CTNNA1 (Catenin alpha-1) variants and mutations
CTNNA1 (also known as Catenin alpha-1) is a human protein-coding gene encoding a catenin alpha-1 protein. It links cadherin-catenin adhesion complexes to the actin cytoskeleton and helps maintain epithelial integrity and tissue architecture. Germline loss-of-function variants can predispose to diffuse gastric cancer, while biallelic variants can cause severe epithelial and skin disease. This analysis covers 1,761 CTNNA1 variants and mutations. Of these, 70% have computational variant effect predictions. Disease context includes Butterfly-shaped pigment dystrophy, Inherited cancer-predisposing syndrome, and hereditary neoplastic syndrome. Example CTNNA1 variants include M1?, M1T, and M1V.
Variant analysis overview
- Gene: CTNNA1
- Protein: Catenin alpha-1
- UniProt accession: P35221
- Organism: Homo sapiens
- Variants analyzed: 1761
- Variant scope: all variants
- Completed: 2026-08-19
Variant and mutation evidence
- Variant composition: 1,633 unspecified-consequence records; 15 frameshift variants; 38 missense variants; 62 synonymous variants; 3 stop-gained variants; 3 splice-region variants; 4 in-frame deletions; 3 substitution
- Prediction scores: 1,227 variants have prediction scores (70% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Butterfly-shaped pigment dystrophy, Inherited cancer-predisposing syndrome, hereditary neoplastic syndrome, hereditary diffuse gastric adenocarcinoma, colorectal cancer, Familial exudative vitreoretinopathy, patterned macular dystrophy 1, exudative vitreoretinopathy, hereditary mixed polyposis syndrome, Retinal dystrophy, Hereditary breast and ovarian cancer syndrome, hereditary breast ovarian cancer syndrome.
Protein structure and variant hotspots
- Protein features: 12 post-translational modification sites.
- PTM context: 21 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 CTNNA1 variants
Examples include M1?, M1T, M1V, T2A, T2M, T2P, T2S, T2T. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1?, NCI-TCGA Cosmic COSV5706, cosmic curated COSV57069, Variant assessed as somatic; high impact.
- M1T (p.Met1Thr), rs2149651722, ClinGen CA361477018, ClinVar RCV001354838, ClinVar RCV004951590, MetaLR 0.51, MetaSVM 0.05, Uncertain significance, Hereditary cancer-predisposing syndrome
- M1V (p.Met1Val), rs2532170047, ClinGen CA361477015, ClinVar RCV003561889, Uncertain significance, not provided
- T2A (p.Thr2Ala), rs1248704890, ClinGen CA361477025, ClinVar RCV001362815, ClinVar RCV002341766, REVEL 0.08, CADD 21.30, Uncertain significance, Hereditary cancer-predisposing syndrome
- T2M (p.Thr2Met), gnomAD 5-138781928-AC-A, CADD 25.50
- T2P (p.Thr2Pro), gnomAD 5-138781928-A-C, REVEL 0.16, CADD 23.50
- T2S (p.Thr2Ser), gnomAD 5-138781929-C-G, REVEL 0.07, CADD 17.70
- T2T (p.Thr2Thr), rs2149651736, gnomAD 5-138781930-T-G, CADD 12.10
- A3G (p.Ala3Gly), rs1410904142, ClinGen CA361477033, ClinVar RCV001980121, ClinVar RCV002370596, REVEL 0.07, CADD 21.10, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- A3V (p.Ala3Val), rs1410904142, ClinGen CA361477034, ClinVar RCV002017205, TOPMed rs1410904142, REVEL 0.07, CADD 22.40, Uncertain significance, not provided
- A3A (p.Ala3Ala), gnomAD 5-138781933-T-C, CADD 11.50
- V4I (p.Val4Ile), rs1307799059, ClinGen CA361477035, ClinVar RCV002430930, ClinVar RCV003101881, AlphaMissense 0.13, MetaLR 0.23, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- V4L (p.Val4Leu), rs1307799059, ClinGen CA361477036, ClinVar RCV001959689, ClinVar RCV003382760, REVEL 0.06, AlphaMissense 0.13, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- V4V (p.Val4Val), gnomAD 5-138781936-C-A, CADD 5.02
- H5R (p.His5Arg), rs1580977954, ClinGen CA361477045, ClinVar RCV001011914, ClinVar RCV002551751, REVEL 0.09, CADD 18.00, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- H5Y (p.His5Tyr), rs1755157382, ClinGen CA361477043, cosmic curated COSV10513, ClinVar RCV001042158, AlphaMissense 0.13, MetaLR 0.22, Uncertain significance, not provided
- H5N (p.His5Asn), gnomAD 5-138781937-C-A, REVEL 0.06, CADD 14.30
- A6K (p.Ala6Lys), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- A6P (p.Ala6Pro), ExAC rs776783618, TOPMed rs776783618, gnomAD rs776783618, Likely benign
- A6T (p.Ala6Thr), rs776783618, ClinGen CA3431329, ClinVar RCV001012793, ClinVar RCV001057956, REVEL 0.09, CADD 0.61, Conflicting interpretations, Hereditary cancer-predisposing syndrome; not provided
- A6V (p.Ala6Val), rs2532170251, ClinGen CA361477053, ClinVar RCV003560814, REVEL 0.12, CADD 20.00, Uncertain significance, not provided
- A6A (p.Ala6Ala), rs1449685929, gnomAD 5-138781942-A-G, CADD 7.90
- G7D (p.Gly7Asp), rs1755158341, ClinGen CA361477059, ClinVar RCV001326720, Ensembl rs1755158341, REVEL 0.20, CADD 21.20, Uncertain significance, not provided
- G7S (p.Gly7Ser), gnomAD 5-138781943-G-A, REVEL 0.13, CADD 21.10
- N8S (p.Asn8Ser), rs1580978002, ClinGen CA361477064, ClinVar RCV000812215, ClinVar RCV004028762, AlphaMissense 0.07, MetaLR 0.45, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- N8Y (p.Asn8Tyr), Ensembl rs2149651797
- N8N (p.Asn8Asn), rs2149651806, gnomAD 5-138781948-C-T, CADD 8.98
- I9T (p.Ile9Thr), rs1292323689, ClinGen CA361477070, cosmic curated COSV57081, ClinVar RCV001301575, REVEL 0.24, CADD 23.30, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- I9V (p.Ile9Val), rs1035752743, ClinGen CA128716439, ClinVar RCV000802612, ClinVar RCV002424857, REVEL 0.08, CADD 17.50, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- F11L (p.Phe11Leu), rs2532170351, ClinGen CA361477089, ClinVar RCV003541898, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- K12E (p.Lys12Glu), rs2532170374, ClinGen CA361477091, ClinVar RCV002459123, ClinVar RCV003679094, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- K12N (p.Lys12Asn), rs1755159437, ClinGen CA361477096, ClinVar RCV003040072, TOPMed rs1755159437, AlphaMissense 0.87, MetaLR 0.28, Uncertain significance, not provided
- K12R (p.Lys12Arg), rs1580978035, ClinGen CA361477094, ClinVar RCV001883302, ClinVar RCV002458701, REVEL 0.18, CADD 22.90, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- K12Q (p.Lys12Gln), gnomAD 5-138781956-T-TC, CADD 26.90
- K12K (p.Lys12Lys), rs1755159437, gnomAD 5-138781960-G-A, AlphaMissense 0.87, MetaLR 0.28
- W13* (p.Trp13Ter), rs2532170453, ClinGen CA361477103, ClinVar RCV003455964, ClinVar RCV006382011, Pathogenic
- W13G (p.Trp13Gly), rs1755159708, ClinGen CA361477100, ClinVar RCV001937268, ClinVar RCV003375386, AlphaMissense 0.95, MetaLR 0.57, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- W13L (p.Trp13Leu), rs955840317, ClinGen CA128716440, ClinVar RCV000808291, ClinVar RCV003307493, REVEL 0.45, CADD 28.80, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- W13R (p.Trp13Arg), rs1755159708, ClinGen CA361477098, ClinVar RCV001894048, Ensembl rs1755159708, AlphaMissense 0.95, MetaLR 0.57, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- D14H (p.Asp14His), rs2532170468, ClinGen CA361477107, ClinVar RCV003674018, Uncertain significance, not provided
- D14Y (p.Asp14Tyr), gnomAD 5-138781964-G-T, REVEL 0.59, CADD 28.30
- D14G (p.Asp14Gly), gnomAD 5-138781965-A-G, REVEL 0.60, CADD 27.80
- P15L (p.Pro15Leu), rs988942117, ClinGen CA361477117, cosmic curated COSV10884, ClinVar RCV001303666, AlphaMissense 0.94, MetaLR 0.61, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- P15R (p.Pro15Arg), rs988942117, ClinGen CA128716441, ClinVar RCV001059959, ClinVar RCV004950212, REVEL 0.49, AlphaMissense 0.94, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- P15S (p.Pro15Ser), rs1755160090, ClinGen CA361477116, cosmic curated COSV10513, ClinVar RCV001048248, REVEL 0.37, CADD 25.40, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- P15H (p.Pro15His), gnomAD 5-138781968-C-A, REVEL 0.45, CADD 26.40
- P15P (p.Pro15Pro), gnomAD 5-138781969-T-C, CADD 13.20
- K16E (p.Lys16Glu), rs759641978, ClinGen CA3431330, NCI-TCGA Cosmic COSV1002, cosmic curated COSV10024, REVEL 0.26, CADD 23.20, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- K16R (p.Lys16Arg), rs1276738001, ClinGen CA361477122, ClinVar RCV002297221, ClinVar RCV003475332, AlphaMissense 0.79, MetaLR 0.57, Uncertain significance, Patterned macular dystrophy 2; not provided
- K16T (p.Lys16Thr), rs1276738001, ClinGen CA361477121, ClinVar RCV001224631, ClinVar RCV002339602, REVEL 0.43, AlphaMissense 0.79, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- S17R (p.Ser17Arg), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- L18P (p.Leu18Pro), rs769832131, ClinGen CA361477137, ClinVar RCV001368275, ClinVar RCV002350705, AlphaMissense 0.99, MetaLR 0.64, Uncertain significance, Hereditary cancer-predisposing syndrome; Patterned macular dystrophy 2; not prov
- L18R (p.Leu18Arg), ExAC rs769832131, gnomAD rs769832131, REVEL 0.60, AlphaMissense 0.99, Uncertain significance
- L18V (p.Leu18Val), rs1755160879, ClinGen CA361477135, ClinVar RCV001220886, ClinVar RCV002348738, REVEL 0.33, CADD 22.40, Uncertain significance, Hereditary cancer-predisposing syndrome
- L18L (p.Leu18Leu), gnomAD 5-138781976-C-T, CADD 12.60
- E19* (p.Glu19Ter), rs1755161249, ClinGen CA916082778, ClinVar RCV001043751, Pathogenic
- E19A (p.Glu19Ala), rs1580978110, ClinGen CA361477141, ClinVar RCV002347540, ClinVar RCV003103216, AlphaMissense 0.95, MetaLR 0.28, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- E19D (p.Glu19Asp), rs1755161812, ClinGen CA361477144, ClinVar RCV001349150, ClinVar RCV002357200, REVEL 0.33, CADD 25.40, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- E19G (p.Glu19Gly), rs1580978110, ClinGen CA361477142, ClinVar RCV000817808, Ensembl rs1580978110, REVEL 0.55, AlphaMissense 0.95, Uncertain significance, not provided
- E19Q (p.Glu19Gln), rs2149651919, ClinGen CA361477138, ClinVar RCV001866485, Ensembl rs2149651919, REVEL 0.25, CADD 24.80, Uncertain significance, not provided
- I20F (p.Ile20Phe), rs1561520304, ClinGen CA361477147, ClinVar RCV000823543, ClinVar RCV001075593, REVEL 0.46, CADD 28.50, Uncertain significance, Retinal dystrophy; Hereditary cancer-predisposing syndrome; not provided
- I20M (p.Ile20Met), rs1249272168, ClinGen CA361477152, ClinVar RCV003737041, REVEL 0.38, CADD 23.60, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- I20V (p.Ile20Val), rs1561520304, ClinGen CA361477146, ClinVar RCV002959170, ClinVar RCV003170742, REVEL 0.18, CADD 22.70, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- R21M (p.Arg21Met), Ensembl rs2149651953
- R21S (p.Arg21Ser), rs1436293141, ClinGen CA361477158, ClinVar RCV002361568, ClinVar RCV003565540, Uncertain significance, Hereditary cancer-predisposing syndrome
- R21R (p.Arg21Arg), rs1436293141, gnomAD 5-138781987-G-A, CADD 12.70
- T22I (p.Thr22Ile), rs1755162650, ClinGen CA361477164, ClinVar RCV001884683, ClinVar RCV005809674, REVEL 0.73, AlphaMissense 1.00, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- T22S (p.Thr22Ser), rs1755162650, ClinGen CA361477165, ClinVar RCV001320550, Ensembl rs1755162650, AlphaMissense 1.00, MetaLR 0.40, Uncertain significance, not provided
- T22T (p.Thr22Thr), rs1189827236, gnomAD 5-138781990-T-C, CADD 14.00
- L23P (p.Leu23Pro), rs762931250, ClinGen CA361477168, ClinVar RCV003571447, AlphaMissense 0.61, MetaLR 0.16, Uncertain significance, not provided
- L23Q (p.Leu23Gln), rs762931250, ClinGen CA3431333, ClinVar RCV001362998, ClinVar RCV002377518, REVEL 0.34, AlphaMissense 0.61, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- L23V (p.Leu23Val), gnomAD 5-138781991-C-G, REVEL 0.18, CADD 20.60
- A24E (p.Ala24Glu), rs1755163589, ClinGen CA361477173, ClinVar RCV001039296, ClinVar RCV002372765, AlphaMissense 0.94, MetaLR 0.11, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- A24S (p.Ala24Ser), rs1472535447, ClinGen CA361477172, ClinVar RCV002367365, AlphaMissense 0.60, MetaLR 0.04, Uncertain significance, Hereditary cancer-predisposing syndrome
- A24T (p.Ala24Thr), gnomAD rs1472535447, Uncertain significance, Hereditary cancer-predisposing syndrome
- A24V (p.Ala24Val), rs1755163589, ClinGen CA361477175, ClinVar RCV001370783, ClinVar RCV004037480, AlphaMissense 0.94, MetaLR 0.11, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- V25A (p.Val25Ala), rs1755163761, ClinGen CA361477181, ClinVar RCV001055005, ClinVar RCV004031740, REVEL 0.66, CADD 28.20, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- V25I (p.Val25Ile), gnomAD 5-138781997-G-A, REVEL 0.22, CADD 24.70
- E26G (p.Glu26Gly), rs2149652026, ClinGen CA361477186, ClinVar RCV001899825, Ensembl rs2149652026, AlphaMissense 0.99, MetaLR 0.34, Uncertain significance, not provided
- E26K (p.Glu26Lys), rs2532170810, ClinGen CA361477182, ClinVar RCV003181629, ClinVar RCV006473791, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- E26* (p.Glu26Ter), gnomAD 5-138782000-G-T, CADD 37.00
- E26E (p.Glu26Glu), gnomAD 5-138782002-G-A, CADD 10.30
- R27K (p.Arg27Lys), rs1755164133, ClinGen CA361477192, ClinVar RCV002007985, ClinVar RCV002423177, REVEL 0.20, CADD 19.40, Conflicting interpretations, not provided; Hereditary cancer-predisposing syndrome
- R27T (p.Arg27Thr), rs1161711503, gnomAD 5-138781999-TGA-T, CADD 32.00
- L28Q (p.Leu28Gln), rs2532170894, ClinGen CA361477199, ClinVar RCV003571444, Uncertain significance, not provided
- L28L (p.Leu28Leu), rs1346100329, gnomAD 5-138782006-C-T, CADD 12.70
- L29W (p.Leu29Trp), rs745411817, gnomAD 5-138782008-GT-G, CADD 24.90
- E30A (p.Glu30Ala), rs763858194, ClinGen CA3431335, ClinVar RCV000792870, ClinVar RCV004609525, REVEL 0.43, CADD 25.40, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- E30D (p.Glu30Asp), rs1755165264, ClinGen CA361477215, ClinVar RCV001248702, ClinVar RCV003294158, REVEL 0.33, CADD 23.50, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided; Hereditary nonpolyposis c
- P31H (p.Pro31His), Ensembl rs2149652075, Uncertain significance
- P31L (p.Pro31Leu), rs2149652075, ClinGen CA361477221, ClinVar RCV002020484, ClinVar RCV004046143, AlphaMissense 1.00, MetaLR 0.36, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- P31R (p.Pro31Arg), rs2149652075, ClinGen CA361477220, ClinVar RCV001872294, Ensembl rs2149652075, AlphaMissense 1.00, MetaLR 0.36, Uncertain significance, not provided
- P31S (p.Pro31Ser), rs1755165546, ClinGen CA361477218, ClinVar RCV001071044, ClinVar RCV003380844, REVEL 0.74, CADD 26.80, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- P31P (p.Pro31Pro), rs2149652081, gnomAD 5-138782017-T-A, CADD 11.80
- L32F (p.Leu32Phe), NCI-TCGA Cosmic COSV5707, cosmic curated COSV57071, Ensembl rs1755165834, REVEL 0.45, CADD 25.10, Variant assessed as somatic; moderate impact.
- L32V (p.Leu32Val), NCI-TCGA Cosmic COSV5707, cosmic curated COSV57073, Variant assessed as somatic; moderate impact.
- L32R (p.Leu32Arg), gnomAD 5-138782018-CTT-C, CADD 29.80
- L32L (p.Leu32Leu), rs1430895867, gnomAD 5-138782020-T-G, CADD 12.00
- V33A (p.Val33Ala), NCI-TCGA Cosmic COSV1002, cosmic curated COSV10024, Uncertain significance, Hereditary cancer-predisposing syndrome
- V33D (p.Val33Asp), rs2532171047, ClinGen CA361477231, ClinVar RCV002387462, REVEL 0.63, CADD 28.90, Uncertain significance, Hereditary cancer-predisposing syndrome
- V33F (p.Val33Phe), gnomAD 5-138782021-G-T, REVEL 0.52, CADD 27.90
- V33V (p.Val33Val), gnomAD 5-138782023-T-C, CADD 9.37
- T34I (p.Thr34Ile), rs2149652103, ClinGen CA361477237, ClinVar RCV001973334, Ensembl rs2149652103, REVEL 0.22, AlphaMissense 0.57, Uncertain significance, not provided
- T34K (p.Thr34Lys), rs2149652103, ClinGen CA361477238, ClinVar RCV002997039, AlphaMissense 0.57, MetaLR 0.06, Uncertain significance, not provided
- T34R (p.Thr34Arg), rs2149652103, ClinGen CA361477239, ClinVar RCV002366904, AlphaMissense 0.57, MetaLR 0.06, Uncertain significance, Hereditary cancer-predisposing syndrome
- T34A (p.Thr34Ala), gnomAD 5-138782024-A-G, REVEL 0.17, CADD 20.80
- Q35R (p.Gln35Arg), rs1580978232, ClinGen CA361477244, ClinVar RCV000794677, ClinVar RCV003372847, REVEL 0.72, CADD 33.00, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- Q35* (p.Gln35Ter), gnomAD 5-138782027-C-T, CADD 39.00
- Q35Q (p.Gln35Gln), rs2149652115, gnomAD 5-138782029-G-A, CADD 23.30
- V36F (p.Val36Phe), gnomAD 5-138783177-G-T, REVEL 0.75, CADD 35.00
- V36V (p.Val36Val), rs1199236107, gnomAD 5-138783179-T-C, CADD 14.60
- T37Y (p.Thr37Tyr), gnomAD 5-138783177-G-GT, CADD 35.00
- T37I (p.Thr37Ile), gnomAD 5-138783178-T-TTA, CADD 28.80
- T38A (p.Thr38Ala), rs2532177792, ClinGen CA361477273, ClinVar RCV002838909, REVEL 0.50, CADD 26.40, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- T38N (p.Thr38Asn), rs754397589, ClinGen CA3431362, ClinVar RCV001989175, ExAC rs754397589, AlphaMissense 0.97, MetaLR 0.23, Uncertain significance, not provided
- T38S (p.Thr38Ser), rs2532177792, ClinGen CA361477272, ClinVar RCV002933688, Uncertain significance, not provided
- T38T (p.Thr38Thr), gnomAD 5-138783185-C-A, CADD 8.55
- L39F (p.Leu39Phe), cosmic curated COSV10513, Ensembl rs2149656006
- L39R (p.Leu39Arg), rs967449848, ClinGen CA128716553, ClinVar RCV001055995, ClinVar RCV003372962, AlphaMissense 1.00, MetaLR 0.42, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- L39V (p.Leu39Val), gnomAD 5-138783186-C-G, REVEL 0.39, CADD 22.90
- V40* (p.Val40Ter), rs2532177853, ClinGen CA2580072835, ClinVar RCV002802215, Pathogenic
- V40A (p.Val40Ala), gnomAD rs1755321271, REVEL 0.70, CADD 24.70, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- V40L (p.Val40Leu), rs1755320989, ClinGen CA361477283, ClinVar RCV001228680, ClinVar RCV006387226, REVEL 0.56, CADD 26.50, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- V40V (p.Val40Val), rs1580983970, gnomAD 5-138783191-A-T, CADD 9.64
- N41H (p.Asn41His), rs1755321895, ClinGen CA361477287, ClinVar RCV001238688, Ensembl rs1755321895, AlphaMissense 0.40, MetaLR 0.25, Uncertain significance, not provided
- N41K (p.Asn41Lys), gnomAD rs1369656663, Uncertain significance, Hereditary cancer-predisposing syndrome
- N41S (p.Asn41Ser), rs1755322192, ClinGen CA361477291, ClinVar RCV001068773, Ensembl rs1755322192, AlphaMissense 0.17, MetaLR 0.09, Uncertain significance, not provided
- N41T (p.Asn41Thr), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- N41N (p.Asn41Asn), rs1369656663, gnomAD 5-138783194-C-T, CADD 11.20
- T42A (p.Thr42Ala), Ensembl rs1755322861, Uncertain significance, Hereditary cancer-predisposing syndrome
- T42S (p.Thr42Ser), rs764691345, ClinGen CA3431363, ClinVar RCV001933026, ClinVar RCV004946872, REVEL 0.06, CADD 19.50, Conflicting interpretations, Hereditary cancer-predisposing syndrome; not provided
- T42T (p.Thr42Thr), rs1561521562, gnomAD 5-138783197-C-T, CADD 11.70
- N43D (p.Asn43Asp), gnomAD rs1162644114, REVEL 0.15, CADD 22.40, Uncertain significance, Hereditary cancer-predisposing syndrome
- N43I (p.Asn43Ile), NCI-TCGA Cosmic COSV5708, cosmic curated COSV57081, gnomAD rs1580984043, REVEL 0.16, CADD 24.20, Uncertain significance
- N43S (p.Asn43Ser), rs1580984043, ClinGen CA361477304, ClinVar RCV000812936, ClinVar RCV002381811, REVEL 0.11, CADD 18.00, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- N43N (p.Asn43Asn), rs977902462, gnomAD 5-138783200-T-C, CADD 8.80
- S44G (p.Ser44Gly), rs1755324870, ClinGen CA361477309, ClinVar RCV001034953, ClinVar RCV005809400, REVEL 0.12, CADD 22.50, Conflicting interpretations, not provided; Hereditary cancer-predisposing syndrome
- S44N (p.Ser44Asn), Ensembl rs2149656114, REVEL 0.09, CADD 16.80, Likely benign, Hereditary cancer-predisposing syndrome
- S44R (p.Ser44Arg), rs1755325154, ClinGen CA361477314, ClinVar RCV001051719, Ensembl rs1755325154, AlphaMissense 0.84, MetaLR 0.05, Uncertain significance, not provided
- S44I (p.Ser44Ile), gnomAD 5-138783198-A-AAT, CADD 28.20
- K45Q (p.Lys45Gln), rs2149656124, ClinGen CA361477316, ClinVar RCV002020319, Ensembl rs2149656124, AlphaMissense 0.37, MetaLR 0.32, Uncertain significance, not provided
- G46A (p.Gly46Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- G46E (p.Gly46Glu), gnomAD rs1755325634, REVEL 0.48, CADD 25.00
- G46W (p.Gly46Trp), rs751978245, ClinGen CA3431364, cosmic curated COSV10024, ClinVar RCV001202348, REVEL 0.51, CADD 32.00, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- p.Gly46 Pro47del, gnomAD 5-138783206-AGGGC, CADD 21.40
- G46G (p.Gly46Gly), rs1755325973, gnomAD 5-138783209-G-A, CADD 7.48
- P47L (p.Pro47Leu), rs757666042, ClinGen CA3431365, cosmic curated COSV10513, ClinVar RCV002389465, REVEL 0.37, CADD 26.30, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- P47S (p.Pro47Ser), rs2149656154, ClinGen CA361477329, cosmic curated COSV10459, ClinVar RCV002389205, AlphaMissense 0.59, MetaLR 0.11, Uncertain significance, Hereditary cancer-predisposing syndrome
- P47P (p.Pro47Pro), rs2149656171, gnomAD 5-138783212-C-T, CADD 7.10
- S48A (p.Ser48Ala), rs1755326643, ClinGen CA361477336, ClinVar RCV001973261, ClinVar RCV003375501, AlphaMissense 0.76, MetaLR 0.17, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- S48C (p.Ser48Cys), rs1580984089, ClinGen CA361477338, ClinVar RCV002023409, ClinVar RCV004046847, REVEL 0.42, AlphaMissense 0.55, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- S48F (p.Ser48Phe), rs1580984089, ClinGen CA361477339, ClinVar RCV000816893, ClinVar RCV002390663, AlphaMissense 0.55, MetaLR 0.30, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- S48P (p.Ser48Pro), rs1755326643, ClinGen CA361477335, ClinVar RCV001243265, Ensembl rs1755326643, AlphaMissense 0.76, MetaLR 0.17, Uncertain significance, not provided
- S48L (p.Ser48Leu), gnomAD 5-138783213-TC-T, CADD 27.60
- N49D (p.Asn49Asp), rs1755327366, ClinGen CA361477341, ClinVar RCV001324654, Ensembl rs1755327366, AlphaMissense 0.45, MetaLR 0.10, Uncertain significance, not provided
- N49K (p.Asn49Lys), rs2149656210, ClinGen CA361477347, ClinVar RCV001365499, ClinVar RCV004036945, AlphaMissense 0.55, MetaLR 0.05, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- N49S (p.Asn49Ser), rs1308395731, ClinGen CA361477345, NCI-TCGA Cosmic COSV5707, cosmic curated COSV57070, REVEL 0.07, CADD 20.30, Uncertain significance, not provided
- N49T (p.Asn49Thr), gnomAD 5-138783217-A-C, REVEL 0.14, CADD 22.10
- N49N (p.Asn49Asn), rs2149656210, gnomAD 5-138783218-T-C, AlphaMissense 0.55, MetaLR 0.05
- K50E (p.Lys50Glu), rs2149656222, ClinGen CA361477349, ClinVar RCV001903183, Ensembl rs2149656222, AlphaMissense 0.97, MetaLR 0.18, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- K50R (p.Lys50Arg), rs1755328184, ClinGen CA361477352, ClinVar RCV001314752, ClinVar RCV003294263, AlphaMissense 0.12, MetaLR 0.09, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- K51E (p.Lys51Glu), rs2532178172, ClinGen CA361477357, ClinVar RCV002392387, Uncertain significance, Hereditary cancer-predisposing syndrome
- K51N (p.Lys51Asn), rs1755328571, ClinGen CA361477363, ClinVar RCV001215374, ClinVar RCV002402644, REVEL 0.15, CADD 23.40, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- K51R (p.Lys51Arg), rs1755328383, ClinGen CA361477361, ClinVar RCV001324820, ClinVar RCV002402908, AlphaMissense 0.15, MetaLR 0.12, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- K51del (p.Lys51del), rs762712870, gnomAD 5-138783218-TAAG-, CADD 21.20
- R52G (p.Arg52Gly), rs2532178209, ClinGen CA361477364, ClinVar RCV002403329, ClinVar RCV003100716, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- R52I (p.Arg52Ile), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- R52T (p.Arg52Thr), rs1755328766, ClinGen CA361477367, ClinVar RCV001351706, ClinVar RCV005550301, REVEL 0.09, CADD 23.90, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- G53D (p.Gly53Asp), rs2532178267, ClinGen CA361477376, ClinVar RCV003568669, REVEL 0.44, CADD 27.00, Uncertain significance, not provided
- G53R (p.Gly53Arg), Ensembl rs1755328949, Uncertain significance
- G53S (p.Gly53Ser), rs1755328949, ClinGen CA361477371, ClinVar RCV001237097, ClinVar RCV002393601, AlphaMissense 1.00, MetaLR 0.27, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- G53G (p.Gly53Gly), rs2149656284, gnomAD 5-138783230-T-G, CADD 12.00
- R54C (p.Arg54Cys), rs781520852, ClinGen CA3431367, NCI-TCGA Cosmic COSV5707, cosmic curated COSV57074, REVEL 0.40, CADD 25.80, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- R54G (p.Arg54Gly), rs781520852, ClinGen CA128716555, ClinVar RCV001040736, ClinVar RCV002400241, REVEL 0.41, CADD 24.20, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- R54H (p.Arg54His), rs746153198, ClinGen CA3431368, ClinVar RCV001059776, ClinVar RCV002402428, REVEL 0.26, CADD 23.80, Conflicting interpretations, Hereditary cancer-predisposing syndrome; Patterned macular dystrophy 2; not prov
- R54S (p.Arg54Ser), rs781520852, ClinGen CA361477377, ClinVar RCV002046864, ExAC rs781520852, REVEL 0.34, CADD 24.20, Uncertain significance, not provided
- S55A (p.Ser55Ala), rs1755329623, ClinGen CA361477382, ClinVar RCV001308360, ClinVar RCV004034167, REVEL 0.18, AlphaMissense 0.89, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- S55C (p.Ser55Cys), rs756329640, ClinGen CA3431369, ClinVar RCV001052043, ClinVar RCV005809415, REVEL 0.46, CADD 26.40, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- S55F (p.Ser55Phe), rs756329640, ClinGen CA361477384, cosmic curated COSV10588, ClinVar RCV002302030, REVEL 0.49, CADD 26.80, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- S55P (p.Ser55Pro), rs1755329623, ClinGen CA361477381, ClinVar RCV002274836, TOPMed rs1755329623, AlphaMissense 0.89, MetaLR 0.18, Uncertain significance, Colorectal cancer
Public CTNNA1 analysis runs
- CTNNA1 analysis run — CTNNA1 (1,761 variants) — completed 2026-08-19