F9 (Coagulation factor IX) variants and mutations
F9 (also known as Coagulation factor IX) is a human protein-coding gene encoding a coagulation factor IX protein. Its activated form combines with factor VIIIa to efficiently activate factor X during coagulation. Pathogenic loss-of-function variants cause X-linked hemophilia B, with bleeding severity determined largely by residual factor IX activity. This analysis covers 905 F9 variants and mutations. Of these, 62% have computational variant effect predictions. Disease context includes hemophilia B, hemophilia A, and thrombophilia, X-linked, due to factor 9 defect. Example F9 variants include M1?, Q2L, and Q2P.
Variant analysis overview
- Gene: F9
- Protein: Coagulation factor IX
- UniProt accession: P00740
- Organism: Homo sapiens
- Variants analyzed: 905
- Variant scope: all variants
- Completed: 2026-08-19
Variant and mutation evidence
- Variant composition: 714 unspecified-consequence records; 84 missense variants; 91 synonymous variants; 4 stop-gained variants; 5 splice-region variants; 1 frameshift variants; 1 in-frame deletions; 5 substitution
- Prediction scores: 561 variants have prediction scores (62% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: hemophilia B, hemophilia A, thrombophilia, X-linked, due to factor 9 defect, x-linked warfarin sensitivity, hemorrhage, venous thromboembolism, hemophilia b leyden, hemophilia, Venous thrombosis, cartilage disease, moderately severe hemophilia B, Abnormality of coagulation.
Protein structure and variant hotspots
- Protein features: 4 domains; 35 binding sites; 25 post-translational modification sites.
- Structural context: 711 variants have structural context.
- PTM context: 47 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 F9 variants
Examples include M1?, Q2L, Q2P, Q2R, R3C, R3H, R3S, R3P. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1?, NCI-TCGA Cosmic COSV9949, cosmic curated COSV99496, Variant assessed as somatic; high impact.
- Q2L (p.Gln2Leu), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- Q2P (p.Gln2Pro), Ensembl rs1603263356
- Q2R (p.Gln2Arg), gnomAD X-139530769-A-G, REVEL 0.23, MetaLR 0.34
- R3C (p.Arg3Cys), rs766259893, ClinGen CA10529705, NCI-TCGA Cosmic COSV9949, cosmic curated COSV99496, REVEL 0.16, MetaLR 0.49, Benign, Hereditary factor IX deficiency disease
- R3H (p.Arg3His), rs148060786, ClinGen CA10529706, ClinVar RCV000861920, ClinVar RCV001081775, REVEL 0.53, MetaLR 0.40, Benign, Hereditary factor IX deficiency disease
- R3S (p.Arg3Ser), rs766259893, ClinGen CA10529704, ClinVar RCV003781836, 1000Genomes rs766259893, REVEL 0.12, MetaLR 0.41, Likely benign, Thrombophilia, X-linked, due to factor 9 defect; Hereditary factor IX deficiency
- R3P (p.Arg3Pro), gnomAD X-139530772-G-C, REVEL 0.10, MetaLR 0.49
- R3R (p.Arg3Arg), rs1335753805, gnomAD X-139530773-C-G, CADD 1.95
- V4A (p.Val4Ala), Ensembl rs1927324698
- V4M (p.Val4Met), ExAC rs758078866, TOPMed rs758078866, gnomAD rs758078866, REVEL 0.27, MetaLR 0.36
- N5I (p.Asn5Ile), gnomAD X-139530778-A-T, REVEL 0.15, MetaLR 0.57
- N5N (p.Asn5Asn), rs1281720529, gnomAD X-139530779-C-T, CADD 1.51
- N5K (p.Asn5Lys), gnomAD X-139530779-C-A, REVEL 0.13, MetaLR 0.50
- M6I (p.Met6Ile), NCI-TCGA Cosmic COSV5438, cosmic curated COSV54380, gnomAD rs1927324989, REVEL 0.15, MetaLR 0.55, Variant assessed as somatic; moderate impact.
- M6V (p.Met6Val), Ensembl rs1603263368
- M6R (p.Met6Arg), gnomAD X-139530781-T-G, REVEL 0.32, MetaLR 0.51
- I7F (p.Ile7Phe), rs150190385, ClinGen CA10529708, cosmic curated COSV54381, ClinVar RCV000291239, REVEL 0.58, MetaLR 0.58, Benign, Hereditary factor IX deficiency disease
- I7M (p.Ile7Met), NCI-TCGA Cosmic COSV9949, cosmic curated COSV99496, REVEL 0.27, MetaLR 0.62, Variant assessed as somatic; moderate impact.
- M8T (p.Met8Thr), rs770709443, NCI-TCGA Cosmic COSV5437, cosmic curated COSV54378, ExAC rs770709443, REVEL 0.64, MetaLR 0.69, Variant assessed as somatic; moderate impact.
- M8V (p.Met8Val), ExAC rs746835466, gnomAD rs746835466, REVEL 0.53, MetaLR 0.68, Uncertain significance, F9-related disorder
- A9E (p.Ala9Glu), ExAC rs781184105, TOPMed rs781184105, gnomAD rs781184105, Uncertain significance
- A9G (p.Ala9Gly), ExAC rs781184105, TOPMed rs781184105, gnomAD rs781184105, REVEL 0.40, MetaLR 0.69, Uncertain significance, F9-related disorder
- E10Q (p.Glu10Gln), gnomAD X-139530792-G-C, REVEL 0.19, MetaLR 0.59
- S11L (p.Ser11Leu), NCI-TCGA Cosmic COSV9949, cosmic curated COSV99496, Variant assessed as somatic; moderate impact.
- S11T (p.Ser11Thr), rs387906480, ClinGen CA255447, ClinVar RCV000011401, TOPMed rs387906480, REVEL 0.21, MetaLR 0.53, Conflicting interpretations, Hereditary factor IX deficiency disease
- S11P (p.Ser11Pro), gnomAD X-139530795-T-C, REVEL 0.35, MetaLR 0.55
- P12L (p.Pro12Leu), ExAC rs745849451, TOPMed rs745849451, gnomAD rs745849451, REVEL 0.21, MetaLR 0.46
- P12Q (p.Pro12Gln), ExAC rs745849451, TOPMed rs745849451, gnomAD rs745849451
- P12T (p.Pro12Thr), NCI-TCGA Cosmic COSV5438, cosmic curated COSV54382, Variant assessed as somatic; moderate impact.
- P12P (p.Pro12Pro), gnomAD X-139530800-A-G, CADD 6.98
- G13A (p.Gly13Ala), Ensembl rs1240713875, REVEL 0.14, MetaLR 0.48
- L14F (p.Leu14Phe), gnomAD X-139530804-C-T, REVEL 0.39, MetaLR 0.77
- L14L (p.Leu14Leu), rs1927326529, gnomAD X-139530806-C-T, CADD 8.57
- I15N (p.Ile15Asn), rs1927326780, ClinGen CA414434301, ClinVar RCV001202940, Ensembl rs1927326780, AlphaMissense 0.27, MetaLR 0.67, Uncertain significance, Hereditary factor IX deficiency disease; Thrombophilia, X-linked, due to factor
- I15V (p.Ile15Val), cosmic curated COSV10876, NCI-TCGA TCGA novel, TOPMed rs1927326656, Variant assessed as somatic; moderate impact.
- I15T (p.Ile15Thr), gnomAD X-139530808-T-C, REVEL 0.29, MetaLR 0.66
- T16A (p.Thr16Ala), NCI-TCGA Cosmic COSV5437, cosmic curated COSV54378, REVEL 0.23, MetaLR 0.54, Variant assessed as somatic; moderate impact.
- T16T (p.Thr16Thr), rs768833956, gnomAD X-139530812-C-A, CADD 9.54
- I17M (p.Ile17Met), ExAC rs774612303, TOPMed rs774612303, gnomAD rs774612303, REVEL 0.35, MetaLR 0.63, Benign, in HEMB
- I17N (p.Ile17Asn), UniProt VAR 006521, Pathogenic, in HEMB
- I17I (p.Ile17Ile), rs774612303, gnomAD X-139530815-C-T, CADD 10.50
- C18R (p.Cys18Arg), rs387906474, ClinGen CA255310, ClinVar RCV000011314, Ensembl rs387906474, AlphaMissense 0.65, MetaLR 0.69, Pathogenic, Hereditary factor IX deficiency disease
- C18S (p.Cys18Ser), gnomAD rs944920007, REVEL 0.28, MetaLR 0.56
- C18Y (p.Cys18Tyr), gnomAD rs944920007
- C18C (p.Cys18Cys), rs1337284408, gnomAD X-139530818-C-T, CADD 9.90
- L19I (p.Leu19Ile), Ensembl rs1927327744, REVEL 0.36, MetaLR 0.70
- L20S (p.Leu20Ser), UniProt VAR 073975, Pathogenic, Hereditary factor IX deficiency disease; Thrombophilia, X-linked, due to factor
- L20L (p.Leu20Leu), rs762082146, gnomAD X-139530824-A-G, CADD 5.38
- G21V (p.Gly21Val), gnomAD X-139530826-G-T, REVEL 0.58, MetaLR 0.62
- Y22C (p.Tyr22Cys), ExAC rs772442973, gnomAD rs772442973, REVEL 0.30, MetaLR 0.63
- L23I (p.Leu23Ile), gnomAD rs1194004315, REVEL 0.40, MetaLR 0.70
- L23P (p.Leu23Pro), rs1927328297, ClinGen CA414434403, ClinVar RCV003484572, TOPMed rs1927328297, AlphaMissense 0.30, MetaLR 0.82, Pathogenic, Hereditary factor IX deficiency disease
- L23R (p.Leu23Arg), gnomAD X-139530832-T-G, REVEL 0.70, MetaLR 0.82
- L24L (p.Leu24Leu), gnomAD X-139530836-C-A, CADD 9.14
- S25N (p.Ser25Asn), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- A26T (p.Ala26Thr), rs1569481567, ClinGen CA414434434, ClinVar RCV002854227, TOPMed rs1569481567, AlphaMissense 0.12, MetaLR 0.53, Uncertain significance, Inborn genetic diseases
- A26A (p.Ala26Ala), gnomAD X-139530842-T-A, CADD 7.12
- E27K (p.Glu27Lys), rs387906475, ClinGen CA255313, ClinVar RCV000011316, ClinVar RCV004689413, AlphaMissense 0.11, MetaLR 0.71, Uncertain significance, not specified
- E27Q (p.Glu27Gln), Ensembl rs387906475, Pathogenic
- E27V (p.Glu27Val), Ensembl rs387906476
- C28R (p.Cys28Arg), rs387906481, ClinGen CA255450, ClinVar RCV000011402, ClinVar RCV001851793, AlphaMissense 0.25, MetaLR 0.58, Pathogenic, Thrombophilia, X-linked, due to factor 9 defect; Hereditary factor IX deficiency
- C28Y (p.Cys28Tyr), UniProt VAR 017343, REVEL 0.63, MetaLR 0.66, Pathogenic, Hereditary factor IX deficiency disease
- T29I (p.Thr29Ile), rs1927329129, ClinGen CA414434494, ClinVar RCV003050656, ClinVar RCV004812464, AlphaMissense 0.15, MetaLR 0.67, Likely pathogenic, Hereditary factor IX deficiency disease
- T29A (p.Thr29Ala), gnomAD X-139530849-A-G, REVEL 0.25, MetaLR 0.36
- T29K (p.Thr29Lys), gnomAD X-139530850-C-A, REVEL 0.37, MetaLR 0.59
- V30D (p.Val30Asp), gnomAD rs1191327804, REVEL 0.92, MetaLR 0.91
- V30I (p.Val30Ile), rs1603263395, ClinGen CA414434500, ClinVar RCV000806960, ClinVar RCV004577534, AlphaMissense 0.12, MetaLR 0.88, Likely pathogenic, Hereditary factor IX deficiency disease
- V30L (p.Val30Leu), rs1603263395, ClinGen CA414434503, ClinVar RCV000852238, Ensembl rs1603263395, AlphaMissense 0.12, MetaLR 0.88, Likely pathogenic, Hereditary factor IX deficiency disease
- F31F (p.Phe31Phe), gnomAD X-139537014-T-C, CADD 8.61
- L32F (p.Leu32Phe), NCI-TCGA Cosmic COSV5438, cosmic curated COSV54382, Variant assessed as somatic; moderate impact.
- L32S (p.Leu32Ser), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- L32H (p.Leu32His), gnomAD X-139537016-T-A, REVEL 0.78, MetaLR 0.89
- D33H (p.Asp33His), Ensembl rs2148356001, REVEL 0.64, MetaLR 0.70
- D33N (p.Asp33Asn), gnomAD X-139537018-G-A, REVEL 0.18, MetaLR 0.59
- H34L (p.His34Leu), gnomAD X-139537022-A-T, REVEL 0.30, MetaLR 0.55
- H34Q (p.His34Gln), gnomAD X-139537023-T-A, REVEL 0.26, MetaLR 0.36
- E35D (p.Glu35Asp), ExAC rs779083411, gnomAD rs779083411, REVEL 0.24, MetaLR 0.65
- E35G (p.Glu35Gly), Ensembl rs928672798
- E35K (p.Glu35Lys), rs756148155, NCI-TCGA Cosmic COSV5438, cosmic curated COSV54381, ExAC rs756148155, AlphaMissense 0.07, MetaLR 0.70, Variant assessed as somatic; moderate impact.
- E35E (p.Glu35Glu), gnomAD X-139537026-A-G, CADD 8.86
- N36D (p.Asn36Asp), rs1169714103, ClinGen CA414435396, ClinVar RCV001393734, TOPMed rs1169714103, REVEL 0.15, MetaLR 0.46, Likely benign, Hereditary factor IX deficiency disease; Thrombophilia, X-linked, due to factor
- N36N (p.Asn36Asn), rs184837275, gnomAD X-139537029-C-T, CADD 7.52
- A37T (p.Ala37Thr), rs367569299, ClinGen CA10529736, cosmic curated COSV54381, ClinVar RCV000990955, REVEL 0.95, MetaLR 0.95, Benign; association, Hereditary factor IX deficiency disease; Thrombophilia, X-linked, due to factor
- A37V (p.Ala37Val), rs1327097914, ClinGen CA414435437, ClinVar RCV000011406, UniProt VAR 083981, REVEL 0.94, MetaLR 0.95, Pathogenic, Warfarin sensitivity, X-linked
- N38K (p.Asn38Lys), 1000Genomes rs745353370, ExAC rs745353370, TOPMed rs745353370, gnomAD rs745353370, REVEL 0.28, MetaLR 0.60, Benign
- N38D (p.Asn38Asp), gnomAD X-139537033-A-G, REVEL 0.26, MetaLR 0.53
- N38N (p.Asn38Asn), rs745353370, gnomAD X-139537035-C-T, CADD 7.26
- K39R (p.Lys39Arg), rs200505648, ClinGen CA10529738, ClinVar RCV001504446, 1000Genomes rs200505648, REVEL 0.34, MetaLR 0.64, Likely benign, Thrombophilia, X-linked, due to factor 9 defect; Hereditary factor IX deficiency
- L41R (p.Leu41Arg), rs371373268, ClinGen CA10529739, ClinVar RCV001035253, ClinVar RCV001827212, REVEL 0.94, MetaLR 0.94, Uncertain significance, Hereditary factor IX deficiency disease; Thrombophilia, X-linked, due to factor
- L41L (p.Leu41Leu), gnomAD X-139537044-G-C, CADD 8.31
- N42Y (p.Asn42Tyr), gnomAD X-139537045-A-T, REVEL 0.22, MetaLR 0.60
- R43L (p.Arg43Leu), rs1275708479, ClinGen CA414435545, ClinVar RCV001812346, ClinVar RCV004753261, AlphaMissense 0.22, MetaLR 0.91, Pathogenic, Hereditary factor IX deficiency disease; not specified; Thrombophilia, X-linked
- R43Q (p.Arg43Gln), rs1275708479, ClinGen CA414435539, cosmic curated COSV54380, ClinVar RCV001000159, AlphaMissense 0.22, MetaLR 0.91, Pathogenic/Likely pathogenic, Hereditary factor IX deficiency disease; Thrombophilia, X-linked, due to factor
- R43W (p.Arg43Trp), rs1603264205, ClinGen CA414435537, NCI-TCGA Cosmic COSV5437, cosmic curated COSV54378, REVEL 0.69, MetaLR 0.89, Pathogenic, Hereditary factor IX deficiency disease; not specified; Thrombophilia, X-linked
- P44S (p.Pro44Ser), rs776894974, ClinGen CA10529740, ClinVar RCV001403195, ClinVar RCV001831431, REVEL 0.14, MetaLR 0.51, Likely benign, Hereditary factor IX deficiency disease
- P44P (p.Pro44Pro), gnomAD X-139537053-A-G, CADD 10.90
- K45E (p.Lys45Glu), TOPMed rs1927492604
- K45N (p.Lys45Asn), UniProt VAR 006527, Pathogenic, in HEMB
- K45K (p.Lys45Lys), gnomAD X-139537056-G-A, CADD 9.69
- R46K (p.Arg46Lys), NCI-TCGA Cosmic COSV9949, cosmic curated COSV99497, Variant assessed as somatic; moderate impact., in HEMB
- R46S (p.Arg46Ser), rs2520744315, ClinVar RCV000011311, UniProt VAR 006528, Pathogenic, Hereditary factor IX deficiency disease
- R46T (p.Arg46Thr), UniProt VAR 006529, Uncertain significance, Thrombophilia, X-linked, due to factor 9 defect
- Y47* (p.Tyr47Ter), rs1556435929, ClinGen CA414435626, ClinVar RCV000497960, Ensembl rs1556435929, Likely pathogenic
- Y47Y (p.Tyr47Tyr), rs1556435929, gnomAD X-139537062-T-C, CADD 5.70
- N48D (p.Asn48Asp), rs1927493197, ClinGen CA414435632, NCI-TCGA Cosmic COSV5438, cosmic curated COSV54380, AlphaMissense 0.31, MetaLR 0.98, Pathogenic, Thrombophilia, X-linked, due to factor 9 defect; Hereditary factor IX deficiency
- N48I (p.Asn48Ile), UniProt VAR 006530, Pathogenic, in HEMB
- N48T (p.Asn48Thr), Ensembl rs2148356070
- N48Y (p.Asn48Tyr), rs1927493197, ClinGen CA414435634, ClinVar RCV001265098, TOPMed rs1927493197, AlphaMissense 0.31, MetaLR 0.98, Pathogenic, Hereditary factor IX deficiency disease
- S49* (p.Ser49Ter), NCI-TCGA Cosmic COSV9949, cosmic curated COSV99496, TOPMed rs1927493396, Variant assessed as somatic; high impact., in HEMB
- S49L (p.Ser49Leu), TOPMed rs1927493396
- S49P (p.Ser49Pro), UniProt VAR 006531, Pathogenic, in HEMB
- S49S (p.Ser49Ser), rs1927493537, gnomAD X-139537068-A-C, CADD 8.89
- G50A (p.Gly50Ala), rs1229048705, ClinGen CA414435680, ClinVar RCV002032039, TOPMed rs1229048705, REVEL 0.75, MetaLR 0.99, Likely pathogenic, Hereditary factor IX deficiency disease; Thrombophilia, X-linked, due to factor
- G50D (p.Gly50Asp), cosmic curated COSV10725, TOPMed rs1229048705, gnomAD rs1229048705, Likely pathogenic, Thrombophilia, X-linked, due to factor 9 defect; Hereditary factor IX deficiency
- G50S (p.Gly50Ser), rs1556435940, ClinGen CA414435668, ClinVar RCV000551608, Ensembl rs1556435940, REVEL 0.82, MetaLR 0.98, Pathogenic, Hereditary factor IX deficiency disease; Thrombophilia, X-linked, due to factor
- L52S (p.Leu52Ser), UniProt VAR 017344, Likely pathogenic, Hereditary factor IX deficiency disease
- L52L (p.Leu52Leu), rs1470729875, gnomAD X-139537075-T-C, CADD 2.65
- E53A (p.Glu53Ala), UniProt VAR 006532, Pathogenic, in HEMB
- E53D (p.Glu53Asp), cosmic curated COSV10804, NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact., in HEMB
- E54D (p.Glu54Asp), UniProt VAR 073976, Uncertain significance, in HEMB
- E54G (p.Glu54Gly), UniProt VAR 006533, Pathogenic, in HEMB
- E54V (p.Glu54Val), rs1569481966, ClinGen CA414435761, ClinVar RCV000756129, Ensembl rs1569481966, AlphaMissense 0.77, MetaLR 0.98, Likely pathogenic, not provided
- F55C (p.Phe55Cys), UniProt VAR 006534, Pathogenic, in HEMB
- F55I (p.Phe55Ile), rs759987427, ClinGen CA10529741, ClinVar RCV001380937, ClinVar RCV005040248, REVEL 0.65, AlphaMissense 0.13, Pathogenic/Likely pathogenic, Hereditary factor IX deficiency disease; Thrombophilia, X-linked, due to factor
- F55L (p.Phe55Leu), rs759987427, ClinGen CA414435768, ClinVar RCV002011308, ClinVar RCV006280903, AlphaMissense 0.13, MetaLR 0.86, Uncertain significance, Thrombophilia, X-linked, due to factor 9 defect; Hereditary factor IX deficiency
- F55S (p.Phe55Ser), TOPMed rs1927494889
- V56A (p.Val56Ala), cosmic curated COSV54381, TOPMed rs1927495027, REVEL 0.40, MetaLR 0.89
- V56F (p.Val56Phe), NCI-TCGA Cosmic COSV9949, cosmic curated COSV99496, Variant assessed as somatic; moderate impact.
- Q57* (p.Gln57Ter), rs137852223, ClinGen CA255307, ClinVar RCV000011313, TOPMed rs137852223, AlphaMissense 0.09, MetaLR 0.89, Pathogenic
- Q57E (p.Gln57Glu), TOPMed rs137852223, gnomAD rs137852223, REVEL 0.56, AlphaMissense 0.09, Pathogenic
- Q57Q (p.Gln57Gln), gnomAD X-139537092-A-G, CADD 9.35
- G58A (p.Gly58Ala), rs1927495541, UniProt VAR 006535, TOPMed rs1927495541, AlphaMissense 0.49, MetaLR 1.00, Pathogenic, in HEMB
- G58E (p.Gly58Glu), rs1927495541, UniProt VAR 073977, TOPMed rs1927495541, AlphaMissense 0.49, MetaLR 1.00, Uncertain significance, in HEMB
- G58R (p.Gly58Arg), rs1927495402, UniProt VAR 006536, TOPMed rs1927495402, AlphaMissense 0.69, MetaLR 1.00, Pathogenic, in HEMB
- G58G (p.Gly58Gly), rs1233835025, gnomAD X-139537095-G-A, CADD 5.16
- N59K (p.Asn59Lys), rs139089559, ClinGen CA10529742, ClinVar RCV001810604, ESP rs139089559, REVEL 0.89, MetaLR 0.98, Uncertain significance, not specified
- N59N (p.Asn59Asn), rs139089559, gnomAD X-139537098-C-T, CADD 4.22
- L60P (p.Leu60Pro), TOPMed rs1927496089, Uncertain significance, Hereditary factor IX deficiency disease; Thrombophilia, X-linked, due to factor
- L60F (p.Leu60Phe), gnomAD X-139537099-C-T, REVEL 0.86, MetaLR 0.99
- E61G (p.Glu61Gly), rs2148356134, ClinGen CA414435890, ClinVar RCV002018373, Ensembl rs2148356134, AlphaMissense 0.49, MetaLR 0.99, Uncertain significance, Thrombophilia, X-linked, due to factor 9 defect; Hereditary factor IX deficiency
- E61Q (p.Glu61Gln), cosmic curated COSV54379, ExAC rs774915238, gnomAD rs774915238
- E61R (p.Glu61Arg), NCI-TCGA Cosmic COSV5438, Variant assessed as somatic; high impact.
- R62I (p.Arg62Ile), NCI-TCGA Cosmic COSV5438, cosmic curated COSV54382, Variant assessed as somatic; moderate impact.
- E63* (p.Glu63Ter), NCI-TCGA Cosmic COSV5438, cosmic curated COSV54381, Variant assessed as somatic; high impact.
- E63D (p.Glu63Asp), rs762447016, ClinGen CA414435937, ClinVar RCV001001243, ExAC rs762447016, AlphaMissense 0.95, MetaLR 1.00, Uncertain significance, not specified
- E63E (p.Glu63Glu), rs762447016, gnomAD X-139537110-A-G, AlphaMissense 0.95, MetaLR 1.00
- C64F (p.Cys64Phe), TOPMed rs1330779541, Pathogenic
- C64R (p.Cys64Arg), rs137852224, ClinGen CA336130710, ClinVar RCV001001440, ClinVar RCV004587010, AlphaMissense 0.99, MetaLR 1.00, Likely pathogenic, not specified; Hereditary factor IX deficiency disease
- C64Y (p.Cys64Tyr), rs1330779541, ClinGen CA414435945, ClinVar RCV001390294, TOPMed rs1330779541, AlphaMissense 0.97, MetaLR 1.00, Pathogenic, Hereditary factor IX deficiency disease; Thrombophilia, X-linked, due to factor
- C64C (p.Cys64Cys), rs1261374056, gnomAD X-139537113-T-C, CADD 3.45
- M65I (p.Met65Ile), rs763568424, ExAC rs763568424, gnomAD rs763568424, NCI-TCGA Cosmic COSV5438, REVEL 0.27, MetaLR 0.70, Variant assessed as somatic; moderate impact.
- M65T (p.Met65Thr), rs1447797624, ClinGen CA414435964, ClinVar RCV003121521, TOPMed rs1447797624, REVEL 0.32, MetaLR 0.90, Uncertain significance, Thrombophilia, X-linked, due to factor 9 defect; Hereditary factor IX deficiency
- M65V (p.Met65Val), gnomAD X-139537114-A-G, REVEL 0.26, MetaLR 0.77
- E66K (p.Glu66Lys), rs1569481975, ClinGen CA414435972, NCI-TCGA Cosmic COSV9949, cosmic curated COSV99496, AlphaMissense 0.82, MetaLR 0.99, Likely pathogenic, Hereditary factor IX deficiency disease
- E66V (p.Glu66Val), UniProt VAR 006538, Likely pathogenic, Hereditary factor IX deficiency disease
- E67K (p.Glu67Lys), rs1410080079, UniProt VAR 006539, TOPMed rs1410080079, AlphaMissense 0.84, MetaLR 1.00, Pathogenic, in HEMB
- E67V (p.Glu67Val), Ensembl rs1927497607
- K68R (p.Lys68Arg), TOPMed rs1364356358, REVEL 0.29, MetaLR 0.83, Uncertain significance, Hereditary factor IX deficiency disease
- K68K (p.Lys68Lys), gnomAD X-139537125-G-A, CADD 6.74
- K68N (p.Lys68Asn), gnomAD X-139537125-G-C, REVEL 0.42, MetaLR 0.93
- C69* (p.Cys69Ter), TOPMed rs1927498102
- C69R (p.Cys69Arg), NCI-TCGA Cosmic COSV5438, cosmic curated COSV54380, Variant assessed as somatic; moderate impact.
- C69S (p.Cys69Ser), rs2148356172, ClinGen CA414436026, ClinVar RCV001812550, Ensembl rs2148356172, AlphaMissense 0.99, MetaLR 1.00, Likely pathogenic, not provided
- C69Y (p.Cys69Tyr), rs1927497998, ClinGen CA414436035, ClinVar RCV001810624, Ensembl rs1927497998, AlphaMissense 0.97, MetaLR 1.00, Pathogenic, not provided
- S70R (p.Ser70Arg), TOPMed rs1927498230
- S70T (p.Ser70Thr), ExAC rs751200298, gnomAD rs751200298, REVEL 0.37, MetaLR 0.92
- F71L (p.Phe71Leu), TOPMed rs1385472584, Uncertain significance, Hereditary factor IX deficiency disease; Thrombophilia, X-linked, due to factor
- F71S (p.Phe71Ser), rs1927498407, UniProt VAR 006540, TOPMed rs1927498407, AlphaMissense 0.45, MetaLR 0.96, Pathogenic, in HEMB
- E72* (p.Glu72Ter), rs1927498635, ClinGen CA414436088, ClinVar RCV001265101, Ensembl rs1927498635, Pathogenic
- E73* (p.Glu73Ter), TOPMed rs137852225
- E73K (p.Glu73Lys), rs137852225, UniProt VAR 006541, TOPMed rs137852225, AlphaMissense 0.81, MetaLR 1.00, Pathogenic, in HEMB
- E73V (p.Glu73Val), rs137852226, ClinGen CA255316, ClinVar RCV000011317, UniProt VAR 006542, AlphaMissense 0.90, MetaLR 0.99, Pathogenic, Hereditary factor IX deficiency disease
- A74V (p.Ala74Val), Ensembl rs868314037
- A74A (p.Ala74Ala), gnomAD X-139537143-A-G, CADD 8.55
- R75* (p.Arg75Ter), rs137852227, ClinGen CA340993, NCI-TCGA Cosmic COSV5437, cosmic curated COSV54378, Pathogenic, in HEMB
- R75Q (p.Arg75Gln), rs137852228, ClinGen CA255318, ClinVar RCV000011319, ClinVar RCV000757260, REVEL 0.90, MetaLR 0.98, Pathogenic, Hereditary factor IX deficiency disease
- E76* (p.Glu76Ter), NCI-TCGA Cosmic COSV5438, NCI-TCGA Cosmic COSV9949, cosmic curated COSV99496, Variant assessed as somatic; high impact.
- E76K (p.Glu76Lys), rs1603264236, ClinGen CA414436158, ClinVar RCV001001434, Ensembl rs1603264236, AlphaMissense 0.85, MetaLR 0.99, Pathogenic, not specified
- E76E (p.Glu76Glu), gnomAD X-139537149-A-G, CADD 8.72
Public F9 analysis runs
- F9 analysis run — F9 (905 variants) — completed 2026-08-19