FAT2 (Protocadherin Fat 2) variants and mutations
FAT2 (also known as Protocadherin Fat 2) is a human protein-coding gene encoding a protocadherin Fat 2 protein. Its annotated function is involved in the regulation of cell migration. It is annotated at the cell membrane. This analysis covers 9,375 FAT2 variants and mutations. Of these, 46% have computational variant effect predictions. Disease context includes Autosomal dominant cerebellar ataxia type 1, vaginal cancer, and metabolic disease. Example FAT2 variants include T2A, T2I, and T2S.
Variant analysis overview
- Gene: FAT2
- Protein: Protocadherin Fat 2
- UniProt accession: Q9NYQ8
- Organism: Homo sapiens
- Variants analyzed: 9375
- Variant scope: all variants
- Completed: 2026-09-10
Variant and mutation evidence
- Variant composition: 9,330 unspecified-consequence records; 184 missense variants; 153 synonymous variants; 18 frameshift variants; 3 in-frame insertions; 15 stop-gained variants; 2 in-frame deletions; 1 splice-region variants
- Prediction scores: 4,348 variants have prediction scores (46% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Autosomal dominant cerebellar ataxia type 1, vaginal cancer, metabolic disease, brain aneurysm, Paralysis, cerebellar ataxia, gastric cancer, non-small cell lung carcinoma, esophageal adenocarcinoma, breast carcinoma, placental abruption, breast cancer.
Protein structure and variant hotspots
- Protein features: 1 transmembrane segments; 35 domains; 38 post-translational modification sites.
- Structural context: 7,749 variants have structural context.
- PTM context: 52 variants overlap post-translational modification sites.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, gnomAD constraint, Open Targets, MaveDB, LitVar.
Notable FAT2 variants
Examples include T2A, T2I, T2S, I3T, A4V, L5V, G7C, G7S. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- T2A (p.Thr2Ala), TOPMed rs1758412829
- T2I (p.Thr2Ile), rs746643917, ClinGen CA3522506, ClinVar RCV004386019, ExAC rs746643917, REVEL 0.09, CADD 11.30, Likely benign, not specified
- T2S (p.Thr2Ser), TOPMed rs1758412829
- I3T (p.Ile3Thr), TOPMed rs1758412565, REVEL 0.17, CADD 16.50
- A4V (p.Ala4Val), NCI-TCGA Cosmic COSV5581, Ensembl rs2127651050, Uncertain significance, not specified
- L5V (p.Leu5Val), rs1488441223, ClinGen CA361819006, ClinVar RCV003427718, ClinVar RCV004289495, REVEL 0.07, CADD 2.63, Conflicting interpretations, not specified; not provided
- G7C (p.Gly7Cys), NCI-TCGA Cosmic COSV5582, Ensembl rs1758411982, Variant assessed as somatic; moderate impact.
- G7S (p.Gly7Ser), Ensembl rs1758411982
- G7V (p.Gly7Val), TOPMed rs1426002430, gnomAD rs1426002430, REVEL 0.24, CADD 10.80
- G7A (p.Gly7Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- F8L (p.Phe8Leu), Ensembl rs2127651027
- F8S (p.Phe8Ser), TOPMed rs1758411485
- A9T (p.Ala9Thr), Ensembl rs2127651024, REVEL 0.07, CADD 5.04
- A9V (p.Ala9Val), ExAC rs772010774, gnomAD rs772010774, REVEL 0.08, CADD 2.37
- F11Y (p.Phe11Tyr), Ensembl rs1758411135
- L12F (p.Leu12Phe), ExAC rs779038265, gnomAD rs779038265, REVEL 0.09, CADD 13.40, Uncertain significance, not provided
- L13F (p.Leu13Phe), TOPMed rs1213943178, gnomAD rs1213943178, REVEL 0.08, CADD 11.80
- H14N (p.His14Asn), Ensembl rs1758410129
- A16E (p.Ala16Glu), rs200899973, ClinGen CA361818783, ClinVar RCV003670098, ClinVar RCV004756525, AlphaMissense 0.07, MetaLR 0.16, Uncertain significance, not provided
- A16S (p.Ala16Ser), ExAC rs756260868, TOPMed rs756260868, gnomAD rs756260868, REVEL 0.05, CADD 4.06
- A16T (p.Ala16Thr), ExAC rs756260868, TOPMed rs756260868, gnomAD rs756260868
- A16V (p.Ala16Val), rs200899973, ClinGen CA3522500, ClinVar RCV002933006, ClinVar RCV004067052, REVEL 0.04, CADD 0.15, Conflicting interpretations, not specified; not provided
- T17C (p.Thr17Cys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- T17A (p.Thr17Ala), NCI-TCGA Cosmic COSV9994, Variant assessed as somatic; moderate impact.
- T17I (p.Thr17Ile), ExAC rs751761404, TOPMed rs751761404, gnomAD rs751761404, REVEL 0.15, CADD 13.20
- T17N (p.Thr17Asn), ExAC rs751761404, TOPMed rs751761404, gnomAD rs751761404, REVEL 0.16, CADD 10.40
- C18R (p.Cys18Arg), Ensembl rs2127650975
- E19D (p.Glu19Asp), TOPMed rs1297368746, Likely benign
- K20R (p.Lys20Arg), rs766681033, ClinGen CA3522496, ClinVar RCV003121821, ExAC rs766681033, REVEL 0.11, CADD 15.60, Conflicting interpretations, not provided
- P21A (p.Pro21Ala), TOPMed rs1438206863, gnomAD rs1438206863, REVEL 0.06, CADD 5.54
- P21R (p.Pro21Arg), TOPMed rs1020501563, REVEL 0.13, CADD 7.56
- P21S (p.Pro21Ser), TOPMed rs1438206863, gnomAD rs1438206863
- L22V (p.Leu22Val), Ensembl rs764497436
- E23K (p.Glu23Lys), ExAC rs758801976, TOPMed rs758801976, gnomAD rs758801976, REVEL 0.16, CADD 14.60
- E23Q (p.Glu23Gln), ExAC rs758801976, TOPMed rs758801976, gnomAD rs758801976, REVEL 0.09, CADD 10.50
- G24E (p.Gly24Glu), Ensembl rs2127650939
- I25M (p.Ile25Met), TOPMed rs1758408189, REVEL 0.16, CADD 4.45
- S27P (p.Ser27Pro), Ensembl rs878881071
- S28Y (p.Ser28Tyr), ExAC rs750925126, gnomAD rs750925126, REVEL 0.23, CADD 24.40
- S29F (p.Ser29Phe), TOPMed rs997947284, gnomAD rs997947284, REVEL 0.24, CADD 23.90
- A30P (p.Ala30Pro), ExAC rs765790212, gnomAD rs765790212, REVEL 0.08, CADD 6.83
- A30T (p.Ala30Thr), ExAC rs765790212, gnomAD rs765790212, REVEL 0.06, CADD 11.80
- A30V (p.Ala30Val), Ensembl rs2127650893
- W31* (p.Trp31Ter), NCI-TCGA TCGA novel, Ensembl rs2127650885, CADD 37.00, Variant assessed as somatic; high impact.
- W31C (p.Trp31Cys), Ensembl rs2127650885
- H32L (p.His32Leu), Ensembl rs2127650875
- H32Q (p.His32Gln), TOPMed rs1758407061
- H32Y (p.His32Tyr), Ensembl rs1758407226
- F33C (p.Phe33Cys), gnomAD rs1422081459, REVEL 0.78, CADD 29.20
- T34C (p.Thr34Cys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- T34I (p.Thr34Ile), ExAC rs762319956, gnomAD rs762319956
- T34K (p.Thr34Lys), ExAC rs762319956, gnomAD rs762319956, REVEL 0.60, CADD 27.40
- H35D (p.His35Asp), gnomAD rs1477860288, REVEL 0.29, CADD 26.30
- H35Q (p.His35Gln), TOPMed rs1278802569, gnomAD rs1278802569, REVEL 0.07, CADD 5.88, Uncertain significance, not specified
- H35R (p.His35Arg), ExAC rs776136665, gnomAD rs776136665, REVEL 0.18, CADD 23.00
- H35Y (p.His35Tyr), gnomAD rs1477860288, REVEL 0.32, CADD 25.80
- S36F (p.Ser36Phe), rs574821566, 1000Genomes rs574821566, ExAC rs574821566, TOPMed rs574821566, REVEL 0.12, CADD 18.00, Uncertain significance, not provided
- S36Y (p.Ser36Tyr), 1000Genomes rs574821566, ExAC rs574821566, TOPMed rs574821566, gnomAD rs574821566, REVEL 0.07, CADD 15.70, Uncertain significance, not specified
- H37Q (p.His37Gln), 1000Genomes rs555362084, ExAC rs555362084, TOPMed rs555362084, gnomAD rs555362084, REVEL 0.02, CADD 8.70
- H37Y (p.His37Tyr), TOPMed rs1217735526
- A40P (p.Ala40Pro), Ensembl rs2127650805
- A40V (p.Ala40Val), Ensembl rs763399208, REVEL 0.04, CADD 15.70
- T41I (p.Thr41Ile), ExAC rs771965604, TOPMed rs771965604, gnomAD rs771965604, REVEL 0.37, CADD 25.40, Uncertain significance, not provided
- I42L (p.Ile42Leu), TOPMed rs1284038964, gnomAD rs1284038964
- I42V (p.Ile42Val), TOPMed rs1284038964, gnomAD rs1284038964, REVEL 0.24, CADD 23.10
- Y43* (p.Tyr43Ter), gnomAD rs1256200973, CADD 33.00
- Y43C (p.Tyr43Cys), gnomAD rs1456422687, REVEL 0.27, CADD 23.20
- E44* (p.Glu44Ter), gnomAD rs1259896022
- E44K (p.Glu44Lys), rs1259896022, NCI-TCGA Cosmic COSV5583, gnomAD rs1259896022, REVEL 0.81, CADD 27.00, Variant assessed as somatic; moderate impact.
- S46F (p.Ser46Phe), gnomAD rs1220614830, REVEL 0.64, CADD 28.40
- P48A (p.Pro48Ala), ExAC rs745727798, gnomAD rs745727798, REVEL 0.20, CADD 22.50
- P48L (p.Pro48Leu), rs1758403542, ClinGen CA361817925, ClinVar RCV003854436, Ensembl rs1758403542, AlphaMissense 0.34, MetaLR 0.49, Uncertain significance, not provided
- T50I (p.Thr50Ile), ESP rs369232293, ExAC rs369232293, TOPMed rs369232293, gnomAD rs369232293, REVEL 0.64, CADD 25.50
- Y51C (p.Tyr51Cys), Ensembl rs1758403109, REVEL 0.55, CADD 27.50
- V52E (p.Val52Glu), TOPMed rs1758402745, gnomAD rs1758402745, REVEL 0.90, CADD 27.50
- S54C (p.Ser54Cys), rs1226846110, ClinGen CA361817820, ClinVar RCV003047957, gnomAD rs1226846110, REVEL 0.59, CADD 25.80, Uncertain significance, not provided
- E56K (p.Glu56Lys), 1000Genomes rs569701735, TOPMed rs569701735, gnomAD rs569701735, REVEL 0.11, CADD 19.40, Uncertain significance, not specified; not provided
- M58I (p.Met58Ile), ExAC rs781293341, gnomAD rs781293341, REVEL 0.35, CADD 24.60
- M58R (p.Met58Arg), ExAC rs749188814, gnomAD rs749188814, REVEL 0.62, CADD 26.00
- G59D (p.Gly59Asp), Ensembl rs2127650717
- I60T (p.Ile60Thr), Ensembl rs2127650714
- L62F (p.Leu62Phe), TOPMed rs1191832137, REVEL 0.17, CADD 21.90
- A63E (p.Ala63Glu), 1000Genomes rs192641187, ExAC rs192641187, TOPMed rs192641187, gnomAD rs192641187, REVEL 0.12, CADD 4.98, Uncertain significance
- A63P (p.Ala63Pro), 1000Genomes rs201874812, ExAC rs201874812, TOPMed rs201874812, gnomAD rs201874812
- A63T (p.Ala63Thr), rs201874812, NCI-TCGA Cosmic COSV5582, 1000Genomes rs201874812, ExAC rs201874812, REVEL 0.05, CADD 0.04, Variant assessed as somatic; moderate impact.
- A63V (p.Ala63Val), rs192641187, ClinGen CA3522478, ClinVar RCV003697608, ClinVar RCV005335856, REVEL 0.11, CADD 4.95, Uncertain significance, not specified; not provided
- E64K (p.Glu64Lys), rs2127650688, ClinGen CA361817693, ClinVar RCV004386004, AlphaMissense 0.08, MetaLR 0.14, Uncertain significance, not specified
- E64Q (p.Glu64Gln), Ensembl rs2127650688, Uncertain significance
- P65A (p.Pro65Ala), Ensembl rs1758400145, REVEL 0.42, CADD 23.90
- P65L (p.Pro65Leu), rs779251901, ClinGen CA3522476, ClinVar RCV003688818, ExAC rs779251901, REVEL 0.25, CADD 22.20, Uncertain significance, not provided
- Q66* (p.Gln66Ter), NCI-TCGA TCGA novel, Ensembl rs2127650672, Variant assessed as somatic; high impact.
- Q66P (p.Gln66Pro), Ensembl rs1554134050
- Q66R (p.Gln66Arg), Ensembl rs1554134050
- W67R (p.Trp67Arg), Ensembl rs2127650650
- A68S (p.Ala68Ser), Ensembl rs1581456000
- A68V (p.Ala68Val), rs150175247, ClinGen CA3522475, ClinVar RCV002903893, ClinVar RCV004066140, REVEL 0.06, CADD 19.10, Uncertain significance, not specified; not provided
- A68C (p.Ala68Cys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- V69A (p.Val69Ala), ExAC rs763633455, gnomAD rs763633455, REVEL 0.37, CADD 23.90
- V69E (p.Val69Glu), ExAC rs763633455, gnomAD rs763633455
- V69M (p.Val69Met), rs116402695, ClinGen CA3522474, ClinVar RCV000966975, 1000Genomes rs116402695, REVEL 0.25, CADD 24.50, Benign, not provided
- R70K (p.Arg70Lys), rs1199210774, NCI-TCGA Cosmic COSV5582, gnomAD rs1199210774, REVEL 0.11, CADD 9.63, Variant assessed as somatic; moderate impact.
- R70S (p.Arg70Ser), Ensembl rs2127650630
- R70W (p.Arg70Trp), TOPMed rs779353820, REVEL 0.37, CADD 22.90
- Y71* (p.Tyr71Ter), Ensembl rs2127650627, CADD 37.00
- Y71D (p.Tyr71Asp), Ensembl rs2127650628
- R72G (p.Arg72Gly), ESP rs147574119, ExAC rs147574119, TOPMed rs147574119, gnomAD rs147574119, Likely benign
- R72P (p.Arg72Pro), ESP rs371264512, ExAC rs371264512, gnomAD rs371264512, Uncertain significance
- R72Q (p.Arg72Gln), rs371264512, ClinGen CA3522471, ClinVar RCV003777530, ClinVar RCV004345452, REVEL 0.35, CADD 23.80, Uncertain significance, not specified; not provided
- R72W (p.Arg72Trp), rs147574119, ClinGen CA3522472, ClinVar RCV001417501, ESP rs147574119, REVEL 0.42, CADD 26.10, Likely benign, not provided
- I74T (p.Ile74Thr), gnomAD rs1323792300, REVEL 0.15, CADD 23.60
- S75C (p.Ser75Cys), NCI-TCGA Cosmic COSV5582, Ensembl rs2127650608, Variant assessed as somatic; moderate impact.
- S75P (p.Ser75Pro), gnomAD rs1758397625
- G76V (p.Gly76Val), Ensembl rs2127650606
- D77E (p.Asp77Glu), Ensembl rs2127650605
- V78E (p.Val78Glu), Ensembl rs2127650600, REVEL 0.07, CADD 13.10
- A79D (p.Ala79Asp), Ensembl rs2127650594
- A79G (p.Ala79Gly), Ensembl rs2127650594
- A79S (p.Ala79Ser), Ensembl rs2127650597
- A79T (p.Ala79Thr), Ensembl rs2127650597
- N80D (p.Asn80Asp), Ensembl rs1581455918
- N80K (p.Asn80Lys), 1000Genomes rs202197076, ExAC rs202197076, TOPMed rs202197076, gnomAD rs202197076
- N80S (p.Asn80Ser), ExAC rs767339469, gnomAD rs767339469, REVEL 0.06, CADD 13.40
- V81E (p.Val81Glu), Ensembl rs1758397065
- V81L (p.Val81Leu), Ensembl rs1758397178
- K83E (p.Lys83Glu), TOPMed rs1758396947
- T84S (p.Thr84Ser), Ensembl rs2127650569
- T84C (p.Thr84Cys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- E85Q (p.Glu85Gln), Ensembl rs2127650562
- E85V (p.Glu85Val), gnomAD rs1311851678, REVEL 0.79, CADD 28.60
- E86D (p.Glu86Asp), Ensembl rs2127650544, REVEL 0.15, CADD 18.20
- E86G (p.Glu86Gly), TOPMed rs1758396589, REVEL 0.30, CADD 27.10
- E86K (p.Glu86Lys), Ensembl rs2127650553
- Y87* (p.Tyr87Ter), gnomAD rs1448203653, CADD 8.77
- Y87C (p.Tyr87Cys), 1000Genomes rs561734616, REVEL 0.26, CADD 23.20
- V88L (p.Val88Leu), gnomAD rs1394345298, REVEL 0.09, CADD 14.10
- V89A (p.Val89Ala), Ensembl rs1561879162, REVEL 0.34, CADD 26.40
- G90C (p.Gly90Cys), Ensembl rs2127650508
- G90D (p.Gly90Asp), rs145029623, ClinGen CA3522468, ClinVar RCV002904212, ClinVar RCV003943554, REVEL 0.72, CADD 26.20, Conflicting interpretations, Spinocerebellar ataxia 45; not provided; not specified
- C93A (p.Cys93Ala), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- C93F (p.Cys93Phe), gnomAD rs1350180601, REVEL 0.62, CADD 26.10
- C93S (p.Cys93Ser), gnomAD rs1350180601
- C93Y (p.Cys93Tyr), gnomAD rs1350180601
- F94L (p.Phe94Leu), Ensembl rs2127650487
- R96T (p.Arg96Thr), Ensembl rs2127650484
- R98S (p.Arg98Ser), ExAC rs770882451, gnomAD rs770882451, REVEL 0.51, CADD 23.80
- T99I (p.Thr99Ile), ExAC rs773073059, gnomAD rs773073059, REVEL 0.66, CADD 26.10
- T99K (p.Thr99Lys), ExAC rs773073059, gnomAD rs773073059, REVEL 0.72, CADD 26.70
- S101I (p.Ser101Ile), Ensembl rs970470171
- S101N (p.Ser101Asn), Ensembl rs970470171
- S102I (p.Ser102Ile), Ensembl rs2127650456
- N103I (p.Asn103Ile), Ensembl rs1758394489
- T104I (p.Thr104Ile), gnomAD rs1758394271, REVEL 0.33, CADD 26.10
- A105P (p.Ala105Pro), TOPMed rs1758394034, gnomAD rs1758394034
- A105S (p.Ala105Ser), TOPMed rs1758394034, gnomAD rs1758394034, REVEL 0.29, CADD 23.80
- A105T (p.Ala105Thr), TOPMed rs1758394034, gnomAD rs1758394034, REVEL 0.39, CADD 26.10
- L106V (p.Leu106Val), Ensembl rs2127650438
- L107P (p.Leu107Pro), Ensembl rs1758393797, REVEL 0.85, CADD 28.40
- N108S (p.Asn108Ser), gnomAD rs1265157758, REVEL 0.53, CADD 25.80
- R109G (p.Arg109Gly), ExAC rs747116146, TOPMed rs747116146, gnomAD rs747116146, REVEL 0.64, CADD 25.60, Uncertain significance, not specified
- E110G (p.Glu110Gly), TOPMed rs1758393363, gnomAD rs1758393363, REVEL 0.81, CADD 29.10
- V111M (p.Val111Met), ExAC rs751812178, gnomAD rs751812178, REVEL 0.26, CADD 25.80
- R112* (p.Arg112Ter), rs1403035184, TOPMed rs1403035184, gnomAD rs1403035184, CADD 37.00, Variant assessed as somatic; high impact.
- R112Q (p.Arg112Gln), TOPMed rs1266048047, gnomAD rs1266048047, REVEL 0.06, CADD 13.90
- D113G (p.Asp113Gly), ExAC rs772213660, TOPMed rs772213660, gnomAD rs772213660, REVEL 0.35, CADD 26.40
- D113H (p.Asp113His), TOPMed rs1011979822, gnomAD rs1011979822, REVEL 0.45, CADD 26.10, Uncertain significance, not specified
- S114T (p.Ser114Thr), Ensembl rs2127650387
- Y115H (p.Tyr115His), ExAC rs746116409, gnomAD rs746116409, REVEL 0.69, CADD 27.40
- Y115S (p.Tyr115Ser), Ensembl rs1581455686
- T116C (p.Thr116Cys), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- T116I (p.Thr116Ile), ExAC rs754343645, TOPMed rs754343645, gnomAD rs754343645, REVEL 0.08, CADD 17.70
- T116P (p.Thr116Pro), ExAC rs757607748, gnomAD rs757607748, REVEL 0.36, CADD 23.60
- T116S (p.Thr116Ser), ExAC rs754343645, TOPMed rs754343645, gnomAD rs754343645
- L117F (p.Leu117Phe), Ensembl rs2127650366
- L117I (p.Leu117Ile), Ensembl rs2127650366
- I118M (p.Ile118Met), Ensembl rs2127650357
- I118N (p.Ile118Asn), TOPMed rs1240135610, gnomAD rs1240135610, REVEL 0.18, CADD 24.10
- I119L (p.Ile119Leu), TOPMed rs1758391472, gnomAD rs1758391472, REVEL 0.10, CADD 14.60
- I119N (p.Ile119Asn), ExAC rs778215535, gnomAD rs778215535
- I119T (p.Ile119Thr), ExAC rs778215535, gnomAD rs778215535, REVEL 0.51, CADD 23.80, Uncertain significance, not specified
- Q120* (p.Gln120Ter), ExAC rs77944146, TOPMed rs77944146, gnomAD rs77944146, CADD 37.00
Public FAT2 analysis runs
- FAT2 analysis run — FAT2 (9,375 variants) — completed 2026-09-10