SMC3 (Q9UQE7) variants and mutations
SMC3 (also known as Q9UQE7) is a human protein-coding gene encoding a structural maintenance of chromosomes protein 3 protein. A cohesin-ring protein involved in chromosome cohesion and genome organization. Pathogenic variants are associated with Cornelia de Lange syndrome. This analysis covers 720 SMC3 variants and mutations. Of these, 91% have computational variant effect predictions. Disease context includes Cornelia de Lange syndrome, hereditary disease, and Wiedemann-Steiner syndrome. Example SMC3 variants include Y2C, Y2*, and I3R.
Variant analysis overview
- Gene: SMC3
- Protein: Q9UQE7
- UniProt accession: Q9UQE7
- Organism: Homo sapiens
- Variants analyzed: 720
- Variant scope: all variants
- Completed: 2026-10-09
Variant and mutation evidence
- Variant composition: 742 unspecified-consequence records; 10 frameshift variants; 4 splice-region variants; 48 missense variants; 26 synonymous variants; 5 stop-gained variants; 2 substitution
- Prediction scores: 655 variants have prediction scores (91% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Cornelia de Lange syndrome, hereditary disease, Wiedemann-Steiner syndrome, Intellectual disability, cardiac arrest, neurodegenerative disease, congenital heart disease, autism spectrum disorder, neurodevelopmental disorder, neuromuscular disease, multiple congenital anomalies/dysmorphic syndrome, hepatocellular carcinoma.
Protein structure and variant hotspots
- Protein features: 1 domains; 1 binding sites; 12 post-translational modification sites.
- Structural context: 56 variants have structural context.
- PTM context: 9 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.
Diseases linked to SMC3
Notable SMC3 variants
Examples include Y2C, Y2*, I3R, I3V, K4N, K4R, Q5H, Q5R. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- Y2C (p.Tyr2Cys), NCI-TCGA TCGA novel, Ensembl rs1860796043, ESM-1b 1.00, AlphaMissense 0.29, Variant assessed as somatic; moderate impact.
- Y2* (p.Tyr2Ter), gnomAD 10-110567819-GTAC, CADD 29.80
- I3R (p.Ile3Arg), rs2493089056, ClinGen CA378367576, ClinVar RCV003612700, ESM-1b 1.00, AlphaMissense 1.00, Uncertain significance, Cornelia de Lange syndrome 3
- I3V (p.Ile3Val), rs1860796091, ClinGen CA378367568, ClinVar RCV001198308, Ensembl rs1860796091, REVEL 0.48, ESM-1b 0.76, Uncertain significance, Cornelia de Lange syndrome 3
- K4N (p.Lys4Asn), gnomAD rs1350338348, REVEL 0.69, ESM-1b 1.00
- K4R (p.Lys4Arg), TOPMed rs890348077, gnomAD rs890348077, REVEL 0.72, ESM-1b 1.00
- Q5H (p.Gln5His), Ensembl rs1860796238, ESM-1b 0.97, AlphaMissense 0.84
- Q5R (p.Gln5Arg), gnomAD 10-110567828-GC-G, CADD 28.10
- Q5Q (p.Gln5Gln), rs1860796238, gnomAD 10-110567831-G-A, CADD 25.00
- I7T (p.Ile7Thr), gnomAD 10-110568942-T-C, REVEL 0.80, ESM-1b 0.00
- I8S (p.Ile8Ser), gnomAD 10-110568941-AT-A, CADD 32.00
- I8V (p.Ile8Val), gnomAD 10-110568944-A-G, REVEL 0.33, ESM-1b 0.00
- I8I (p.Ile8Ile), gnomAD 10-110568946-C-A, CADD 13.40
- Q9K (p.Gln9Lys), gnomAD 10-110568947-C-A, REVEL 0.30, ESM-1b 1.00
- Q9Q (p.Gln9Gln), gnomAD 10-110568949-G-A, CADD 10.20
- G10S (p.Gly10Ser), gnomAD 10-110568950-G-A, REVEL 0.97, ESM-1b 1.00
- G10D (p.Gly10Asp), gnomAD 10-110568951-G-A, REVEL 0.96, ESM-1b 1.00
- F11F (p.Phe11Phe), gnomAD 10-110568955-T-C, CADD 14.10
- Y14* (p.Tyr14Ter), gnomAD 10-110568964-C-A, CADD 35.00
- D16A (p.Asp16Ala), gnomAD 10-110568969-A-C, REVEL 0.91, ESM-1b 1.00
- T18K (p.Thr18Lys), gnomAD 10-110568975-C-A, REVEL 0.87, ESM-1b 1.00
- T18I (p.Thr18Ile), gnomAD 10-110568975-C-T, REVEL 0.82, ESM-1b 1.00
- T18T (p.Thr18Thr), gnomAD 10-110568976-A-T, CADD 11.40
- V20A (p.Val20Ala), gnomAD 10-110568981-T-C, REVEL 0.85, ESM-1b 1.00
- V20V (p.Val20Val), gnomAD 10-110568982-A-G, CADD 14.00
- P22T (p.Pro22Thr), gnomAD 10-110568986-C-A, REVEL 0.70, ESM-1b 1.00
- P22L (p.Pro22Leu), gnomAD 10-110568987-C-T, REVEL 0.72, ESM-1b 1.00
- F23L (p.Phe23Leu), gnomAD 10-110568991-C-A, REVEL 0.56, ESM-1b 1.00
- F23F (p.Phe23Phe), rs756514651, gnomAD 10-110568991-C-T, CADD 16.70
- S24N (p.Ser24Asn), ExAC rs780355125, gnomAD rs780355125, REVEL 0.30, ESM-1b 0.96
- S24R (p.Ser24Arg), TOPMed rs1860825918, gnomAD rs1860825918, REVEL 0.53, ESM-1b 1.00
- S25* (p.Ser25Ter), gnomAD 10-110568996-C-A, CADD 39.00
- K26R (p.Lys26Arg), gnomAD 10-110568999-A-G, REVEL 0.36, ESM-1b 0.00
- H27R (p.His27Arg), gnomAD rs1248980460, ESM-1b 1.00, AlphaMissense 0.97
- H27N (p.His27Asn), gnomAD 10-110569001-C-A, REVEL 0.42, ESM-1b 1.00
- N28K (p.Asn28Lys), rs762983740, gnomAD 10-110569003-T-TA, CADD 33.00
- N28D (p.Asn28Asp), gnomAD 10-110569004-A-G, REVEL 0.87, ESM-1b 1.00
- V29V (p.Val29Val), gnomAD 10-110569009-G-A, CADD 11.30
- I30W (p.Ile30Trp), rs1230381435, gnomAD 10-110569007-GTGA, CADD 32.00
- V31M (p.Val31Met), gnomAD 10-110569013-G-A, REVEL 0.86, ESM-1b 1.00
- V31V (p.Val31Val), gnomAD 10-110573708-G-A, CADD 22.30
- G32A (p.Gly32Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- G32D (p.Gly32Asp), gnomAD 10-110573710-G-A, REVEL 0.97, ESM-1b 1.00
- G32G (p.Gly32Gly), gnomAD 10-110573711-C-A, CADD 8.93
- N34S (p.Asn34Ser), gnomAD 10-110573716-A-G, REVEL 0.92, ESM-1b 1.00
- N34N (p.Asn34Asn), rs1259426787, gnomAD 10-110573717-T-C, CADD 11.10
- G35E (p.Gly35Glu), NCI-TCGA TCGA novel, Ensembl rs1860907080, ESM-1b 1.00, AlphaMissense 1.00, Variant assessed as somatic; moderate impact.
- G35R (p.Gly35Arg), gnomAD 10-110573718-G-A, REVEL 0.99, ESM-1b 1.00
- G35G (p.Gly35Gly), gnomAD 10-110573720-A-G, CADD 19.80
- S36Y (p.Ser36Tyr), gnomAD 10-110573722-C-A, REVEL 0.92, ESM-1b 1.00
- S36S (p.Ser36Ser), gnomAD 10-110573723-T-C, CADD 11.00
- G37T (p.Gly37Thr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- G37E (p.Gly37Glu), gnomAD 10-110573723-TG-T, CADD 34.00
- G37* (p.Gly37Ter), gnomAD 10-110573724-G-T, CADD 44.00
- G37R (p.Gly37Arg), gnomAD 10-110573724-G-A, REVEL 0.94, ESM-1b 1.00
- K38E (p.Lys38Glu), Ensembl rs79203236, REVEL 0.99, ESM-1b 1.00
- S39N (p.Ser39Asn), gnomAD 10-110573731-G-A, REVEL 0.95, ESM-1b 1.00
- N40K (p.Asn40Lys), TOPMed rs1182362356, ESM-1b 1.00, AlphaMissense 1.00
- F41F (p.Phe41Phe), gnomAD 10-110573738-T-C, CADD 10.70
- F42S (p.Phe42Ser), rs1554881901, ClinGen CA378369475, ClinVar RCV000534058, Ensembl rs1554881901, ESM-1b 1.00, AlphaMissense 1.00, Uncertain significance, Cornelia de Lange syndrome 3
- Y43C (p.Tyr43Cys), Ensembl rs1860907356, ESM-1b 1.00, AlphaMissense 0.37
- Y43M (p.Tyr43Met), rs1466680694, gnomAD 10-110573735-CT-C, CADD 32.00
- Y43L (p.Tyr43Leu), gnomAD 10-110573735-C-CT, CADD 33.00
- A44E (p.Ala44Glu), gnomAD 10-110575336-C-A, REVEL 0.90, ESM-1b 1.00
- I45V (p.Ile45Val), rs1488636661, NCI-TCGA Cosmic COSV6242, gnomAD rs1488636661, REVEL 0.69, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- F47L (p.Phe47Leu), rs863225258, ClinGen CA279574, ClinVar RCV000201864, Ensembl rs863225258, ESM-1b 1.00, AlphaMissense 1.00, Pathogenic, Cornelia de Lange syndrome 3
- V48L (p.Val48Leu), gnomAD rs1176119437, REVEL 0.56, ESM-1b 1.00
- V48I (p.Val48Ile), gnomAD 10-110575347-G-A, REVEL 0.56, ESM-1b 0.63
- V48V (p.Val48Val), gnomAD 10-110575349-T-C, CADD 11.50
- L49I (p.Leu49Ile), gnomAD 10-110575350-C-A, REVEL 0.72, ESM-1b 1.00
- S50R (p.Ser50Arg), Ensembl rs2134715938, ESM-1b 1.00, AlphaMissense 1.00
- D51V (p.Asp51Val), gnomAD rs1860932207, REVEL 0.93, ESM-1b 1.00
- D51E (p.Asp51Glu), gnomAD 10-110575358-T-A, REVEL 0.75, ESM-1b 0.00
- E52A (p.Glu52Ala), Ensembl rs879158286, ESM-1b 0.00, AlphaMissense 0.89
- E52K (p.Glu52Lys), TOPMed rs1214949585, ESM-1b 1.00, AlphaMissense 0.98
- E52D (p.Glu52Asp), gnomAD 10-110575361-G-C, REVEL 0.31, ESM-1b 1.00
- F53L (p.Phe53Leu), gnomAD 10-110575362-T-C, REVEL 0.46, ESM-1b 1.00
- F53F (p.Phe53Phe), rs774284203, gnomAD 10-110575364-T-C, CADD 11.70
- S54N (p.Ser54Asn), gnomAD rs1473519917, REVEL 0.13, ESM-1b 1.00
- H55R (p.His55Arg), gnomAD rs1159760043, REVEL 0.64, ESM-1b 1.00
- H55Y (p.His55Tyr), gnomAD 10-110575368-C-T, REVEL 0.56, ESM-1b 1.00
- L56F (p.Leu56Phe), ExAC rs747590114, gnomAD rs747590114, REVEL 0.74, ESM-1b 1.00
- L56P (p.Leu56Pro), gnomAD 10-110575372-T-C, REVEL 0.92, ESM-1b 1.00
- L56L (p.Leu56Leu), rs1459624851, gnomAD 10-110575373-T-G, CADD 10.10
- R57C (p.Arg57Cys), rs771561635, NCI-TCGA Cosmic COSV6242, ExAC rs771561635, gnomAD rs771561635, REVEL 0.88, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- R57H (p.Arg57His), rs1564788385, Ensembl rs1564788385, ESM-1b 1.00, AlphaMissense 0.79, Variant assessed as somatic; moderate impact.
- R57S (p.Arg57Ser), gnomAD 10-110575374-C-A, REVEL 0.79, ESM-1b 1.00
- R57R (p.Arg57Arg), gnomAD 10-110575376-T-C, CADD 13.30
- Q60H (p.Gln60His), Ensembl rs1860932595, REVEL 0.30, ESM-1b 1.00
- Q60* (p.Gln60Ter), gnomAD 10-110575383-C-T, CADD 38.00
- R61W (p.Arg61Trp), rs866273473, ClinGen CA213226657, ClinVar RCV000760292, Ensembl rs866273473, ESM-1b 1.00, AlphaMissense 1.00, Conflicting interpretations, Cornelia de Lange syndrome 3; SMC3-related disorder
- L62W (p.Leu62Trp), gnomAD 10-110575390-T-G, REVEL 0.40, ESM-1b 1.00
- L62F (p.Leu62Phe), gnomAD 10-110575391-G-C, REVEL 0.24, ESM-1b 0.20
- A63A (p.Ala63Ala), gnomAD 10-110575394-T-A, CADD 14.00
- L65* (p.Leu65Ter), TOPMed rs1353379013
- L65L (p.Leu65Leu), rs772652388, gnomAD 10-110575398-T-C, CADD 12.20
- H66R (p.His66Arg), TOPMed rs1287384889, gnomAD rs1287384889, REVEL 0.68, ESM-1b 1.00
- H66N (p.His66Asn), gnomAD 10-110575401-C-A, REVEL 0.60, ESM-1b 1.00
- H66Y (p.His66Tyr), gnomAD 10-110575401-C-T, REVEL 0.59, ESM-1b 1.00
- H66H (p.His66His), rs2134715990, gnomAD 10-110575403-T-C, CADD 15.00
- G68C (p.Gly68Cys), NCI-TCGA Cosmic COSV6242, Variant assessed as somatic; moderate impact.
- G68S (p.Gly68Ser), gnomAD 10-110577424-G-A, REVEL 0.78, ESM-1b 1.00
- G68D (p.Gly68Asp), gnomAD 10-110577425-G-A, REVEL 0.83, ESM-1b 1.00
- G68A (p.Gly68Ala), gnomAD 10-110577425-G-C, REVEL 0.81, ESM-1b 1.00
- G68G (p.Gly68Gly), rs1860969100, gnomAD 10-110577426-T-C, CADD 10.70
- T69A (p.Thr69Ala), Ensembl rs2134718741, REVEL 0.32, ESM-1b 0.75
- T69I (p.Thr69Ile), gnomAD 10-110577428-C-T, REVEL 0.56, ESM-1b 1.00
- G70V (p.Gly70Val), TOPMed rs1860969172, ESM-1b 1.00, AlphaMissense 1.00
- G70A (p.Gly70Ala), NCI-TCGA Cosmic COSV1006, Variant assessed as somatic; moderate impact.
- G70C (p.Gly70Cys), gnomAD 10-110577430-G-T, REVEL 0.77, ESM-1b 1.00
- P71T (p.Pro71Thr), gnomAD 10-110577433-C-A, REVEL 0.34, ESM-1b 1.00
- R72C (p.Arg72Cys), gnomAD 10-110577436-C-T, REVEL 0.65, ESM-1b 1.00
- S75F (p.Ser75Phe), gnomAD 10-110577446-C-T, REVEL 0.62, ESM-1b 1.00
- A76T (p.Ala76Thr), Ensembl rs1261608909, ESM-1b 1.00, AlphaMissense 0.99
- F77F (p.Phe77Phe), gnomAD 10-110577453-T-C, CADD 11.00
- V78V (p.Val78Val), rs1860969312, gnomAD 10-110577456-G-A, CADD 13.80
- I80V (p.Ile80Val), Ensembl rs2134718775, REVEL 0.35, ESM-1b 0.36
- I80I (p.Ile80Ile), gnomAD 10-110577462-T-A, CADD 12.90
- I81M (p.Ile81Met), gnomAD 10-110577465-T-G, REVEL 0.58, ESM-1b 1.00
- F82L (p.Phe82Leu), gnomAD 10-110577463-AT-A, CADD 31.00
- D83D (p.Asp83Asp), gnomAD 10-110577471-T-C, CADD 9.40
- S85S (p.Ser85Ser), rs146433240, gnomAD 10-110577477-A-T, CADD 5.71
- D86A (p.Asp86Ala), rs1554882236, ClinGen CA378371928, ClinVar RCV000501814, Ensembl rs1554882236, ESM-1b 1.00, AlphaMissense 0.92, Uncertain significance, not specified
- D86E (p.Asp86Glu), gnomAD 10-110577480-C-A, REVEL 0.54, ESM-1b 1.00
- R88Q (p.Arg88Gln), rs2493105845, ClinGen CA378372033, ClinVar RCV003503884, REVEL 0.60, ESM-1b 1.00, Uncertain significance, Cornelia de Lange syndrome 3
- R88W (p.Arg88Trp), gnomAD 10-110577484-C-T, REVEL 0.61, ESM-1b 1.00
- R88R (p.Arg88Arg), gnomAD 10-110577484-C-A, CADD 13.20
- L89* (p.Leu89Ter), gnomAD 10-110577488-T-G, CADD 37.00
- L89L (p.Leu89Leu), gnomAD 10-110577489-A-G, CADD 11.30
- P90Q (p.Pro90Gln), gnomAD 10-110577491-C-A, REVEL 0.44, ESM-1b 1.00
- P90P (p.Pro90Pro), rs1860969562, gnomAD 10-110577492-A-G, CADD 14.00
- I91S (p.Ile91Ser), gnomAD rs1860975738, REVEL 0.57, ESM-1b 1.00
- I91V (p.Ile91Val), TOPMed rs1345184300, gnomAD rs1345184300, REVEL 0.29, ESM-1b 0.00
- D92E (p.Asp92Glu), ExAC rs199936534, TOPMed rs199936534, gnomAD rs199936534, REVEL 0.25, ESM-1b 1.00, Benign
- D92Y (p.Asp92Tyr), rs1554882266, ClinGen CA378372335, ClinVar RCV000501682, Ensembl rs1554882266, ESM-1b 1.00, AlphaMissense 0.89, Uncertain significance, not specified
- K93E (p.Lys93Glu), rs869312672, Likely pathogenic
- E95K (p.Glu95Lys), rs869312672, ClinGen CA090929, ClinVar RCV000209912, ClinVar RCV004017489, REVEL 0.77, ESM-1b 1.00, Likely pathogenic, De Lange syndrome; Cornelia de Lange syndrome 3
- V96I (p.Val96Ile), ExAC rs769145720, gnomAD rs769145720, REVEL 0.33, ESM-1b 1.00
- S97L (p.Ser97Leu), gnomAD rs1860976121, REVEL 0.34, ESM-1b 1.00
- S97P (p.Ser97Pro), TOPMed rs1860976083, gnomAD rs1860976083, REVEL 0.46, ESM-1b 1.00
- R100K (p.Arg100Lys), rs2134719390, ClinGen CA378372530, ClinVar RCV002252374, Ensembl rs2134719390, ESM-1b 1.00, AlphaMissense 0.99, Uncertain significance, See cases
- V101I (p.Val101Ile), gnomAD rs1407886381, REVEL 0.28, ESM-1b 0.00
- K105E (p.Lys105Glu), rs2134719396, ClinGen CA378372629, ClinVar RCV001768829, Ensembl rs2134719396, ESM-1b 1.00, AlphaMissense 1.00, Uncertain significance, not provided
- K106Q (p.Lys106Gln), Ensembl rs2134719400, ESM-1b 1.00, AlphaMissense 0.99
- D112A (p.Asp112Ala), ExAC rs774721996, gnomAD rs774721996, REVEL 0.77, ESM-1b 1.00
- T117M (p.Thr117Met), Ensembl rs1860976420, REVEL 0.64, ESM-1b 1.00, Uncertain significance, not provided; Cornelia de Lange syndrome 3
- T117C (p.Thr117Cys), NCI-TCGA Cosmic COSV6241, NCI-TCGA Cosmic COSV6242, Variant assessed as somatic; moderate impact.
- N119S (p.Asn119Ser), gnomAD rs1207398077, REVEL 0.18, ESM-1b 0.00
- D120G (p.Asp120Gly), Ensembl rs1860990560, ESM-1b 1.00, AlphaMissense 0.99
- N123Y (p.Asn123Tyr), rs1554882313, ClinGen CA378373735, ClinVar RCV000623304, Ensembl rs1554882313, ESM-1b 1.00, AlphaMissense 0.75, Uncertain significance, Inborn genetic diseases
- L124R (p.Leu124Arg), rs1590553017, ClinGen CA378373770, NCI-TCGA Cosmic COSV6242, ClinVar RCV000790518, ESM-1b 1.00, AlphaMissense 0.99, Uncertain significance, Cornelia de Lange syndrome 3
- E126G (p.Glu126Gly), rs113411202, ClinGen CA272635, ClinVar RCV000147597, Ensembl rs113411202, ESM-1b 1.00, AlphaMissense 0.99, Uncertain significance, Cornelia de Lange syndrome 3
- S127R (p.Ser127Arg), rs748876063, ClinGen CA378373836, ClinVar RCV000857247, ClinVar RCV003372893, REVEL 0.67, ESM-1b 1.00, Likely pathogenic, De Lange syndrome; Inborn genetic diseases
- A128T (p.Ala128Thr), Ensembl rs1860990873, REVEL 0.72, ESM-1b 1.00
- G129V (p.Gly129Val), rs2493107856, ClinGen CA378373872, ClinVar RCV002294841, ESM-1b 1.00, AlphaMissense 1.00, Uncertain significance, Cornelia de Lange syndrome 3
- S131Y (p.Ser131Tyr), rs1163438093, NCI-TCGA Cosmic COSV6241, gnomAD rs1163438093, REVEL 0.86, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- N134I (p.Asn134Ile), rs2493107869, ClinGen CA378373976, ClinVar RCV003312176, ESM-1b 1.00, AlphaMissense 0.99, Uncertain significance, not provided
- N134S (p.Asn134Ser), rs2493107869, ClinGen CA378373969, ClinVar RCV003441520, ESM-1b 1.00, AlphaMissense 0.85, Likely pathogenic, not provided
- Y137H (p.Tyr137His), ESP rs370788296, ExAC rs370788296, gnomAD rs370788296, ESM-1b 1.00, AlphaMissense 0.99
- G142R (p.Gly142Arg), rs1554882316, ClinGen CA378374140, NCI-TCGA Cosmic COSV1006, ClinVar RCV000541678, ESM-1b 1.00, AlphaMissense 1.00, Uncertain significance, Cornelia de Lange syndrome 3
- N145K (p.Asn145Lys), rs2493111001, ClinGen CA378375071, ClinVar RCV003485953, REVEL 0.67, ESM-1b 1.00, Likely pathogenic, Cornelia de Lange syndrome 3
- N145R (p.Asn145Arg), rs2493110995, ClinGen CA2580616897, ClinVar RCV003314959, ESM-1b 1.00, AlphaMissense 0.99, Uncertain significance
- N145S (p.Asn145Ser), Ensembl rs1861020608, REVEL 0.56, ESM-1b 0.29
- M147V (p.Met147Val), Ensembl rs1405221526, REVEL 0.77, ESM-1b 1.00
- A148G (p.Ala148Gly), NCI-TCGA TCGA novel, ESM-1b 1.00, AlphaMissense 0.96, Variant assessed as somatic; moderate impact.
- A150S (p.Ala150Ser), ExAC rs747493783, ESM-1b 1.00, AlphaMissense 0.18, Uncertain significance, Inborn genetic diseases
- A150V (p.Ala150Val), rs2493111025, ClinGen CA378375177, ClinVar RCV003109958, ESM-1b 1.00, AlphaMissense 0.90, Uncertain significance, not provided
- R155G (p.Arg155Gly), rs2493111036, ClinGen CA378375268, ClinVar RCV003984930, ESM-1b 1.00, AlphaMissense 1.00, Likely pathogenic, Cornelia de Lange syndrome 3
- L159V (p.Leu159Val), gnomAD rs1188423288, REVEL 0.80, ESM-1b 1.00
- G164T (p.Gly164Thr), NCI-TCGA Cosmic COSV1006, NCI-TCGA Cosmic COSV6242, Variant assessed as somatic; moderate impact.
- T165S (p.Thr165Ser), TOPMed rs1861020918, ESM-1b 1.00, AlphaMissense 0.95
- V167M (p.Val167Met), Ensembl rs1861020947, ESM-1b 1.00, AlphaMissense 0.97
- E170K (p.Glu170Lys), gnomAD rs1861021107, REVEL 0.70, ESM-1b 1.00
- I176V (p.Ile176Val), TOPMed rs1386121584, gnomAD rs1386121584, REVEL 0.33, ESM-1b 0.00
- K180Q (p.Lys180Gln), rs2493111137, ClinGen CA378375675, ClinVar RCV003054858, ESM-1b 1.00, AlphaMissense 0.23, Uncertain significance, Cornelia de Lange syndrome 3
- G184A (p.Gly184Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- R186W (p.Arg186Trp), NCI-TCGA TCGA novel, gnomAD rs1861037421, REVEL 0.63, ESM-1b 1.00, Variant assessed as somatic; moderate impact.
- K188E (p.Lys188Glu), rs1057521663, ClinGen CA16605599, ClinVar RCV000443224, Ensembl rs1057521663, ESM-1b 1.00, AlphaMissense 0.99, Likely pathogenic, not provided
- N190S (p.Asn190Ser), gnomAD rs1861037687, REVEL 0.34, ESM-1b 0.00, Uncertain significance, Inborn genetic diseases
- I196T (p.Ile196Thr), rs797045070, ClinGen CA276168, ClinVar RCV000191131, ClinVar RCV004721289, ESM-1b 1.00, AlphaMissense 0.99, Pathogenic/Likely pathogenic, Cornelia de Lange syndrome 3; not provided
Public SMC3 analysis runs
- SMC3 analysis run — SMC3 (720 variants) — completed 2026-10-09