MSH3 (DNA mismatch repair protein Msh3) variants and mutations
MSH3 (also known as DNA mismatch repair protein Msh3) is a human protein-coding gene encoding a DNA mismatch repair protein. Together with MSH2, it recognizes larger insertion-deletion loops and certain DNA secondary structures during mismatch repair. Variation can modify the behavior of repeat-expansion disorders, while biallelic loss has been associated with a recessive adenomatous-polyposis phenotype. This analysis covers 3,034 MSH3 variants and mutations. Of these, 78% have computational variant effect predictions. Disease context includes familial adenomatous polyposis 4, endometrial carcinoma, and hereditary neoplastic syndrome. Example MSH3 variants include M1I, M1L, and M1T.
Variant analysis overview
- Gene: MSH3
- Protein: DNA mismatch repair protein Msh3
- UniProt accession: P20585
- Organism: Homo sapiens
- Variants analyzed: 3034
- Variant scope: all variants
- Completed: 2026-08-21
Variant and mutation evidence
- Variant composition: 2,850 unspecified-consequence records; 41 missense variants; 65 synonymous variants; 19 in-frame insertions; 38 frameshift variants; 20 in-frame deletions; 1 splice-region variants; 1 substitution
- Prediction scores: 2,355 variants have prediction scores (78% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: familial adenomatous polyposis 4, endometrial carcinoma, hereditary neoplastic syndrome, Inherited cancer-predisposing syndrome, endometrial cancer, endometrial neoplasm, neurodegenerative disease, X-linked dystonia-parkinsonism, response to simvastatin, response to fenofibrate, Huntington disease, cancer.
Protein structure and variant hotspots
- Protein features: 1 binding sites; 2 post-translational modification sites.
- PTM context: 11 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 MSH3 variants
Examples include M1I, M1L, M1T, M1V, S2C, S2F, S2T, S2P. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1I (p.Met1Ile), rs2112796836, ClinGen CA360264733, ClinVar RCV002031141, ClinGen CA360264736, MetaLR 0.75, MetaSVM 0.52, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- M1L (p.Met1Leu), rs775714088, ClinGen CA3327412, ClinVar RCV000821779, ClinVar RCV001013981, MetaLR 0.73, MetaSVM 0.48, Uncertain significance, not provided
- M1T (p.Met1Thr), rs543854925, ClinGen CA3327413, ClinVar RCV000818648, ClinVar RCV001017957, MetaLR 0.74, MetaSVM 0.52, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- M1V (p.Met1Val), rs775714088, ClinGen CA360264724, ClinVar RCV000816198, ClinVar RCV002422831, MetaLR 0.73, MetaSVM 0.48, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- S2C (p.Ser2Cys), rs768844493, ClinGen CA360264744, ClinVar RCV001963670, ExAC rs768844493, AlphaMissense 0.15, MetaLR 0.50, Uncertain significance, not provided
- S2F (p.Ser2Phe), rs768844493, ClinGen CA3327414, ClinVar RCV001070709, ClinVar RCV002355101, REVEL 0.25, AlphaMissense 0.15, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- S2T (p.Ser2Thr), rs2546709729, ClinGen CA360264738, ClinVar RCV003470226, Uncertain significance, Endometrial carcinoma
- S2P (p.Ser2Pro), gnomAD 5-80654731-T-C, REVEL 0.19, CADD 11.60
- S2S (p.Ser2Ser), gnomAD 5-80654733-T-C, CADD 11.70
- R3C (p.Arg3Cys), rs774455792, ClinGen CA3327415, ClinVar RCV001059419, ClinVar RCV002418511, REVEL 0.37, AlphaMissense 0.62, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided; Endometrial carcinoma
- R3G (p.Arg3Gly), rs774455792, ClinGen CA360264750, ClinVar RCV002419162, ClinVar RCV003099811, AlphaMissense 0.62, MetaLR 0.67, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided; Endometrial carcinoma
- R3H (p.Arg3His), rs1391784097, ClinGen CA360264753, ClinVar RCV001244351, ClinVar RCV002375293, REVEL 0.31, CADD 28.30, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- R3P (p.Arg3Pro), rs1391784097, ClinGen CA360264756, ClinVar RCV002019982, TOPMed rs1391784097, REVEL 0.43, CADD 29.30, Uncertain significance, not provided
- R3S (p.Arg3Ser), gnomAD 5-80654734-C-A, REVEL 0.40, CADD 23.60
- R4Q (p.Arg4Gln), rs1442281976, ClinGen CA360264763, ClinVar RCV001064010, ClinVar RCV003283947, REVEL 0.29, CADD 24.10, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- R4W (p.Arg4Trp), rs761912573, ClinGen CA3327416, ClinVar RCV001245568, ClinVar RCV004944952, REVEL 0.40, CADD 25.80, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- K5E (p.Lys5Glu), rs2546709757, ClinGen CA360264769, ClinVar RCV003704782, ClinVar RCV005439153, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- K5M (p.Lys5Met), rs1275624430, ClinGen CA360264776, ClinVar RCV001224174, ClinVar RCV002393546, REVEL 0.47, AlphaMissense 0.40, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- K5N (p.Lys5Asn), rs563338833, ClinGen CA3327418, ClinVar RCV000796995, ClinVar RCV002397593, REVEL 0.36, CADD 23.60, Uncertain significance, Endometrial carcinoma; not provided; Hereditary cancer-predisposing syndrome
- K5Q (p.Lys5Gln), rs2546709757, ClinGen CA360264768, ClinVar RCV004513650, Uncertain significance, Hereditary cancer-predisposing syndrome
- K5R (p.Lys5Arg), rs1275624430, ClinGen CA360264775, ClinVar RCV001071481, ClinVar RCV005372545, AlphaMissense 0.40, MetaLR 0.71, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- K5K (p.Lys5Lys), rs563338833, gnomAD 5-80654742-G-A, CADD 11.50
- P6A (p.Pro6Ala), rs374904719, ClinGen CA360264783, ClinVar RCV001976158, ClinVar RCV005370099, REVEL 0.12, CADD 16.80, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- P6L (p.Pro6Leu), rs2546709769, ClinGen CA360264788, ClinVar RCV002890876, ClinVar RCV004642058, REVEL 0.08, CADD 17.10, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- P6S (p.Pro6Ser), rs374904719, ClinGen CA3327419, ClinVar RCV000805347, ClinVar RCV001012792, REVEL 0.05, CADD 17.70, Uncertain significance, Familial adenomatous polyposis 4; Hereditary cancer-predisposing syndrome; MSH3
- P6T (p.Pro6Thr), gnomAD 5-80654743-C-A, REVEL 0.14, CADD 21.10
- P6R (p.Pro6Arg), gnomAD 5-80654744-C-G, REVEL 0.20, CADD 17.10
- P6H (p.Pro6His), gnomAD 5-80654744-C-A, REVEL 0.23, CADD 22.90
- P6P (p.Pro6Pro), gnomAD 5-80654745-T-C, CADD 9.99
- A7E (p.Ala7Glu), NCI-TCGA Cosmic COSV5415, Variant assessed as somatic; moderate impact.
- A7G (p.Ala7Gly), rs1580537658, ClinGen CA360264797, ClinVar RCV000805858, ClinVar RCV004028227, AlphaMissense 0.10, MetaLR 0.41, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- A7T (p.Ala7Thr), rs1749187065, ClinGen CA360264789, ClinVar RCV001207714, Ensembl rs1749187065, AlphaMissense 0.12, MetaLR 0.41, Uncertain significance, not provided
- A7V (p.Ala7Val), rs1580537658, ClinGen CA360264796, ClinVar RCV000796558, ClinVar RCV004649323, REVEL 0.09, AlphaMissense 0.10, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- A7A (p.Ala7Ala), rs6151597, gnomAD 5-80654748-G-A, CADD 8.45
- S8A (p.Ser8Ala), TOPMed rs1313510221, gnomAD rs1313510221, Uncertain significance
- S8L (p.Ser8Leu), rs2546709784, ClinGen CA360264803, ClinVar RCV003461900, ClinVar RCV003720918, REVEL 0.15, CADD 14.30, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided; Endometrial carcinoma
- S8P (p.Ser8Pro), rs1313510221, ClinGen CA360264800, ClinVar RCV000794081, ClinVar RCV002424802, REVEL 0.21, AlphaMissense 0.07, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided; Endometrial carcinoma
- S8T (p.Ser8Thr), rs1313510221, ClinGen CA360264799, ClinVar RCV001044427, ClinVar RCV003307837, AlphaMissense 0.07, MetaLR 0.42, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- S8S (p.Ser8Ser), rs1320023097, gnomAD 5-80654751-G-C, CADD 3.54
- G9A (p.Gly9Ala), rs369278563, ClinGen CA360264814, ClinVar RCV001205984, ClinVar RCV002451437, REVEL 0.08, CADD 19.00, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- G9D (p.Gly9Asp), rs369278563, ClinGen CA3327421, ClinVar RCV000797567, ClinVar RCV002440650, REVEL 0.11, CADD 19.80, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- G9S (p.Gly9Ser), rs2546709789, ClinGen CA360264808, ClinVar RCV002591701, ClinVar RCV005445798, REVEL 0.09, CADD 16.80, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- G9V (p.Gly9Val), rs369278563, ClinGen CA360264815, ClinVar RCV001210126, ClinVar RCV002282484, REVEL 0.24, CADD 20.50, Uncertain significance, Hereditary cancer-predisposing syndrome; not specified; Endometrial carcinoma
- G9C (p.Gly9Cys), gnomAD 5-80654752-G-T, REVEL 0.24, CADD 22.40
- G9G (p.Gly9Gly), rs1749188036, gnomAD 5-80654754-C-G, CADD 7.65
- G10A (p.Gly10Ala), rs1580537703, ClinGen CA360264824, ClinVar RCV001017899, ClinVar RCV003688895, AlphaMissense 0.08, MetaLR 0.52, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- G10C (p.Gly10Cys), rs2112796965, ClinGen CA360264817, ClinVar RCV001993814, Ensembl rs2112796965, AlphaMissense 0.22, MetaLR 0.56, Uncertain significance, not provided
- G10R (p.Gly10Arg), rs2112796965, ClinGen CA360264819, ClinVar RCV001918400, ClinVar RCV002441017, AlphaMissense 0.22, MetaLR 0.56, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- G10S (p.Gly10Ser), rs2112796965, ClinGen CA360264820, ClinVar RCV002259246, ClinVar RCV003738170, REVEL 0.13, AlphaMissense 0.22, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- G10D (p.Gly10Asp), gnomAD 5-80654756-G-A, REVEL 0.11, CADD 15.30
- G10G (p.Gly10Gly), rs2112796969, gnomAD 5-80654757-C-T, CADD 8.60
- L11F (p.Leu11Phe), rs372442835, ClinGen CA360264829, ClinVar RCV002612964, ClinVar RCV004065639, REVEL 0.21, CADD 0.08, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- L11I (p.Leu11Ile), 1000Genomes rs372442835, ESP rs372442835, ExAC rs372442835, gnomAD rs372442835, REVEL 0.18, CADD 0.12, Uncertain significance
- L11R (p.Leu11Arg), ExAC rs777602777, gnomAD rs777602777, REVEL 0.16, CADD 13.20
- L11V (p.Leu11Val), rs372442835, ClinGen CA3327422, ClinVar RCV000801693, ClinVar RCV002325540, REVEL 0.17, CADD 0.04, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- L11L (p.Leu11Leu), rs564921007, gnomAD 5-80654760-C-T, CADD 4.51
- A12G (p.Ala12Gly), rs969715234, ClinGen CA121287683, ClinVar RCV003293254, Ensembl rs969715234, REVEL 0.23, CADD 9.33, Uncertain significance, Hereditary cancer-predisposing syndrome
- A12P (p.Ala12Pro), rs1580537725, ClinGen CA360264837, ClinVar RCV003821236, ClinVar RCV005377580, AlphaMissense 0.09, MetaLR 0.37, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- A12S (p.Ala12Ser), rs1580537725, ClinGen CA360264838, ClinVar RCV001240520, ClinVar RCV003166501, REVEL 0.15, AlphaMissense 0.09, Conflicting interpretations, Hereditary cancer-predisposing syndrome; not provided
- A12T (p.Ala12Thr), rs1580537725, ClinGen CA360264835, ClinVar RCV000795775, Ensembl rs1580537725, REVEL 0.10, AlphaMissense 0.09, Conflicting interpretations, not provided; Hereditary cancer-predisposing syndrome
- A12V (p.Ala12Val), rs969715234, ClinGen CA360264842, ClinVar RCV001053269, ClinVar RCV002451221, REVEL 0.16, CADD 15.30, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- A12D (p.Ala12Asp), gnomAD 5-80654762-C-A, REVEL 0.19, CADD 15.00
- A12A (p.Ala12Ala), rs1749188879, gnomAD 5-80654763-T-C, CADD 6.36
- A13D (p.Ala13Asp), rs756843242, ClinGen CA3327425, ClinVar RCV001913632, ClinVar RCV002359407, REVEL 0.11, CADD 10.80, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- A13T (p.Ala13Thr), rs2546709827, ClinGen CA360264843, ClinVar RCV002355172, ClinVar RCV006558964, REVEL 0.13, CADD 7.79, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- A13V (p.Ala13Val), gnomAD 5-80654765-C-T, REVEL 0.10, CADD 11.90
- A13A (p.Ala13Ala), gnomAD 5-80654766-C-G, CADD 5.67
- S14A (p.Ser14Ala), rs2112797022, ClinGen CA360264853, ClinVar RCV004513713, AlphaMissense 0.07, MetaLR 0.33, Likely benign, Hereditary cancer-predisposing syndrome
- S14F (p.Ser14Phe), rs2112797030, ClinGen CA360265103, ClinVar RCV001989702, Ensembl rs2112797030, AlphaMissense 0.15, MetaLR 0.36, Uncertain significance, not provided
- S14P (p.Ser14Pro), Ensembl rs2112797022, REVEL 0.13, AlphaMissense 0.07
- S14S (p.Ser14Ser), gnomAD 5-80654769-C-A, CADD 6.94
- S15G (p.Ser15Gly), rs1414195684, ClinGen CA360265106, ClinVar RCV001337753, ClinVar RCV006406912, REVEL 0.20, CADD 0.97, Conflicting interpretations, not provided; Hereditary cancer-predisposing syndrome
- S15N (p.Ser15Asn), rs2546709853, ClinGen CA360265113, ClinVar RCV003477307, ClinVar RCV004943063, REVEL 0.20, CADD 10.80, Conflicting interpretations, Hereditary cancer-predisposing syndrome; not provided
- S15R (p.Ser15Arg), rs2112797042, ClinGen CA360265117, ClinVar RCV002824081, ClinVar RCV004946057, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- S15T (p.Ser15Thr), rs2546709853, ClinGen CA360265110, ClinVar RCV002962476, Uncertain significance, not provided
- S15S (p.Ser15Ser), rs2112797042, gnomAD 5-80654772-C-T, CADD 8.56
- S16* (p.Ser16Ter), rs944680882, ClinGen CA121287684, ClinVar RCV003091448, ClinVar RCV003367986, CADD 35.00, Pathogenic
- S16T (p.Ser16Thr), rs2546709856, ClinGen CA360265118, ClinVar RCV003293241, Uncertain significance, Hereditary cancer-predisposing syndrome
- p.Ser16dup, rs1254174829, gnomAD 5-80654764-G-GCCT, CADD 10.20
- S16L (p.Ser16Leu), gnomAD 5-80654774-C-T, REVEL 0.24, CADD 20.50
- S16S (p.Ser16Ser), rs976119718, gnomAD 5-80654775-A-T, CADD 7.94
- A17G (p.Ala17Gly), rs1749189749, ClinGen CA360265133, ClinVar RCV001066125, ClinVar RCV004944840, AlphaMissense 0.09, MetaLR 0.38, Conflicting interpretations, not provided; Hereditary cancer-predisposing syndrome
- A17T (p.Ala17Thr), rs1176057750, ClinGen CA360265126, ClinVar RCV001220271, ClinVar RCV002339582, REVEL 0.18, CADD 17.00, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- A17V (p.Ala17Val), rs1749189749, ClinGen CA360265134, ClinVar RCV001218095, ClinVar RCV003294051, REVEL 0.24, AlphaMissense 0.09, Conflicting interpretations, Hereditary cancer-predisposing syndrome; not provided
- P18L (p.Pro18Leu), rs1749189883, ClinGen CA360265142, ClinVar RCV003461916, AlphaMissense 0.11, MetaLR 0.44, Uncertain significance, Endometrial carcinoma
- P18R (p.Pro18Arg), rs1749189883, ClinGen CA360265141, ClinVar RCV001324727, ClinVar RCV002350599, AlphaMissense 0.11, MetaLR 0.44, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- P18T (p.Pro18Thr), rs2112797069, ClinGen CA360265136, ClinVar RCV001875550, Ensembl rs2112797069, AlphaMissense 0.08, MetaLR 0.37, Uncertain significance, not provided
- P18A (p.Pro18Ala), gnomAD 5-80654779-C-G, REVEL 0.14, CADD 9.98
- A19G (p.Ala19Gly), rs780785898, ClinGen CA3327426, ClinVar RCV001205761, ClinVar RCV002348673, REVEL 0.13, CADD 11.40, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- A19P (p.Ala19Pro), rs2546709873, ClinGen CA360265147, ClinVar RCV003041868, ClinVar RCV003459706, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided; Endometrial carcinoma
- A19T (p.Ala19Thr), rs2546709873, ClinGen CA360265144, ClinVar RCV004513716, ClinVar RCV005104874, CADD 2.54, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- A19V (p.Ala19Val), ExAC rs780785898, gnomAD rs780785898, REVEL 0.23, CADD 18.70, Uncertain significance, Hereditary cancer-predisposing syndrome
- A19E (p.Ala19Glu), gnomAD 5-80654783-C-A, REVEL 0.25, CADD 18.50
- A19A (p.Ala19Ala), rs1447333327, gnomAD 5-80654784-G-T, CADD 6.36
- R20G (p.Arg20Gly), rs2546709886, ClinGen CA360265152, ClinVar RCV002355680, ClinVar RCV003718528, REVEL 0.62, CADD 18.10, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- R20K (p.Arg20Lys), rs1580537787, ClinGen CA360265156, ClinVar RCV000820855, ClinVar RCV002352453, REVEL 0.43, AlphaMissense 0.09, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided; Endometrial carcinoma
- R20M (p.Arg20Met), rs1580537787, ClinGen CA360265159, ClinVar RCV002357956, AlphaMissense 0.09, MetaLR 0.53, Uncertain significance, Hereditary cancer-predisposing syndrome
- R20S (p.Arg20Ser), rs1416287946, ClinGen CA360265163, ClinVar RCV001900802, ClinVar RCV002359371, REVEL 0.57, CADD 21.20, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- R20T (p.Arg20Thr), rs1580537787, ClinGen CA360265158, ClinVar RCV002005203, Ensembl rs1580537787, AlphaMissense 0.09, MetaLR 0.53, Uncertain significance, not provided
- R20R (p.Arg20Arg), rs1416287946, gnomAD 5-80654787-G-A, CADD 9.71
- Q21* (p.Gln21Ter), rs2546709890, ClinGen CA360265167, ClinVar RCV003459134, Pathogenic
- Q21L (p.Gln21Leu), rs2546709895, ClinGen CA360265171, ClinVar RCV003552505, Uncertain significance, not provided
- Q21K (p.Gln21Lys), gnomAD 5-80654788-C-A, REVEL 0.38, CADD 24.40
- Q21Q (p.Gln21Gln), rs1168176656, gnomAD 5-80654790-A-G, CADD 6.75
- A22E (p.Ala22Glu), rs1749190564, ClinGen CA360265180, ClinVar RCV001306496, ClinVar RCV002375378, REVEL 0.08, AlphaMissense 0.29, Uncertain significance, Hereditary cancer-predisposing syndrome; not specified; not provided
- A22G (p.Ala22Gly), rs1749190564, ClinGen CA360265182, ClinVar RCV003720948, AlphaMissense 0.29, MetaLR 0.39, Uncertain significance, not provided
- A22S (p.Ala22Ser), Ensembl rs1749190439, REVEL 0.06, AlphaMissense 0.14, Uncertain significance
- A22T (p.Ala22Thr), rs1749190439, ClinGen CA360265175, ClinVar RCV003026139, Ensembl rs1749190439, AlphaMissense 0.14, MetaLR 0.40, Uncertain significance, not provided
- A22V (p.Ala22Val), Ensembl rs1749190564, REVEL 0.12, AlphaMissense 0.29, Uncertain significance
- A22A (p.Ala22Ala), rs1580537815, gnomAD 5-80654793-G-C, CADD 5.94
- V23A (p.Val23Ala), rs2112797142, ClinGen CA360265190, ClinVar RCV002378060, ClinVar RCV003120953, AlphaMissense 0.55, MetaLR 0.71, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- V23D (p.Val23Asp), Ensembl rs2112797142
- V23F (p.Val23Phe), rs1353893324, ClinGen CA360265187, ClinVar RCV001315937, ClinVar RCV005372640, AlphaMissense 0.20, MetaLR 0.72, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- V23G (p.Val23Gly), Ensembl rs2112797142
- V23I (p.Val23Ile), rs1353893324, ClinGen CA360265184, ClinVar RCV001056454, ClinVar RCV002365713, REVEL 0.30, AlphaMissense 0.20, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- L24F (p.Leu24Phe), rs2112797155, ClinGen CA360265201, ClinVar RCV001935672, ClinVar RCV006392253, REVEL 0.47, CADD 25.30, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- L24L (p.Leu24Leu), rs2112797155, gnomAD 5-80654799-G-A, CADD 13.20
- S25G (p.Ser25Gly), rs746455200, ClinGen CA3327427, ClinVar RCV001995173, ExAC rs746455200, REVEL 0.55, CADD 27.60, Uncertain significance, not provided
- S25N (p.Ser25Asn), rs1749191144, ClinGen CA360265208, ClinVar RCV001038238, ClinVar RCV004031068, REVEL 0.41, CADD 26.80, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- S25R (p.Ser25Arg), rs879145456, ClinGen CA360265215, ClinVar RCV001230805, Ensembl rs879145456, AlphaMissense 0.62, MetaLR 0.67, Uncertain significance, not provided
- S25S (p.Ser25Ser), rs879145456, gnomAD 5-80654802-C-T, AlphaMissense 0.62, MetaLR 0.67
- R26* (p.Arg26Ter), rs770190473, ClinGen CA3327428, ClinVar RCV001383336, ClinVar RCV002404898, CADD 37.00, Pathogenic
- R26L (p.Arg26Leu), rs780517196, ClinGen CA360265220, ClinVar RCV003569268, ExAC rs780517196, REVEL 0.59, AlphaMissense 0.38, Uncertain significance, not provided
- R26P (p.Arg26Pro), rs780517196, ClinGen CA360265219, ClinVar RCV001956779, ClinVar RCV004571764, AlphaMissense 0.38, MetaLR 0.63, Uncertain significance, not provided; Endometrial carcinoma; Hereditary cancer-predisposing syndrome
- R26Q (p.Arg26Gln), rs780517196, ClinGen CA3327429, ClinVar RCV001026824, ClinVar RCV001042443, REVEL 0.39, AlphaMissense 0.38, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- F27L (p.Phe27Leu), rs749586225, ClinGen CA360265234, ClinVar RCV004513726, ExAC rs749586225, REVEL 0.53, CADD 22.60, Uncertain significance, Hereditary cancer-predisposing syndrome
- F27V (p.Phe27Val), rs1465875645, ClinGen CA360265226, ClinVar RCV001370013, ClinVar RCV002420827, REVEL 0.62, CADD 24.80, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- F27C (p.Phe27Cys), gnomAD 5-80654807-T-G, REVEL 0.69, CADD 29.20
- F27F (p.Phe27Phe), rs749586225, gnomAD 5-80654808-C-T, CADD 13.20
- F28L (p.Phe28Leu), Ensembl rs2112797206
- F28V (p.Phe28Val), rs2546709932, ClinGen CA360265237, ClinVar RCV003690358, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- F28Y (p.Phe28Tyr), gnomAD 5-80654810-T-A, REVEL 0.52, CADD 28.00
- Q29* (p.Gln29Ter), rs1283575037, ClinGen CA360265252, ClinVar RCV003459065, gnomAD rs1283575037, CADD 38.00, Pathogenic
- Q29H (p.Gln29His), rs768967342, ClinGen CA3327431, ClinVar RCV001997985, ClinVar RCV002442956, REVEL 0.13, CADD 11.70, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- Q29K (p.Gln29Lys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- Q29P (p.Gln29Pro), rs1580537878, ClinGen CA360265254, ClinVar RCV002373410, ClinVar RCV003103526, REVEL 0.25, AlphaMissense 0.06, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- Q29R (p.Gln29Arg), rs1580537878, ClinGen CA360265256, ClinVar RCV000817963, ClinVar RCV004944214, AlphaMissense 0.06, MetaLR 0.31, Conflicting interpretations, not provided; Hereditary cancer-predisposing syndrome
- S30A (p.Ser30Ala), rs1749192322, ClinGen CA360265264, ClinVar RCV001217113, ClinVar RCV002375191, REVEL 0.11, AlphaMissense 0.07, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- S30C (p.Ser30Cys), rs1580537891, ClinGen CA360265269, ClinVar RCV002299321, ClinVar RCV002373084, AlphaMissense 0.18, MetaLR 0.49, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- S30F (p.Ser30Phe), rs1580537891, ClinGen CA360265268, ClinVar RCV000814997, ClinVar RCV004028835, REVEL 0.27, AlphaMissense 0.18, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- S30P (p.Ser30Pro), rs1749192322, ClinGen CA360265262, ClinVar RCV001071074, ClinVar RCV002375002, AlphaMissense 0.07, MetaLR 0.39, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- S30T (p.Ser30Thr), rs1749192322, ClinGen CA360265261, ClinVar RCV003368174, ClinVar RCV003669391, AlphaMissense 0.07, MetaLR 0.39, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- S30S (p.Ser30Ser), gnomAD 5-80654817-T-G, CADD 10.00
- T31A (p.Thr31Ala), rs1212322787, ClinGen CA360265273, ClinVar RCV000813159, ClinVar RCV002372289, REVEL 0.14, AlphaMissense 0.06, Conflicting interpretations, Hereditary cancer-predisposing syndrome; not provided
- T31M (p.Thr31Met), rs1580537911, ClinGen CA360265279, ClinVar RCV000824036, Ensembl rs1580537911, REVEL 0.19, CADD 21.60, Uncertain significance, not provided
- T31P (p.Thr31Pro), rs1212322787, ClinGen CA360265271, ClinVar RCV002378948, AlphaMissense 0.06, MetaLR 0.26, Uncertain significance, Hereditary cancer-predisposing syndrome
- T31T (p.Thr31Thr), gnomAD 5-80654820-G-T, CADD 7.38
- G32A (p.Gly32Ala), ExAC rs774577965, gnomAD rs774577965, REVEL 0.36, CADD 23.10
- G32R (p.Gly32Arg), rs2112797247, ClinGen CA360265281, ClinVar RCV002048586, ClinVar RCV003161252, AlphaMissense 0.17, MetaLR 0.75, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- G32G (p.Gly32Gly), rs145429648, gnomAD 5-80654823-A-C, CADD 13.80
- S33G (p.Ser33Gly), rs772142059, ClinGen CA360265291, ClinVar RCV001067465, ClinVar RCV002379603, REVEL 0.19, CADD 22.90, Uncertain significance, Endometrial carcinoma; not provided; Familial adenomatous polyposis 4
- S33I (p.Ser33Ile), rs1489972731, ClinGen CA360265296, ClinVar RCV004513730, AlphaMissense 0.07, MetaLR 0.41, Uncertain significance, Hereditary cancer-predisposing syndrome
- S33N (p.Ser33Asn), rs1489972731, ClinGen CA360265293, ClinVar RCV001209776, ClinVar RCV002379796, REVEL 0.17, AlphaMissense 0.07, Conflicting interpretations, Hereditary cancer-predisposing syndrome; not provided; Endometrial carcinoma
- S33R (p.Ser33Arg), rs772142059, ClinGen CA3327434, ClinVar RCV001050847, ClinVar RCV002374904, REVEL 0.28, CADD 21.80, Uncertain significance, not provided
- S33T (p.Ser33Thr), TOPMed rs1489972731, gnomAD rs1489972731, Likely benign
- S33A (p.Ser33Ala), gnomAD 5-80654822-GA-G, CADD 23.70
- S33S (p.Ser33Ser), gnomAD 5-80654826-C-T, CADD 12.50
- L34Q (p.Leu34Gln), rs2112797278, ClinGen CA360265303, ClinVar RCV001904787, Ensembl rs2112797278, AlphaMissense 0.06, MetaLR 0.73, Uncertain significance, not provided
- L34L (p.Leu34Leu), rs2112797274, gnomAD 5-80654827-C-T, CADD 11.80
- L34M (p.Leu34Met), gnomAD 5-80654827-C-A, REVEL 0.25, CADD 23.60
- L34P (p.Leu34Pro), gnomAD 5-80654828-T-C, REVEL 0.40, CADD 28.80
- K35N (p.Lys35Asn), Ensembl rs2112797284
- K35E (p.Lys35Glu), gnomAD 5-80654830-A-G, REVEL 0.37, CADD 24.30
- S36A (p.Ser36Ala), rs773158640, ClinGen CA3327435, ClinVar RCV000802127, ClinVar RCV002406778, REVEL 0.21, AlphaMissense 0.08, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- S36C (p.Ser36Cys), rs1470213668, ClinGen CA360265323, ClinVar RCV001009835, ClinVar RCV001220916, REVEL 0.30, AlphaMissense 0.14, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- S36F (p.Ser36Phe), rs1470213668, ClinGen CA360265324, ClinVar RCV002024120, ClinVar RCV004945899, AlphaMissense 0.14, MetaLR 0.51, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- S36P (p.Ser36Pro), rs773158640, ClinGen CA360265320, ClinVar RCV003368187, ExAC rs773158640, AlphaMissense 0.08, MetaLR 0.47, Uncertain significance, Hereditary cancer-predisposing syndrome
- S36Y (p.Ser36Tyr), rs1470213668, ClinGen CA360265322, ClinVar RCV002424253, AlphaMissense 0.14, MetaLR 0.51, Uncertain significance, Hereditary cancer-predisposing syndrome
- T37I (p.Thr37Ile), rs759573423, ClinGen CA3327436, ClinVar RCV003682477, ExAC rs759573423, REVEL 0.14, CADD 18.00, Uncertain significance, not provided
- T37N (p.Thr37Asn), rs759573423, ClinGen CA121287710, ClinVar RCV000796937, ClinVar RCV002424827, REVEL 0.11, CADD 16.90, Conflicting interpretations, Hereditary cancer-predisposing syndrome; not provided; Endometrial carcinoma
- T37S (p.Thr37Ser), gnomAD 5-80654836-A-T, REVEL 0.18, CADD 8.19
- T37T (p.Thr37Thr), gnomAD 5-80654838-C-G, CADD 1.46
- S38F (p.Ser38Phe), rs1184865419, ClinGen CA360265341, ClinVar RCV000802703, ClinVar RCV002458475, REVEL 0.15, CADD 16.30, Uncertain significance, Hereditary cancer-predisposing syndrome; not provided
- S38S (p.Ser38Ser), rs368081203, gnomAD 5-80654841-C-G, CADD 5.22
- S39A (p.Ser39Ala), rs1580538013, ClinGen CA360265346, ClinVar RCV001991168, ClinVar RCV002352694, REVEL 0.19, AlphaMissense 0.06, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome; Endometrial carcinoma
- S39C (p.Ser39Cys), rs2112797345, ClinGen CA360265348, ClinVar RCV002619652, AlphaMissense 0.10, MetaLR 0.41, Uncertain significance, not provided
- S39F (p.Ser39Phe), rs2112797345, ClinGen CA360265350, ClinVar RCV001998218, ClinVar RCV002331555, REVEL 0.34, AlphaMissense 0.10, Uncertain significance, not provided; Hereditary cancer-predisposing syndrome
- S39P (p.Ser39Pro), rs1580538013, ClinGen CA360265345, ClinVar RCV000807580, TOPMed rs1580538013, AlphaMissense 0.06, MetaLR 0.37, Uncertain significance, not provided
- S39T (p.Ser39Thr), rs1580538013, ClinGen CA360265343, ClinVar RCV000803297, ClinVar RCV002370129, REVEL 0.14, AlphaMissense 0.06, Uncertain significance, Familial adenomatous polyposis 4; not provided; Hereditary cancer-predisposing s
- S39S (p.Ser39Ser), rs762866873, gnomAD 5-80654844-C-T, CADD 8.55
Public MSH3 analysis runs
- MSH3 analysis run — MSH3 (3,034 variants) — completed 2026-08-21