FANCA (Fanconi anemia group A protein) variants and mutations
FANCA (also known as Fanconi anemia group A protein) is a human protein-coding gene encoding a fanconi anemia group A protein. It helps assemble the Fanconi-anemia core complex that monoubiquitinates FANCD2 and FANCI after DNA interstrand crosslinks stall replication. Biallelic loss-of-function variants are the most common cause of Fanconi anemia, with bone-marrow failure and cancer predisposition. This analysis covers 3,556 FANCA variants and mutations. Of these, 80% have computational variant effect predictions. Disease context includes Fanconi anemia complementation group A, Fanconi anemia, and acute myeloid leukemia. Example FANCA variants include M1?, M1C, and M1I.
Variant analysis overview
- Gene: FANCA
- Protein: Fanconi anemia group A protein
- UniProt accession: O15360
- Organism: Homo sapiens
- Variants analyzed: 3556
- Variant scope: all variants
- Completed: 2026-08-18
Variant and mutation evidence
- Variant composition: 3,282 unspecified-consequence records; 5 stop lost; 84 synonymous variants; 140 missense variants; 8 in-frame deletions; 4 stop-gained variants; 29 frameshift variants; 1 stop retained variant; 1 in-frame insertions; 2 substitution
- Prediction scores: 2,848 variants have prediction scores (80% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Fanconi anemia complementation group A, Fanconi anemia, acute myeloid leukemia, myelodysplastic syndrome, Abnormality of skin pigmentation, leukemia, hereditary disease, Abnormality of blood and blood-forming tissues, head and neck squamous cell carcinoma, prostate carcinoma, head and neck cancer, lung carcinoma.
Protein structure and variant hotspots
- Protein features: 1 post-translational modification sites.
- PTM context: 4 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 FANCA variants
Examples include M1?, M1C, M1I, M1L, M1R, M1T, M1V, S2A. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1?, rs769479800, ClinGen CA397484674, ClinVar RCV000672220, ClinVar RCV005240441, MetaLR 0.63, MetaSVM 0.31, Pathogenic
- M1C (p.Met1Cys), rs2544395419, ClinGen CA2580092356, ClinVar RCV003079207, Pathogenic
- M1I (p.Met1Ile), rs1555581729, ClinGen CA397484665, ClinVar RCV000671694, MetaLR 0.36, MetaSVM -0.31, Likely pathogenic, not provided
- M1L (p.Met1Leu), rs772751654, ClinGen CA397484677, ClinVar RCV000669511, ClinVar RCV001387726, MetaLR 0.40, MetaSVM -0.39, Pathogenic
- M1R (p.Met1Arg), rs769479800, ClinGen CA397484671, ClinVar RCV001202859, ClinVar RCV001256436, MetaLR 0.63, MetaSVM 0.31, Pathogenic
- M1T (p.Met1Thr), rs769479800, ClinGen CA8253279, ClinVar RCV000669920, ClinVar RCV000699054, MetaLR 0.63, MetaSVM 0.31, Pathogenic
- M1V (p.Met1Val), rs772751654, ClinGen CA397484679, ClinVar RCV000500370, ClinVar RCV001383377, MetaLR 0.40, MetaSVM -0.39, Pathogenic
- S2A (p.Ser2Ala), rs2041144813, ClinGen CA397484660, ClinVar RCV001925306, TOPMed rs2041144813, REVEL 0.15, CADD 2.52, Uncertain significance, Fanconi anemia
- S2C (p.Ser2Cys), rs928016876, ClinGen CA286612860, ClinVar RCV002257111, ClinVar RCV005008497, REVEL 0.30, CADD 21.50, Uncertain significance, Fanconi anemia; Fanconi anemia complementation group A
- S2F (p.Ser2Phe), rs928016876, ClinGen CA286612857, ClinVar RCV001035136, ClinVar RCV005021341, REVEL 0.30, CADD 21.90, Uncertain significance
- S2P (p.Ser2Pro), TOPMed rs2041144813, gnomAD rs2041144813, REVEL 0.12, CADD 5.86, Uncertain significance
- S2T (p.Ser2Thr), rs2041144813, ClinGen CA397484662, ClinVar RCV003237514, TOPMed rs2041144813, REVEL 0.15, CADD 7.72, Uncertain significance, not provided
- D3A (p.Asp3Ala), rs1183087111, ClinGen CA397484649, ClinVar RCV001945719, ClinVar RCV002558465, REVEL 0.10, CADD 0.01, Uncertain significance, Inborn genetic diseases; Fanconi anemia
- D3H (p.Asp3His), rs1246636933, ClinGen CA397484652, ClinVar RCV001349027, TOPMed rs1246636933, REVEL 0.19, CADD 16.90, Uncertain significance, Fanconi anemia
- D3N (p.Asp3Asn), TOPMed rs1246636933, gnomAD rs1246636933, REVEL 0.13, CADD 15.20, Uncertain significance
- D3Y (p.Asp3Tyr), rs1246636933, ClinGen CA397484654, ClinVar RCV000693528, TOPMed rs1246636933, REVEL 0.21, CADD 16.80, Uncertain significance
- S4* (p.Ser4Ter), rs1484087361, ClinGen CA397484637, ClinVar RCV000666866, ClinVar RCV001387348, CADD 36.00, Pathogenic
- S4L (p.Ser4Leu), rs1484087361, ClinGen CA397484635, ClinVar RCV003092069, ClinVar RCV005021557, REVEL 0.12, CADD 7.05, Uncertain significance, Fanconi anemia complementation group A; not provided; Fanconi anemia
- W5* (p.Trp5Ter), rs2041143697, ClinGen CA397484625, ClinVar RCV001256437, Ensembl rs2041143697, CADD 37.00, Pathogenic
- W5C (p.Trp5Cys), rs2143731999, ClinGen CA397484618, ClinVar RCV001372794, Ensembl rs2143731999, REVEL 0.09, CADD 14.30, Uncertain significance, Inborn genetic diseases
- W5G (p.Trp5Gly), gnomAD rs1204745684, REVEL 0.08, CADD 8.44
- W5R (p.Trp5Arg), gnomAD rs1204745684, REVEL 0.09, CADD 1.11
- V6F (p.Val6Phe), rs1348835311, ClinGen CA397484610, ClinVar RCV003524853, ClinVar RCV005014807, REVEL 0.22, CADD 10.50, Conflicting interpretations, Fanconi anemia; Fanconi anemia complementation group A
- V6A (p.Val6Ala), 1000Genomes rs1800282, ESP rs1800282, ExAC rs1800282, TOPMed rs1800282, REVEL 0.10, CADD 1.59, Benign
- V6D (p.Val6Asp), rs1800282, ClinGen CA159226, cosmic curated COSV66881, ClinVar RCV000120910, REVEL 0.16, CADD 14.30, Benign
- V6G (p.Val6Gly), rs1800282, ClinGen CA397484605, ClinVar RCV001935866, 1000Genomes rs1800282, REVEL 0.17, CADD 8.25, Uncertain significance, Fanconi anemia
- V6I (p.Val6Ile), TOPMed rs1348835311, gnomAD rs1348835311, REVEL 0.13, CADD 13.50, Likely benign
- P7A (p.Pro7Ala), rs780667753, ClinGen CA286612836, ClinVar RCV001362227, ClinVar RCV004980368, REVEL 0.07, CADD 2.85, Uncertain significance, Inborn genetic diseases; Fanconi anemia
- P7L (p.Pro7Leu), ExAC rs772712346, TOPMed rs772712346, gnomAD rs772712346, REVEL 0.11, CADD 6.88, Uncertain significance, Inborn genetic diseases
- P7Q (p.Pro7Gln), rs772712346, ClinGen CA8253277, ClinVar RCV001354987, ClinVar RCV002493817, REVEL 0.09, CADD 4.08, Uncertain significance, Inborn genetic diseases; Fanconi anemia; Fanconi anemia complementation group A
- P7R (p.Pro7Arg), rs772712346, ClinGen CA397484599, ClinVar RCV001879044, ClinVar RCV002551650, REVEL 0.08, CADD 2.47, Uncertain significance, not provided; Inborn genetic diseases; Fanconi anemia
- P7S (p.Pro7Ser), rs780667753, ClinGen CA8253278, cosmic curated COSV10891, ClinVar RCV001304743, REVEL 0.12, CADD 4.86, Conflicting interpretations, Fanconi anemia; Fanconi anemia complementation group A
- P7T (p.Pro7Thr), rs780667753, ClinGen CA397484602, ClinVar RCV003087659, ClinVar RCV005335647, REVEL 0.12, CADD 4.51, Uncertain significance, Inborn genetic diseases; Fanconi anemia
- N8I (p.Asn8Ile), rs757468756, ClinGen CA397484587, ClinVar RCV001202667, ClinVar RCV006347499, REVEL 0.15, CADD 1.25, Likely benign, in FANCA
- N8K (p.Asn8Lys), rs76275444, ClinGen CA159223, ClinVar RCV000120909, ClinVar RCV000371007, REVEL 0.06, CADD 0.54, Uncertain significance, Fanconi anemia
- N8S (p.Asn8Ser), rs757468756, ClinGen CA8253274, ClinVar RCV000470449, ClinVar RCV003237862, REVEL 0.07, CADD 0.00, Likely benign, in FANCA
- S9C (p.Ser9Cys), rs752776388, ClinGen CA286612810, ClinVar RCV002027416, ClinVar RCV004976181, REVEL 0.09, CADD 13.90, Uncertain significance, Inborn genetic diseases; Fanconi anemia
- S9F (p.Ser9Phe), rs752776388, ClinGen CA8253272, ClinVar RCV001247242, ClinVar RCV003387442, REVEL 0.15, CADD 14.70, Uncertain significance
- S9L (p.Ser9Leu), rs2143731757, ClinGen CA2573152816, ClinVar RCV002254864, ClinVar RCV003094180, Uncertain significance, Fanconi anemia complementation group A; Fanconi anemia
- S9P (p.Ser9Pro), ExAC rs777991781, TOPMed rs777991781, gnomAD rs777991781, REVEL 0.17, CADD 12.60
- S9Y (p.Ser9Tyr), rs752776388, ClinGen CA8253271, ClinVar RCV001931866, ExAC rs752776388, REVEL 0.16, CADD 13.70, Uncertain significance, Fanconi anemia
- A10T (p.Ala10Thr), rs965036018, ClinGen CA286612791, ClinVar RCV000803976, ClinVar RCV001120660, REVEL 0.08, CADD 11.80, Uncertain significance, Fanconi anemia; Inborn genetic diseases; Fanconi anemia complementation group A
- S11* (p.Ser11Ter), TOPMed rs1019317682, gnomAD rs1019317682, CADD 37.00
- S11L (p.Ser11Leu), TOPMed rs1019317682, gnomAD rs1019317682, REVEL 0.20, CADD 8.51
- S11P (p.Ser11Pro), Ensembl rs2143731639, REVEL 0.15, CADD 7.31
- G12A (p.Gly12Ala), TOPMed rs899666953, gnomAD rs899666953, REVEL 0.13, CADD 1.76
- G12D (p.Gly12Asp), TOPMed rs899666953, gnomAD rs899666953, REVEL 0.15, CADD 1.35
- G12S (p.Gly12Ser), Ensembl rs2041141674, REVEL 0.12, CADD 0.99, Uncertain significance, Fanconi anemia complementation group A
- G12V (p.Gly12Val), TOPMed rs899666953, gnomAD rs899666953, REVEL 0.19, CADD 4.38
- Q13E (p.Gln13Glu), rs766131144, ClinGen CA8253267, ClinVar RCV001543114, ClinVar RCV005341022, REVEL 0.13, CADD 0.09, Uncertain significance, Fanconi anemia; Inborn genetic diseases
- Q13H (p.Gln13His), rs1486155993, ClinGen CA397484523, ClinVar RCV001246397, ClinVar RCV004978207, REVEL 0.11, CADD 3.14, Likely benign
- Q13P (p.Gln13Pro), TOPMed rs1264855885, gnomAD rs1264855885, REVEL 0.13, CADD 0.12, Uncertain significance, Inborn genetic diseases
- Q13R (p.Gln13Arg), rs1264855885, ClinGen CA397484527, ClinVar RCV001323317, ClinVar RCV002493689, REVEL 0.10, CADD 0.07, Uncertain significance, Fanconi anemia; Inborn genetic diseases; not provided
- D14A (p.Asp14Ala), ExAC rs762648754, TOPMed rs762648754, gnomAD rs762648754, Benign
- D14E (p.Asp14Glu), rs750021837, ClinGen CA286612760, ClinVar RCV001957844, TOPMed rs750021837, REVEL 0.08, CADD 0.55, Uncertain significance, Fanconi anemia
- D14G (p.Asp14Gly), rs762648754, ClinGen CA8253266, ClinVar RCV000233505, ClinVar RCV000665027, REVEL 0.09, CADD 10.90, Benign
- D14N (p.Asp14Asn), gnomAD rs1239434360, REVEL 0.02, CADD 10.20
- D14Y (p.Asp14Tyr), gnomAD rs1239434360, REVEL 0.09, CADD 16.10
- P15A (p.Pro15Ala), TOPMed rs1567660116, REVEL 0.11, CADD 0.05
- P15L (p.Pro15Leu), rs2041140210, ClinGen CA397484496, ClinVar RCV003842716, ClinVar RCV006347928, REVEL 0.13, CADD 10.40, Uncertain significance, Inborn genetic diseases; Fanconi anemia
- P15S (p.Pro15Ser), TOPMed rs1567660116, REVEL 0.05, CADD 0.15
- G16E (p.Gly16Glu), rs908258968, ClinGen CA286612753, ClinVar RCV001242343, ClinVar RCV002564025, REVEL 0.14, CADD 7.65, Uncertain significance
- G16R (p.Gly16Arg), rs943773590, ClinGen CA16615039, ClinVar RCV000461194, ClinVar RCV002489041, REVEL 0.10, CADD 6.01, Uncertain significance, Fanconi anemia
- G17A (p.Gly17Ala), rs1326963514, ClinGen CA397484477, ClinVar RCV001927092, gnomAD rs1326963514, AlphaMissense 0.11, MetaLR 0.22, Uncertain significance, Fanconi anemia
- G17C (p.Gly17Cys), rs982957228, ClinGen CA286612747, ClinVar RCV002592468, ClinVar RCV004621725, REVEL 0.21, CADD 18.20, Uncertain significance, not provided; Fanconi anemia; Fanconi anemia complementation group A
- G17D (p.Gly17Asp), rs1326963514, ClinGen CA397484479, ClinVar RCV003522587, ClinVar RCV004585050, REVEL 0.23, AlphaMissense 0.11, Uncertain significance, Inborn genetic diseases; Fanconi anemia; not provided
- G17V (p.Gly17Val), rs1326963514, ClinGen CA397484476, ClinVar RCV003477201, ClinVar RCV005335779, REVEL 0.17, AlphaMissense 0.11, Uncertain significance, not provided; Inborn genetic diseases
- R18C (p.Arg18Cys), gnomAD rs1287222023, REVEL 0.08, CADD 13.70
- R18G (p.Arg18Gly), gnomAD rs1287222023
- R18H (p.Arg18His), rs772693509, ClinGen CA8253264, ClinVar RCV002589406, ClinVar RCV004973475, REVEL 0.14, CADD 8.44, Uncertain significance, Inborn genetic diseases; Fanconi anemia; Fanconi anemia complementation group A
- R18S (p.Arg18Ser), gnomAD rs1287222023, REVEL 0.16, CADD 8.94
- R19G (p.Arg19Gly), TOPMed rs1300733063, gnomAD rs1300733063, REVEL 0.35, CADD 19.20, Uncertain significance, Inborn genetic diseases
- R19Q (p.Arg19Gln), gnomAD rs1446775327, REVEL 0.28, CADD 19.60
- R19W (p.Arg19Trp), rs1300733063, ClinGen CA397484465, ClinVar RCV001299597, ClinVar RCV001760347, REVEL 0.29, CADD 22.70, Uncertain significance, Inborn genetic diseases; not provided; Fanconi anemia complementation group A
- R20G (p.Arg20Gly), Ensembl rs2143731084, REVEL 0.30, CADD 24.10
- R20K (p.Arg20Lys), rs376307136, ClinGen CA8253263, ClinVar RCV000306986, ClinVar RCV003477894, REVEL 0.06, CADD 11.80, Likely benign
- R20S (p.Arg20Ser), rs1321607523, ClinGen CA397484450, ClinVar RCV002800736, TOPMed rs1321607523, REVEL 0.29, CADD 18.00, Likely benign, Fanconi anemia
- A21G (p.Ala21Gly), TOPMed rs1300380574, gnomAD rs1300380574, REVEL 0.14, CADD 22.80
- A21P (p.Ala21Pro), gnomAD rs1459330448, REVEL 0.15, CADD 0.75, Uncertain significance, Inborn genetic diseases
- W22* (p.Trp22Ter), rs761341952, ClinGen CA8253262, cosmic curated COSV66880, ClinVar RCV000665314, CADD 43.00, Pathogenic
- W22G (p.Trp22Gly), Ensembl rs2143730974, REVEL 0.22, CADD 25.40
- W22R (p.Trp22Arg), Ensembl rs2143730974, REVEL 0.30, CADD 24.90
- W22S (p.Trp22Ser), rs761341952, ClinGen CA397484429, ClinVar RCV001879636, ExAC rs761341952, REVEL 0.21, CADD 23.80, Uncertain significance, Fanconi anemia
- A23D (p.Ala23Asp), rs776297241, ClinGen CA397484413, ClinVar RCV002923167, ClinVar RCV005343533, REVEL 0.07, CADD 19.30, Uncertain significance, Inborn genetic diseases; Fanconi anemia; Fanconi anemia complementation group A
- A23G (p.Ala23Gly), rs776297241, ClinGen CA397484412, ClinVar RCV001062373, ClinVar RCV002555811, REVEL 0.05, CADD 20.50, Likely benign
- A23T (p.Ala23Thr), TOPMed rs2041138122, REVEL 0.04, CADD 4.76, Uncertain significance, Inborn genetic diseases
- A23V (p.Ala23Val), rs776297241, ClinGen CA8253261, ClinVar RCV001327579, ClinVar RCV002504516, REVEL 0.03, CADD 16.50, Conflicting interpretations, Inborn genetic diseases; not provided; Fanconi anemia
- E24* (p.Glu24Ter), rs1311396994, ClinGen CA397484403, ClinVar RCV001234856, TOPMed rs1311396994, CADD 44.00, Pathogenic
- E24D (p.Glu24Asp), gnomAD rs1415989135, REVEL 0.11, CADD 23.00, Uncertain significance, Inborn genetic diseases
- E24G (p.Glu24Gly), Ensembl rs2143730844, REVEL 0.26, CADD 26.00, Uncertain significance, Inborn genetic diseases
- E24K (p.Glu24Lys), cosmic curated COSV66884, TOPMed rs1311396994, gnomAD rs1311396994, REVEL 0.19, CADD 24.40, Uncertain significance, Inborn genetic diseases
- E24V (p.Glu24Val), Ensembl rs2143730844, REVEL 0.31, CADD 24.70, Uncertain significance, Fanconi anemia
- L25M (p.Leu25Met), rs2544394660, ClinGen CA397484391, ClinVar RCV003215141, REVEL 0.39, CADD 24.00, Uncertain significance, Inborn genetic diseases
- L25R (p.Leu25Arg), rs886052489, ClinGen CA10648407, ClinVar RCV000395518, Ensembl rs886052489, AlphaMissense 0.44, MetaLR 0.75, Uncertain significance
- L26V (p.Leu26Val), rs2041137276, ClinGen CA397484385, ClinVar RCV001277949, Ensembl rs2041137276, REVEL 0.32, CADD 24.60, Uncertain significance, Fanconi anemia complementation group A
- A27G (p.Ala27Gly), ExAC rs765679791, TOPMed rs765679791, gnomAD rs765679791, REVEL 0.19, CADD 22.70, Uncertain significance, Inborn genetic diseases
- A27V (p.Ala27Val), rs765679791, ClinGen CA397483816, ClinVar RCV002760888, ExAC rs765679791, REVEL 0.17, CADD 22.80, Uncertain significance, Fanconi anemia
- G28* (p.Gly28Ter), rs2544390572, ClinGen CA2580092402, ClinVar RCV002881341, Pathogenic
- G28E (p.Gly28Glu), gnomAD rs1336535353, REVEL 0.40, CADD 24.30
- R29G (p.Arg29Gly), rs2143724622, ClinGen CA397483794, ClinVar RCV003477204, ClinVar RCV005567507, REVEL 0.53, CADD 24.50, Uncertain significance, not provided; Inborn genetic diseases
- R29K (p.Arg29Lys), ExAC rs764561391, TOPMed rs764561391, gnomAD rs764561391, REVEL 0.34, AlphaMissense 0.40, Uncertain significance, not provided; Inborn genetic diseases
- R29M (p.Arg29Met), rs764561391, ClinGen CA8253182, ClinVar RCV000822301, ClinVar RCV001274664, AlphaMissense 0.40, MetaLR 0.75, Uncertain significance
- R29S (p.Arg29Ser), ExAC rs760787108, TOPMed rs760787108, gnomAD rs760787108, REVEL 0.43, CADD 20.60, Uncertain significance, Inborn genetic diseases; Fanconi anemia
- V30D (p.Val30Asp), Ensembl rs2143724515
- V30F (p.Val30Phe), rs1160471115, ClinGen CA397483774, ClinVar RCV001037405, ClinVar RCV005338507, REVEL 0.25, CADD 21.20, Uncertain significance
- V30I (p.Val30Ile), rs1160471115, ClinGen CA397483772, ClinVar RCV001235093, ClinVar RCV005340708, REVEL 0.09, CADD 15.40, Uncertain significance
- K31* (p.Lys31Ter), rs2041101553, ClinGen CA397483745, ClinVar RCV001052431, Ensembl rs2041101553, AlphaMissense 0.15, MetaLR 0.27, Pathogenic
- K31E (p.Lys31Glu), Ensembl rs2041101553, REVEL 0.10, AlphaMissense 0.15, Pathogenic
- K31N (p.Lys31Asn), rs759630319, ExAC rs759630319, TOPMed rs759630319, gnomAD rs759630319, REVEL 0.09, CADD 14.10, Likely benign
- K31R (p.Lys31Arg), rs2041101472, ClinGen CA397483738, ClinVar RCV001338074, TOPMed rs2041101472, REVEL 0.04, CADD 10.30, Uncertain significance, Fanconi anemia; Inborn genetic diseases
- R32G (p.Arg32Gly), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- R32K (p.Arg32Lys), cosmic curated COSV10654, ExAC rs770984577, TOPMed rs770984577, gnomAD rs770984577, REVEL 0.04, CADD 6.42, Uncertain significance
- R32T (p.Arg32Thr), rs770984577, ClinGen CA8253176, ClinVar RCV000534176, ClinVar RCV005338225, REVEL 0.14, CADD 20.00, Uncertain significance
- E33* (p.Glu33Ter), rs2041101017, ClinGen CA397483696, ClinVar RCV003108462, ClinVar RCV004572846, CADD 36.00, Pathogenic
- E33G (p.Glu33Gly), rs372857989, ClinGen CA8253175, ClinVar RCV003080634, ClinVar RCV006342801, REVEL 0.03, CADD 18.40, Uncertain significance, Inborn genetic diseases; Fanconi anemia
- E33K (p.Glu33Lys), rs2041101017, ClinGen CA397483691, cosmic curated COSV66883, ClinVar RCV001948296, REVEL 0.03, CADD 13.60, Uncertain significance, Inborn genetic diseases; Fanconi anemia
- K34* (p.Lys34Ter), rs772858764, ClinGen CA8253174, ClinVar RCV000668648, ClinVar RCV001211107, CADD 35.00, Pathogenic
- K34R (p.Lys34Arg), ExAC rs769578985, TOPMed rs769578985, gnomAD rs769578985, REVEL 0.02, CADD 9.23
- Y35* (p.Tyr35Ter), rs747928827, ClinGen CA397483628, ClinVar RCV003468103, Likely pathogenic
- Y35C (p.Tyr35Cys), TOPMed rs1460652102, gnomAD rs1460652102, REVEL 0.02, CADD 0.14
- Y35S (p.Tyr35Ser), TOPMed rs1460652102, gnomAD rs1460652102, REVEL 0.04, CADD 0.06, Uncertain significance, Inborn genetic diseases
- N36K (p.Asn36Lys), TOPMed rs1326495878, gnomAD rs1326495878, REVEL 0.03, CADD 0.04
- N36S (p.Asn36Ser), rs1210459454, ClinGen CA397483607, ClinVar RCV001321312, ClinVar RCV004035031, REVEL 0.02, CADD 3.36, Uncertain significance, Inborn genetic diseases; Fanconi anemia
- P37L (p.Pro37Leu), cosmic curated COSV10532, ExAC rs754642453, gnomAD rs754642453, REVEL 0.10, CADD 17.20
- P37S (p.Pro37Ser), rs780833865, ClinGen CA8253171, ClinVar RCV001905007, ClinVar RCV002482523, REVEL 0.03, CADD 4.45, Uncertain significance, Inborn genetic diseases; Fanconi anemia; Fanconi anemia complementation group A
- E38A (p.Glu38Ala), rs957315731, ClinGen CA286612259, ClinVar RCV002923489, ClinVar RCV005019491, REVEL 0.07, CADD 13.70, Uncertain significance, Inborn genetic diseases; Fanconi anemia; Fanconi anemia complementation group A
- E38K (p.Glu38Lys), NCI-TCGA Cosmic COSV6687, cosmic curated COSV66879, REVEL 0.06, CADD 18.00, Variant assessed as somatic; moderate impact.
- E38Q (p.Glu38Gln), gnomAD rs2041099874, REVEL 0.09, CADD 18.60
- R39K (p.Arg39Lys), rs151089298, ClinGen CA8253167, ClinVar RCV000803891, ClinVar RCV001276569, REVEL 0.05, CADD 6.21, Likely benign
- R39S (p.Arg39Ser), TOPMed rs2041099499, Uncertain significance, Inborn genetic diseases
- R39T (p.Arg39Thr), rs151089298, ClinGen CA8253168, ClinVar RCV001801132, ClinVar RCV002541345, REVEL 0.05, CADD 6.20, Uncertain significance, Inborn genetic diseases; Fanconi anemia; not specified
- R39W (p.Arg39Trp), 1000Genomes rs17232091, ESP rs17232091, ExAC rs17232091, TOPMed rs17232091, Benign
- A40E (p.Ala40Glu), cosmic curated COSV66882, Ensembl rs563060518, Uncertain significance
- A40T (p.Ala40Thr), ExAC rs754419548, gnomAD rs754419548, REVEL 0.04, CADD 8.76, Uncertain significance, Inborn genetic diseases
- A40V (p.Ala40Val), rs563060518, ClinGen CA397483528, ClinVar RCV001318609, ClinVar RCV002493667, REVEL 0.05, CADD 0.79, Uncertain significance, Inborn genetic diseases; Fanconi anemia; Fanconi anemia complementation group A
- Q41* (p.Gln41Ter), ExAC rs764533094, gnomAD rs764533094, CADD 37.00, Uncertain significance
- Q41E (p.Gln41Glu), rs764533094, ClinGen CA397483519, ClinVar RCV001302030, ExAC rs764533094, REVEL 0.05, CADD 14.40, Uncertain significance, Fanconi anemia; Inborn genetic diseases
- Q41H (p.Gln41His), NCI-TCGA Cosmic COSV1012, REVEL 0.04, CADD 13.60, Uncertain significance, Inborn genetic diseases
- Q41P (p.Gln41Pro), TOPMed rs1305209243, gnomAD rs1305209243, REVEL 0.17, CADD 13.60
- K42N (p.Lys42Asn), ExAC rs756432890, gnomAD rs756432890, REVEL 0.01, CADD 15.50, Likely benign
- L43* (p.Leu43Ter), rs1158456786, ClinGen CA397483468, ClinVar RCV001256539, ClinVar RCV003523089, CADD 37.00, Pathogenic
- K44N (p.Lys44Asn), cosmic curated COSV10654, 1000Genomes rs200428379, ExAC rs200428379, TOPMed rs200428379, REVEL 0.04, CADD 18.60, Likely benign
- K44R (p.Lys44Arg), TOPMed rs912608081, gnomAD rs912608081, REVEL 0.04, CADD 8.88
- K44T (p.Lys44Thr), TOPMed rs912608081, gnomAD rs912608081, Uncertain significance, Inborn genetic diseases
- E45* (p.Glu45Ter), ESP rs142990858, ExAC rs142990858, TOPMed rs142990858, gnomAD rs142990858, Pathogenic
- E45G (p.Glu45Gly), gnomAD rs1443801693, REVEL 0.08, CADD 17.00
- E45K (p.Glu45Lys), rs142990858, ClinGen CA8253162, ClinVar RCV000457577, ClinVar RCV005010357, REVEL 0.05, CADD 18.00, Pathogenic
- S46* (p.Ser46Ter), rs2041098068, ClinGen CA397483405, ClinVar RCV001939493, Ensembl rs2041098068, AlphaMissense 0.20, MetaLR 0.18, Pathogenic
- S46L (p.Ser46Leu), rs2041098068, ClinGen CA397483403, cosmic curated COSV10469, ClinVar RCV001068775, REVEL 0.12, AlphaMissense 0.20, Pathogenic
- S46P (p.Ser46Pro), rs2041098152, ClinGen CA397483414, ClinVar RCV001914479, NCI-TCGA TCGA novel, REVEL 0.16, CADD 21.40, Uncertain significance, Inborn genetic diseases; Fanconi anemia
- A47P (p.Ala47Pro), rs1190475225, ClinGen CA397483388, ClinVar RCV003524462, TOPMed rs1190475225, REVEL 0.28, CADD 24.80, Uncertain significance, Fanconi anemia
- A47T (p.Ala47Thr), rs1190475225, ClinGen CA397483390, cosmic curated COSV10971, ClinVar RCV000799065, REVEL 0.17, CADD 24.60, Uncertain significance
- A47V (p.Ala47Val), NCI-TCGA Cosmic COSV6688, cosmic curated COSV66881, Ensembl rs2041097798, Uncertain significance, Inborn genetic diseases
- R49C (p.Arg49Cys), TOPMed rs929925295, gnomAD rs929925295, REVEL 0.04, CADD 21.30, Uncertain significance, Inborn genetic diseases
- R49G (p.Arg49Gly), rs929925295, ClinGen CA286612195, ClinVar RCV000689475, ClinVar RCV003478407, REVEL 0.02, CADD 18.70, Uncertain significance
- R49H (p.Arg49His), rs766611067, ClinGen CA8253159, ClinVar RCV002904191, ClinVar RCV006342624, REVEL 0.02, CADD 1.54, Uncertain significance, Fanconi anemia; Inborn genetic diseases
- R49S (p.Arg49Ser), rs929925295, ClinGen CA397483365, ClinVar RCV002923172, TOPMed rs929925295, REVEL 0.01, CADD 14.20, Uncertain significance, Fanconi anemia
- L50F (p.Leu50Phe), TOPMed rs2041097480, REVEL 0.13, CADD 25.30
- L50P (p.Leu50Pro), rs2143723758, ClinGen CA397483347, ClinVar RCV002024830, Ensembl rs2143723758, REVEL 0.47, CADD 27.50, Uncertain significance, Fanconi anemia
- L51M (p.Leu51Met), NCI-TCGA Cosmic COSV6688, cosmic curated COSV66881, Variant assessed as somatic; moderate impact.
- L51V (p.Leu51Val), rs1287320584, ClinGen CA397483341, ClinVar RCV002258492, gnomAD rs1287320584, REVEL 0.16, CADD 23.40, Uncertain significance, Fanconi anemia
- R52* (p.Arg52Ter), rs773159223, ClinGen CA8253157, ClinVar RCV000409456, ClinVar RCV001245476, CADD 36.00, Pathogenic
- R52L (p.Arg52Leu), NCI-TCGA Cosmic COSV6688, cosmic curated COSV66883, Variant assessed as somatic; moderate impact.
- R52P (p.Arg52Pro), NCI-TCGA Cosmic COSV6688, cosmic curated COSV66883, Variant assessed as somatic; moderate impact.
- R52Q (p.Arg52Gln), rs2143723686, ClinGen CA397483327, cosmic curated COSV66881, ClinVar RCV003062962, AlphaMissense 0.10, MetaLR 0.13, Uncertain significance, Fanconi anemia
- S53G (p.Ser53Gly), ExAC rs61757383, TOPMed rs61757383, gnomAD rs61757383, REVEL 0.04, CADD 0.31, Uncertain significance
- S53R (p.Ser53Arg), TOPMed rs1437967277, gnomAD rs1437967277, REVEL 0.07, CADD 13.20, Uncertain significance, not provided
- S53T (p.Ser53Thr), rs761614742, ClinGen CA8253155, ClinVar RCV001911226, ClinVar RCV005343111, REVEL 0.05, CADD 16.00, Uncertain significance, Inborn genetic diseases; Fanconi anemia
- H54Y (p.His54Tyr), rs1383572316, ClinGen CA397483308, ClinVar RCV001240545, gnomAD rs1383572316, REVEL 0.07, CADD 22.70, Uncertain significance
- Q55* (p.Gln55Ter), rs1555580427, ClinGen CA397483293, ClinVar RCV000665360, ClinVar RCV001387347, CADD 37.00, Pathogenic
- Q55R (p.Gln55Arg), Ensembl rs2143723600
- D56A (p.Asp56Ala), rs2544389615, ClinGen CA397483277, ClinVar RCV003638066, Uncertain significance, Fanconi anemia
- D56N (p.Asp56Asn), rs1360481164, ClinGen CA397483282, cosmic curated COSV66881, ClinVar RCV001323193, REVEL 0.03, CADD 2.62, Conflicting interpretations, Inborn genetic diseases; Fanconi anemia
- L57Q (p.Leu57Gln), gnomAD rs1351638021, REVEL 0.19, CADD 23.90
- L57V (p.Leu57Val), ESP rs368828271, ExAC rs368828271, TOPMed rs368828271, gnomAD rs368828271, REVEL 0.09, CADD 0.14, Likely benign
- N58* (p.Asn58Ter), rs2041096125, ClinGen CA1139664997, ClinVar RCV001256540, ClinVar RCV003635953, Pathogenic
- N58D (p.Asn58Asp), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- N58I (p.Asn58Ile), ExAC rs746705026, gnomAD rs746705026, REVEL 0.08, CADD 6.24, Uncertain significance, Fanconi anemia complementation group A
- A59S (p.Ala59Ser), ExAC rs779519169, gnomAD rs779519169, REVEL 0.02, CADD 12.50
- A59V (p.Ala59Val), gnomAD rs1165398420, REVEL 0.02, CADD 15.70
Public FANCA analysis runs
- FANCA analysis run — FANCA (3,556 variants) — completed 2026-08-18