (p.Gly15Ser), rs2145721270, ClinGen CA404053961, ClinVar RCV003617390, Ensembl rs2145721270, AlphaMissense 0.89, MetaLR 0.64, Uncertain significance, Rhabdoid tumor predisposition syndrome 2
- G15V (p.Gly15Val), rs1060502077, ClinGen CA16616097, ClinVar RCV000475490, ClinVar RCV004948327, AlphaMissense 0.85, MetaLR 0.61, Uncertain significance
- P16A (p.Pro16Ala), Ensembl rs2145721371
- P16R (p.Pro16Arg), rs2513932881, ClinGen CA404053979, ClinVar RCV002337865, ClinVar RCV003102633, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- P16S (p.Pro16Ser), cosmic curated COSV60796, Ensembl rs2145721371
- P16T (p.Pro16Thr), Ensembl rs2145721371
- S17F (p.Ser17Phe), rs2085806321, ClinGen CA404053992, cosmic curated COSV10524, ClinVar RCV001227359, AlphaMissense 0.65, MetaLR 0.75, Uncertain significance, Rhabdoid tumor predisposition syndrome 2
- S17P (p.Ser17Pro), Ensembl rs2145721468
- S17C (p.Ser17Cys), gnomAD 19-10984201-C-G, REVEL 0.57, CADD 25.80
- S17S (p.Ser17Ser), rs1438233071, gnomAD 19-10984202-C-T, CADD 4.67
- P18A (p.Pro18Ala), gnomAD rs2085806713, Uncertain significance, Hereditary cancer-predisposing syndrome
- P18L (p.Pro18Leu), rs1060502087, ClinGen CA16615866, cosmic curated COSV10817, ClinVar RCV000470492, REVEL 0.44, CADD 24.30, Uncertain significance
- P18Q (p.Pro18Gln), cosmic curated COSV10075, Ensembl rs1060502087, Uncertain significance
- P18S (p.Pro18Ser), cosmic curated COSV60803, gnomAD rs2085806713, REVEL 0.54, CADD 24.30, Uncertain significance
- P18P (p.Pro18Pro), rs529632222, gnomAD 19-10984205-G-A, CADD 1.02
- G19A (p.Gly19Ala), rs1222542093, ClinGen CA404054013, ClinVar RCV001947646, TOPMed rs1222542093, AlphaMissense 0.90, MetaLR 0.76, Uncertain significance, Rhabdoid tumor predisposition syndrome 2
- G19D (p.Gly19Asp), rs1222542093, TOPMed rs1222542093, AlphaMissense 0.90, MetaLR 0.76, Uncertain significance, Rhabdoid tumor predisposition syndrome 2
- G19R (p.Gly19Arg), rs2145721640, ClinGen CA404054008, ClinVar RCV004525726, Ensembl rs2145721640, AlphaMissense 0.21, MetaLR 0.76, Uncertain significance, Hereditary cancer-predisposing syndrome
- G19S (p.Gly19Ser), cosmic curated COSV10465, Ensembl rs2145721640, Uncertain significance
- G19V (p.Gly19Val), rs1222542093, ClinGen CA404054015, ClinVar RCV003342013, AlphaMissense 0.90, MetaLR 0.76, Uncertain significance, Hereditary cancer-predisposing syndrome
- G19G (p.Gly19Gly), rs778795986, gnomAD 19-10984208-C-T, CADD 10.80
- P20A (p.Pro20Ala), Ensembl rs2145721758
- P20H (p.Pro20His), Ensembl rs2145721800
- P20L (p.Pro20Leu), Ensembl rs2145721800
- P20S (p.Pro20Ser), Ensembl rs2145721758, Uncertain significance, Hereditary cancer-predisposing syndrome
- P20T (p.Pro20Thr), Ensembl rs2145721758, Uncertain significance, Hereditary cancer-predisposing syndrome
- P20P (p.Pro20Pro), rs2145721831, gnomAD 19-10984211-T-G, CADD 1.26
- G21A (p.Gly21Ala), Ensembl rs2145721852
- G21D (p.Gly21Asp), Ensembl rs2145721852
- G21V (p.Gly21Val), Ensembl rs2145721852
- P22A (p.Pro22Ala), rs2085807805, ClinGen CA404054042, ClinVar RCV002802212, Ensembl rs2085807805, AlphaMissense 0.24, MetaLR 0.65, Uncertain significance, Rhabdoid tumor predisposition syndrome 2
- P22H (p.Pro22His), rs1227659334, ClinGen CA404054047, NCI-TCGA Cosmic COSV6080, ClinVar RCV000646848, AlphaMissense 0.60, MetaLR 0.71, Uncertain significance, Hereditary cancer-predisposing syndrome; Intellectual disability, autosomal domi
- P22L (p.Pro22Leu), rs1227659334, ClinGen CA404054046, ClinVar RCV000561555, ClinVar RCV001206995, REVEL 0.47, AlphaMissense 0.60, Uncertain significance, Hereditary cancer-predisposing syndrome; Intellectual disability, autosomal domi
- P22R (p.Pro22Arg), rs1227659334, ClinGen CA404054049, ClinVar RCV000527918, ClinVar RCV002367899, AlphaMissense 0.60, MetaLR 0.71, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposi
- P22S (p.Pro22Ser), rs2085807805, ClinGen CA404054044, ClinVar RCV001036294, Ensembl rs2085807805, AlphaMissense 0.24, MetaLR 0.65, Uncertain significance, Rhabdoid tumor predisposition syndrome 2
- p.Pro22 Gly25del, gnomAD 19-10984207-GCCCT, CADD 21.00
- P22P (p.Pro22Pro), rs2145722014, gnomAD 19-10984217-T-C, CADD 9.78
- S23C (p.Ser23Cys), rs1555750712, ClinGen CA404054059, ClinVar RCV001042156, Ensembl rs1555750712, AlphaMissense 0.65, MetaLR 0.75, Uncertain significance, Rhabdoid tumor predisposition syndrome 2
- S23F (p.Ser23Phe), rs1555750712, ClinGen CA404054060, ClinVar RCV001975884, ClinVar RCV004946959, REVEL 0.62, AlphaMissense 0.65, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- S23Y (p.Ser23Tyr), rs1555750712, ClinGen CA404054057, ClinVar RCV000571054, ClinVar RCV003617835, AlphaMissense 0.65, MetaLR 0.75, Uncertain significance, Rhabdoid tumor predisposition syndrome 2; Hereditary cancer-predisposing syndrom
- S23S (p.Ser23Ser), rs772658698, gnomAD 19-10984220-C-T, CADD 4.24
- P24A (p.Pro24Ala), rs1060502057, ClinGen CA16616100, ClinVar RCV000462210, ClinVar RCV000571106, REVEL 0.41, CADD 24.50, Likely benign
- P24L (p.Pro24Leu), ExAC rs772230026, gnomAD rs772230026, REVEL 0.52, AlphaMissense 0.45, Uncertain significance, Hereditary cancer-predisposing syndrome
- P24R (p.Pro24Arg), rs772230026, ClinGen CA16616101, ClinVar RCV000475042, ClinVar RCV001026148, AlphaMissense 0.45, MetaLR 0.72, Uncertain significance
- P24S (p.Pro24Ser), rs1060502057, ClinGen CA404054062, ClinVar RCV001035580, ClinVar RCV005492916, REVEL 0.41, CADD 23.70, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- P24T (p.Pro24Thr), TOPMed rs1060502057, gnomAD rs1060502057, Likely benign
- P24P (p.Pro24Pro), rs780223957, gnomAD 19-10984223-T-C, CADD 8.71
- G25* (p.Gly25Ter), Ensembl rs1568416887, Uncertain significance
- G25R (p.Gly25Arg), rs1568416887, Ensembl rs1568416887, ClinGen CA404054067, ClinVar RCV000698344, AlphaMissense 0.87, MetaLR 0.63, Uncertain significance, Rhabdoid tumor predisposition syndrome 2; Hereditary cancer-predisposing syndrom
- G25A (p.Gly25Ala), Ensembl rs2145722317
- G25E (p.Gly25Glu), Ensembl rs2145722317
- G25V (p.Gly25Val), Ensembl rs2145722317
- G25del (p.Gly25del), rs1568416902, gnomAD 19-10984223-TGGA-, CADD 22.40
- G25G (p.Gly25Gly), rs2145722351, gnomAD 19-10984226-A-G, CADD 13.60
- A26D (p.Ala26Asp), Ensembl rs1599928845, Uncertain significance
- A26G (p.Ala26Gly), Ensembl rs1599928845, Uncertain significance, Hereditary cancer-predisposing syndrome
- A26P (p.Ala26Pro), rs145867502, ClinGen CA404054080, ClinVar RCV002400593, 1000Genomes rs145867502, AlphaMissense 0.09, MetaLR 0.51, Uncertain significance, Hereditary cancer-predisposing syndrome
- A26T (p.Ala26Thr), rs145867502, ClinGen CA162137, ClinVar RCV000122060, ClinVar RCV000566087, REVEL 0.27, AlphaMissense 0.09, Benign
- A26V (p.Ala26Val), rs1599928845, ClinGen CA404054088, cosmic curated COSV60797, ClinVar RCV000815719, AlphaMissense 0.63, MetaLR 0.51, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- A26A (p.Ala26Ala), rs2145722449, gnomAD 19-10984229-C-A, CADD 11.50
- M27I (p.Met27Ile), Ensembl rs2145722576
- M27K (p.Met27Lys), Ensembl rs2145722539, Uncertain significance
- M27L (p.Met27Leu), ExAC rs768328175, TOPMed rs768328175, gnomAD rs768328175, Likely benign
- M27R (p.Met27Arg), Ensembl rs2145722539, Uncertain significance
- M27T (p.Met27Thr), rs2145722539, ClinGen CA404054097, ClinVar RCV002587798, Ensembl rs2145722539, AlphaMissense 0.86, MetaLR 0.62, Uncertain significance, Rhabdoid tumor predisposition syndrome 2
- M27V (p.Met27Val), rs768328175, ClinGen CA9203393, ClinVar RCV000475634, ClinVar RCV000575563, REVEL 0.50, CADD 23.50, Likely benign
- L28Q (p.Leu28Gln), Ensembl rs2145722667
- L28M (p.Leu28Met), rs776688705, ClinGen CA9203394, ClinVar RCV000646807, ClinVar RCV005278625, REVEL 0.26, CADD 14.20, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- L28L (p.Leu28Leu), gnomAD 19-10984233-C-T, CADD 8.25
- G29A (p.Gly29Ala), Ensembl rs2145722799, Uncertain significance
- G29D (p.Gly29Asp), rs2145722799, ClinGen CA404054120, ClinVar RCV001986348, Ensembl rs2145722799, AlphaMissense 0.44, MetaLR 0.80, Uncertain significance, Rhabdoid tumor predisposition syndrome 2
- G29R (p.Gly29Arg), Ensembl rs2085810311
- G29S (p.Gly29Ser), Ensembl rs2085810311
- G29V (p.Gly29Val), rs2145722799, ClinGen CA404054124, ClinVar RCV002449719, ClinVar RCV003100004, AlphaMissense 0.44, MetaLR 0.80, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- G29G (p.Gly29Gly), rs1330706074, gnomAD 19-10984238-C-T, CADD 11.40
- P30H (p.Pro30His), Ensembl rs2145722893, REVEL 0.52, AlphaMissense 0.52
- P30L (p.Pro30Leu), rs2145722893, ClinGen CA404054139, ClinVar RCV002376324, AlphaMissense 0.52, MetaLR 0.74, Uncertain significance, Hereditary cancer-predisposing syndrome
- P30R (p.Pro30Arg), Ensembl rs2145722893, REVEL 0.70, AlphaMissense 0.52, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- P30S (p.Pro30Ser), rs1599928968, ClinGen CA404054128, cosmic curated COSV10441, ClinVar RCV000804536, AlphaMissense 0.27, MetaLR 0.74, Uncertain significance, Intellectual disability, autosomal dominant 16; Hereditary cancer-predisposing s
- P30P (p.Pro30Pro), rs2145722926, gnomAD 19-10984241-T-C, CADD 9.57
- S31C (p.Ser31Cys), Ensembl rs2145722956, REVEL 0.58, CADD 26.10
- S31G (p.Ser31Gly), Ensembl rs2145722956
- S31I (p.Ser31Ile), Ensembl rs2145722981
- S31N (p.Ser31Asn), cosmic curated COSV60806, Ensembl rs2145722981
- S31R (p.Ser31Arg), Ensembl rs2145722956, Uncertain significance, Hereditary cancer-predisposing syndrome
- S31T (p.Ser31Thr), Ensembl rs2145722981
- P32L (p.Pro32Leu), rs910095001, ClinGen CA9203395, cosmic curated COSV10606, ClinVar RCV000472108, REVEL 0.48, AlphaMissense 0.70, Uncertain significance
- P32R (p.Pro32Arg), rs910095001, ClinGen CA404054169, ClinVar RCV002374350, ClinVar RCV003094839, AlphaMissense 0.70, MetaLR 0.77, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- P32S (p.Pro32Ser), rs1304026031, ClinGen CA404054162, ClinVar RCV000817110, ClinVar RCV001019415, REVEL 0.41, CADD 25.30, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- P32P (p.Pro32Pro), rs761597013, gnomAD 19-10984247-G-A, CADD 0.67
- G33D (p.Gly33Asp), NCI-TCGA Cosmic COSV6079, cosmic curated COSV60791, Variant assessed as somatic; moderate impact.
- G33R (p.Gly33Arg), rs1060502096, ClinGen CA16616108, ClinVar RCV000466701, TOPMed rs1060502096, REVEL 0.56, CADD 27.60, Uncertain significance
- G33V (p.Gly33Val), rs2513935029, ClinGen CA404054192, ClinVar RCV002387461, Uncertain significance, Hereditary cancer-predisposing syndrome
- G33A (p.Gly33Ala), gnomAD 19-10984249-G-C, REVEL 0.47, CADD 26.00
- G33G (p.Gly33Gly), rs2145723182, gnomAD 19-10984250-T-C, CADD 4.89
- P34L (p.Pro34Leu), cosmic curated COSV10524, Uncertain significance, Hereditary cancer-predisposing syndrome; Rhabdoid tumor predisposition syndrome
- P34R (p.Pro34Arg), rs2085811631, ClinGen CA404054208, ClinVar RCV001205057, gnomAD rs2085811631, REVEL 0.63, CADD 25.10, Uncertain significance, Rhabdoid tumor predisposition syndrome 2; Hereditary cancer-predisposing syndrom
- P34P (p.Pro34Pro), rs769349881, gnomAD 19-10984253-C-T, CADD 8.82
- S35* (p.Ser35Ter), 1000Genomes rs563079629, ExAC rs563079629, TOPMed rs563079629, gnomAD rs563079629, Benign
- S35L (p.Ser35Leu), rs563079629, ClinGen CA9203399, cosmic curated COSV60799, ClinVar RCV000539954, REVEL 0.47, CADD 24.60, Benign
- S35P (p.Ser35Pro), cosmic curated COSV10441, Ensembl rs2145723296
- S35T (p.Ser35Thr), Ensembl rs2145723296
- S35W (p.Ser35Trp), 1000Genomes rs563079629, ExAC rs563079629, TOPMed rs563079629, gnomAD rs563079629, Benign
- S35S (p.Ser35Ser), rs762531687, gnomAD 19-10984256-G-A, CADD 0.06
- P36L (p.Pro36Leu), rs766176476, ClinGen CA9203401, ClinVar RCV000470350, ClinVar RCV000571867, REVEL 0.55, CADD 23.70, Uncertain significance
- P36Q (p.Pro36Gln), ExAC rs766176476, TOPMed rs766176476, gnomAD rs766176476, Uncertain significance
Public SMARCA4 analysis runs
- SMARCA4 analysis run — SMARCA4 (7,890 variants) — completed 2026-08-18