SMAD2 (SMAD family member 2) variants and mutations
SMAD2 (also known as SMAD family member 2) is a human protein-coding gene encoding a SMAD family member 2 protein. It carries activated TGF-beta and activin signals from receptors to the nucleus and regulates developmental and extracellular-matrix gene programs. Heterozygous pathogenic variants can cause syndromic thoracic aortic aneurysm and dissection with variable craniofacial and cardiovascular features. This analysis covers 1,791 SMAD2 variants and mutations. Of these, 26% have computational variant effect predictions. Disease context includes Loeys-Dietz syndrome 6, congenital heart defects, multiple types, 8, with or without heterotaxy, and Loeys-Dietz syndrome. Example SMAD2 variants include M1?, S2*, and S2L.
Variant analysis overview
- Gene: SMAD2
- Protein: SMAD family member 2
- UniProt accession: Q15796
- Organism: Homo sapiens
- Variants analyzed: 1791
- Variant scope: all variants
- Completed: 2026-08-19
Variant and mutation evidence
- Variant composition: 1,630 unspecified-consequence records; 96 synonymous variants; 49 missense variants; 3 stop lost; 3 stop-gained variants; 3 frameshift variants; 5 splice-region variants; 1 in-frame deletions; 1 substitution
- Prediction scores: 469 variants have prediction scores (26% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Loeys-Dietz syndrome 6, congenital heart defects, multiple types, 8, with or without heterotaxy, Loeys-Dietz syndrome, colorectal adenocarcinoma, cancer, hereditary disease, prostate carcinoma, familial thoracic aortic aneurysm and aortic dissection, colon adenocarcinoma, cervical carcinoma, gastric carcinoma, congenital heart disease.
Protein structure and variant hotspots
- Protein features: 2 domains; 4 binding sites; 13 post-translational modification sites.
- Structural context: 1,474 variants have structural context.
- PTM context: 48 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 SMAD2 variants
Examples include M1?, S2*, S2L, S2P, S2W, S3C, S3F, I4M. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1?, cosmic curated COSV51014
- S2* (p.Ser2Ter), cosmic curated COSV50994
- S2L (p.Ser2Leu), rs2033454515, ClinGen CA402503739, cosmic curated COSV10005, ClinVar RCV003666407, REVEL 0.48, CADD 25.80, Uncertain significance, not provided
- S2P (p.Ser2Pro), cosmic curated COSV51007
- S2W (p.Ser2Trp), NCI-TCGA Cosmic COSV1000, NCI-TCGA Cosmic COSV5099, Variant assessed as somatic; moderate impact.
- S3C (p.Ser3Cys), Ensembl rs2144475446
- S3F (p.Ser3Phe), cosmic curated COSV51077, Ensembl rs2144475446
- I4M (p.Ile4Met), rs2511383810, ClinGen CA402503712, ClinVar RCV002597629, REVEL 0.19, CADD 22.10, Uncertain significance, not provided
- P6A (p.Pro6Ala), Ensembl rs1170786282, REVEL 0.38, CADD 25.70
- P6L (p.Pro6Leu), Ensembl rs2144475400
- P6S (p.Pro6Ser), Ensembl rs1170786282, REVEL 0.34, CADD 22.20
- F7S (p.Phe7Ser), cosmic curated COSV51082
- T8A (p.Thr8Ala), Ensembl rs892572826
- T8M (p.Thr8Met), rs1341462958, ClinGen CA402503657, ClinVar RCV002027186, gnomAD rs1341462958, REVEL 0.55, CADD 28.50, Uncertain significance, not provided
- T8S (p.Thr8Ser), Ensembl rs892572826
- P9L (p.Pro9Leu), rs749758342, ClinGen CA8956348, ClinVar RCV003822811, ClinVar RCV005485555, REVEL 0.64, CADD 31.00, Uncertain significance, Inborn genetic diseases; not provided
- P9Q (p.Pro9Gln), rs749758342, ClinGen CA402503649, ClinVar RCV002437385, REVEL 0.54, CADD 31.00, Uncertain significance, Inborn genetic diseases
- V12L (p.Val12Leu), cosmic curated COSV50993
- L16V (p.Leu16Val), NCI-TCGA Cosmic COSV1000, cosmic curated COSV10005, Variant assessed as somatic; moderate impact.
- G17* (p.Gly17Ter), cosmic curated COSV51073
- G17R (p.Gly17Arg), Ensembl rs2144475191
- W18* (p.Trp18Ter), rs1555658568, ClinGen CA402503551, ClinVar RCV000578545, Ensembl rs1555658568, Likely pathogenic
- K19E (p.Lys19Glu), rs2144475139, ClinGen CA402503536, ClinVar RCV002029002, Ensembl rs2144475139, AlphaMissense 0.90, MetaLR 0.56, Uncertain significance, not provided
- K20N (p.Lys20Asn), cosmic curated COSV10005
- S21* (p.Ser21Ter), Ensembl rs2144475107
- S21L (p.Ser21Leu), cosmic curated COSV51057, REVEL 0.25, CADD 23.80
- A22V (p.Ala22Val), cosmic curated COSV50995, Ensembl rs2144475079
- G23D (p.Gly23Asp), cosmic curated COSV51002
- G24E (p.Gly24Glu), Ensembl rs2144475059, REVEL 0.41, CADD 24.80
- G24R (p.Gly24Arg), rs747301606, ClinGen CA402503418, ClinVar RCV002367358, ExAC rs747301606, REVEL 0.46, CADD 26.10, Uncertain significance, Inborn genetic diseases
- G24V (p.Gly24Val), Ensembl rs2144475059
- S25C (p.Ser25Cys), rs143058641, ClinGen CA8956341, ClinVar RCV002676328, ESP rs143058641, REVEL 0.32, CADD 23.40, Uncertain significance, not provided
- G26R (p.Gly26Arg), gnomAD rs2033451522, REVEL 0.26, CADD 24.10
- G27* (p.Gly27Ter), cosmic curated COSV51060
- G27E (p.Gly27Glu), TOPMed rs1186363719, gnomAD rs1186363719, REVEL 0.34, CADD 26.30
- G27R (p.Gly27Arg), Ensembl rs2144475006
- G27V (p.Gly27Val), TOPMed rs1186363719, gnomAD rs1186363719, REVEL 0.38, CADD 26.40
- A28V (p.Ala28Val), Ensembl rs2144474984
- G29S (p.Gly29Ser), cosmic curated COSV51003
- G30A (p.Gly30Ala), TOPMed rs1239673820, gnomAD rs1239673820
- G30E (p.Gly30Glu), cosmic curated COSV50993, TOPMed rs1239673820, gnomAD rs1239673820
- G30R (p.Gly30Arg), cosmic curated COSV51000, gnomAD rs2033450905, REVEL 0.38, CADD 23.10
- G30V (p.Gly30Val), TOPMed rs1239673820, gnomAD rs1239673820, REVEL 0.40, CADD 24.10
- G31R (p.Gly31Arg), Ensembl rs2144474902
- E32* (p.Glu32Ter), Ensembl rs2144474870
- E32K (p.Glu32Lys), Ensembl rs2144474870
- Q33* (p.Gln33Ter), cosmic curated COSV50993, Ensembl rs2144474848
- N34I (p.Asn34Ile), gnomAD rs1239631809, REVEL 0.56, CADD 28.20
- G35E (p.Gly35Glu), Ensembl rs2144474814
- Q36* (p.Gln36Ter), Ensembl rs2144474800
- E37G (p.Glu37Gly), Ensembl rs2033450316
- E38* (p.Glu38Ter), cosmic curated COSV10005
- E38K (p.Glu38Lys), cosmic curated COSV51002, Ensembl rs2144474767, Uncertain significance, not provided
- E38V (p.Glu38Val), Ensembl rs2144474750
- K39R (p.Lys39Arg), gnomAD rs1178643701, REVEL 0.60, CADD 28.70
- W40* (p.Trp40Ter), Ensembl rs2144474718
- W40G (p.Trp40Gly), cosmic curated COSV51063
- C41R (p.Cys41Arg), TOPMed rs2033449914, REVEL 0.83, CADD 29.10
- C41Y (p.Cys41Tyr), Ensembl rs1421425152, REVEL 0.80, CADD 27.40
- E42D (p.Glu42Asp), rs2144474665, ClinGen CA402503154, ClinVar RCV002898795, Uncertain significance, not provided
- E42Q (p.Glu42Gln), cosmic curated COSV51041
- K43* (p.Lys43Ter), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- K43E (p.Lys43Glu), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- A44T (p.Ala44Thr), cosmic curated COSV51010, gnomAD rs1456954386, REVEL 0.69, CADD 27.60
- A44V (p.Ala44Val), Ensembl rs2144474620
- V49M (p.Val49Met), rs2511383422, ClinGen CA402503070, ClinVar RCV002847737, Uncertain significance, not provided
- K51N (p.Lys51Asn), Ensembl rs2144474572
- K53E (p.Lys53Glu), cosmic curated COSV51077
- K53N (p.Lys53Asn), NCI-TCGA Cosmic COSV5099, cosmic curated COSV50996, Variant assessed as somatic; moderate impact.
- K54I (p.Lys54Ile), gnomAD rs1445838443, REVEL 0.65, CADD 29.20
- K54T (p.Lys54Thr), cosmic curated COSV50995
- T55A (p.Thr55Ala), NCI-TCGA TCGA novel, REVEL 0.38, CADD 23.90, Variant assessed as somatic; moderate impact.
- G56A (p.Gly56Ala), Ensembl rs2144474517
- G56E (p.Gly56Glu), cosmic curated COSV99030, Ensembl rs2144474517
- G56R (p.Gly56Arg), Ensembl rs2144474530
- R57* (p.Arg57Ter), NCI-TCGA Cosmic COSV5099, cosmic curated COSV50994, gnomAD rs2033448263, CADD 37.00, Variant assessed as somatic; high impact.
- R57Q (p.Arg57Gln), rs2033448101, ClinGen CA402502958, NCI-TCGA Cosmic COSV5099, cosmic curated COSV50994, REVEL 0.18, CADD 22.50, Uncertain significance, Inborn genetic diseases
- L58* (p.Leu58Ter), rs1131691755, ClinGen CA402502947, ClinVar RCV000494088, Ensembl rs1131691755, Pathogenic
- D59E (p.Asp59Glu), ESP rs375368905, ExAC rs375368905, gnomAD rs375368905
- D59N (p.Asp59Asn), cosmic curated COSV50993
- L61F (p.Leu61Phe), Ensembl rs2144474427
- L61R (p.Leu61Arg), cosmic curated COSV51048, Ensembl rs2144474416
- L61V (p.Leu61Val), Ensembl rs2144474427
- E62K (p.Glu62Lys), Ensembl rs2144474403
- K63Q (p.Lys63Gln), NCI-TCGA Cosmic COSV1000, cosmic curated COSV10005, Variant assessed as somatic; moderate impact.
- K63T (p.Lys63Thr), TOPMed rs2033447566
- A64V (p.Ala64Val), NCI-TCGA TCGA novel, Ensembl rs2144474353, Variant assessed as somatic; moderate impact.
- I65V (p.Ile65Val), gnomAD rs1242869146, REVEL 0.22, CADD 22.60
- T66I (p.Thr66Ile), TOPMed rs2033447144, gnomAD rs2033447144, REVEL 0.60, CADD 26.10
- Q68* (p.Gln68Ter), cosmic curated COSV10633
- Q68P (p.Gln68Pro), cosmic curated COSV10957
- N71D (p.Asn71Asp), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- T72A (p.Thr72Ala), NCI-TCGA Cosmic COSV5099, cosmic curated COSV50992, TOPMed rs1830929483, Variant assessed as somatic; moderate impact.
- C74L (p.Cys74Leu), cosmic curated COSV51009
- V75A (p.Val75Ala), cosmic curated COSV50999
- V75F (p.Val75Phe), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- V75I (p.Val75Ile), Ensembl rs2144474247
- T76A (p.Thr76Ala), gnomAD rs1374795369, REVEL 0.83, CADD 26.90
- I77K (p.Ile77Lys), gnomAD rs1326742866, REVEL 0.96, CADD 28.00
- I77M (p.Ile77Met), Ensembl rs1045339800
- P78Q (p.Pro78Gln), rs761359766, ClinGen CA8956334, ClinVar RCV002862156, ExAC rs761359766, REVEL 0.76, CADD 28.40, Uncertain significance, not provided
- P78T (p.Pro78Thr), Ensembl rs2144474197
- S79N (p.Ser79Asn), gnomAD rs2033445825, REVEL 0.14, CADD 26.90
- S79R (p.Ser79Arg), Ensembl rs2144384959, REVEL 0.29, CADD 22.00
- T80I (p.Thr80Ile), Ensembl rs2144384922
- T80P (p.Thr80Pro), Ensembl rs2144384937
- T80S (p.Thr80Ser), Ensembl rs2144384937
- C81F (p.Cys81Phe), rs908853616, ClinGen CA300260225, ClinVar RCV001968695, ClinVar RCV002458902, REVEL 0.58, CADD 22.60, Uncertain significance, not provided; not specified; Inborn genetic diseases
- C81S (p.Cys81Ser), rs908853616, ClinGen CA402502454, ClinVar RCV003702362, REVEL 0.38, CADD 21.30, Uncertain significance, not provided
- C81W (p.Cys81Trp), Ensembl rs2144384884
- S82C (p.Ser82Cys), NCI-TCGA Cosmic COSV5099, cosmic curated COSV50997, Ensembl rs2144384859, Variant assessed as somatic; moderate impact.
- S82F (p.Ser82Phe), Ensembl rs2144384859
- S82P (p.Ser82Pro), rs2511354421, ClinGen CA402502449, ClinVar RCV003568809, Uncertain significance, not provided
- S82Y (p.Ser82Tyr), Ensembl rs2144384859
- E83G (p.Glu83Gly), Ensembl rs2144384812
- E83K (p.Glu83Lys), Ensembl rs2144384821
- E83Q (p.Glu83Gln), Ensembl rs2144384821
- E83V (p.Glu83Val), Ensembl rs2144384812
- I84F (p.Ile84Phe), gnomAD rs1418778323, REVEL 0.24, CADD 21.20
- I84M (p.Ile84Met), Ensembl rs2144384754
- W85C (p.Trp85Cys), cosmic curated COSV10005, REVEL 0.72, CADD 25.30
- W85L (p.Trp85Leu), cosmic curated COSV10585
- G86* (p.Gly86Ter), Ensembl rs2144384734
- G86A (p.Gly86Ala), Ensembl rs2144384717
- G86E (p.Gly86Glu), Ensembl rs2144384717, REVEL 0.69, CADD 23.00
- G86R (p.Gly86Arg), Ensembl rs2144384734
- G86V (p.Gly86Val), Ensembl rs2144384717
- L87M (p.Leu87Met), Ensembl rs2144384707
- L87P (p.Leu87Pro), cosmic curated COSV50993, ExAC rs779006352, TOPMed rs779006352, gnomAD rs779006352, REVEL 0.73, AlphaMissense 0.12, Uncertain significance, not provided
- L87Q (p.Leu87Gln), rs779006352, ClinGen CA402502412, ClinVar RCV004523807, ClinVar RCV005100524, AlphaMissense 0.12, MetaLR 0.82, Uncertain significance, Inborn genetic diseases; not provided
- L87R (p.Leu87Arg), cosmic curated COSV51083
- L87V (p.Leu87Val), Ensembl rs2144384707
- S88C (p.Ser88Cys), Ensembl rs2144384663
- S88G (p.Ser88Gly), Ensembl rs2144384663
- S88I (p.Ser88Ile), gnomAD rs1173764083, Uncertain significance
- S88N (p.Ser88Asn), rs1173764083, ClinGen CA402502407, cosmic curated COSV10940, ClinVar RCV004523808, REVEL 0.42, CADD 21.60, Uncertain significance, Inborn genetic diseases; not provided
- S88R (p.Ser88Arg), Ensembl rs2144384634, cosmic curated COSV51055
- S88T (p.Ser88Thr), gnomAD rs1173764083, Uncertain significance
- T89I (p.Thr89Ile), Ensembl rs2144384609
- T89R (p.Thr89Arg), Ensembl rs2144384609
- T89S (p.Thr89Ser), Ensembl rs2144384624
- P90A (p.Pro90Ala), cosmic curated COSV50992, ExAC rs756023240, TOPMed rs756023240, gnomAD rs756023240, Uncertain significance
- P90L (p.Pro90Leu), Ensembl rs2144384567
- P90Q (p.Pro90Gln), Ensembl rs2144384567
- P90S (p.Pro90Ser), rs756023240, ClinGen CA8956319, ClinVar RCV001969323, ExAC rs756023240, REVEL 0.30, CADD 18.80, Uncertain significance, not provided
- P90T (p.Pro90Thr), ExAC rs756023240, TOPMed rs756023240, gnomAD rs756023240, REVEL 0.30, CADD 19.60, Uncertain significance
- N91D (p.Asn91Asp), rs750419429, ClinGen CA8956318, ClinVar RCV001898342, ClinVar RCV004041489, REVEL 0.29, CADD 22.50, Uncertain significance, not provided; Inborn genetic diseases
- N91K (p.Asn91Lys), Ensembl rs2144384541
- T92M (p.Thr92Met), rs984513669, ClinGen CA402502381, cosmic curated COSV51038, ClinVar RCV002439471, REVEL 0.53, CADD 24.20, Uncertain significance, Inborn genetic diseases; not provided
- T92R (p.Thr92Arg), TOPMed rs984513669, gnomAD rs984513669, REVEL 0.38, CADD 22.70, Uncertain significance, Inborn genetic diseases
- T92S (p.Thr92Ser), Ensembl rs2144384529
- I93K (p.Ile93Lys), cosmic curated COSV10608, Ensembl rs2144384492, Uncertain significance, Inborn genetic diseases
- I93L (p.Ile93Leu), cosmic curated COSV51028
- I93V (p.Ile93Val), Ensembl rs1568066891, REVEL 0.31, CADD 16.90
- D94E (p.Asp94Glu), Ensembl rs2144384439
- D94H (p.Asp94His), ExAC rs780848010, gnomAD rs780848010
- D94N (p.Asp94Asn), ExAC rs780848010, gnomAD rs780848010
- D94Y (p.Asp94Tyr), ExAC rs780848010, gnomAD rs780848010
- Q95* (p.Gln95Ter), ExAC rs757084234, gnomAD rs757084234
- Q95E (p.Gln95Glu), ExAC rs757084234, gnomAD rs757084234, REVEL 0.41, CADD 22.80, Uncertain significance, not provided
- Q95H (p.Gln95His), NCI-TCGA TCGA novel, Ensembl rs2144384397, REVEL 0.53, CADD 23.60, Variant assessed as somatic; moderate impact.
- Q95K (p.Gln95Lys), ExAC rs757084234, gnomAD rs757084234, REVEL 0.49, CADD 23.10
- Q95L (p.Gln95Leu), gnomAD rs1445556377
- Q95R (p.Gln95Arg), gnomAD rs1445556377, REVEL 0.48, CADD 23.20
- W96* (p.Trp96Ter), cosmic curated COSV10438, Ensembl rs2031867213
- W96C (p.Trp96Cys), Ensembl rs2144384355
- W96R (p.Trp96Arg), Ensembl rs2144384386
- W96S (p.Trp96Ser), Ensembl rs2031867213
- D97A (p.Asp97Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- D97E (p.Asp97Glu), Ensembl rs2144384331, Uncertain significance, Inborn genetic diseases
- D97H (p.Asp97His), rs2144384343, ClinGen CA402502348, ClinVar RCV004523809, Ensembl rs2144384343, AlphaMissense 0.40, MetaLR 0.84, Uncertain significance, Inborn genetic diseases
- D97N (p.Asp97Asn), Ensembl rs2144384343, Uncertain significance
- T98A (p.Thr98Ala), TOPMed rs1204906548
- T98I (p.Thr98Ile), gnomAD rs1312562947, REVEL 0.36, CADD 23.10
- T98R (p.Thr98Arg), gnomAD rs1312562947
- T98S (p.Thr98Ser), TOPMed rs1204906548
- T99P (p.Thr99Pro), Ensembl rs2144384293, Uncertain significance
- T99R (p.Thr99Arg), Ensembl rs2144384277
- T99S (p.Thr99Ser), Ensembl rs2144384293, Uncertain significance, Inborn genetic diseases
- G100A (p.Gly100Ala), TOPMed rs1234431657
Public SMAD2 analysis runs
- SMAD2 analysis run — SMAD2 (1,791 variants) — completed 2026-08-19