NCF2 (Neutrophil cytosol factor 2) variants and mutations
NCF2 (also known as Neutrophil cytosol factor 2) is a human protein-coding gene encoding a neutrophil cytosol factor 2 protein. It helps activate the phagocyte NADPH oxidase by assembling with membrane and cytosolic partners during the respiratory burst. Biallelic loss-of-function variants cause chronic granulomatous disease and impaired killing of catalase-positive bacteria and fungi. This analysis covers 898 NCF2 variants and mutations. Of these, 89% have computational variant effect predictions. Disease context includes chronic granulomatous disease, systemic lupus erythematosus, and celiac disease. Example NCF2 variants include M1L, M1T, and S2A.
Variant analysis overview
- Gene: NCF2
- Protein: Neutrophil cytosol factor 2
- UniProt accession: P19878
- Organism: Homo sapiens
- Variants analyzed: 898
- Variant scope: all variants
- Completed: 2026-08-22
Variant and mutation evidence
- Variant composition: 697 unspecified-consequence records; 1 stop retained variant; 74 synonymous variants; 4 in-frame insertions; 27 frameshift variants; 9 stop-gained variants; 80 missense variants; 5 splice-region variants; 2 in-frame deletions; 1 substitution
- Prediction scores: 803 variants have prediction scores (89% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: chronic granulomatous disease, systemic lupus erythematosus, celiac disease, rheumatoid arthritis, autoimmune disorder of musculoskeletal system, systemic sclerosis, myositis disease, cutaneous lupus erythematosus, lupus erythematosus, hereditary disease, smoking initiation, Bicuspid aortic valve.
Protein structure and variant hotspots
- Protein features: 3 domains; 2 post-translational modification sites.
- Structural context: 377 variants have structural context.
- PTM context: 2 variants overlap post-translational modification sites.
- Experimental data: 75 protein positions have experimental scores. Source: NCF2 SH3 domain domainome 1.0, NCF2 PB1 domain domainome 1.0.
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 NCF2 variants
Examples include M1L, M1T, S2A, S2F, V4G, E5G, A6G, A6S. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1L (p.Met1Leu), rs780810631, ClinGen CA343685515, ClinVar RCV002002386, MetaLR 0.61, MetaSVM 0.28, Conflicting interpretations, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- M1T (p.Met1Thr), rs2528040305, ClinGen CA343685509, ClinVar RCV003498798, Pathogenic, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- S2A (p.Ser2Ala), rs987968831, ClinGen CA33993127, ClinVar RCV003091115, ClinVar RCV005675111, REVEL 0.17, MetaLR 0.49, Uncertain significance, Inborn genetic diseases; Granulomatous disease, chronic, autosomal recessive, cy
- S2F (p.Ser2Phe), cosmic curated COSV10083
- V4G (p.Val4Gly), Ensembl rs1572181770
- E5G (p.Glu5Gly), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- A6G (p.Ala6Gly), gnomAD rs1404705904
- A6S (p.Ala6Ser), Ensembl rs1673585904
- A6V (p.Ala6Val), cosmic curated COSV62316
- I7M (p.Ile7Met), rs995270345, ClinGen CA33993122, ClinVar RCV000791651, TOPMed rs995270345, REVEL 0.40, MetaLR 0.39, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- I7T (p.Ile7Thr), Ensembl rs1572181746
- I7V (p.Ile7Val), Ensembl rs1558109278
- S8I (p.Ser8Ile), rs368880633, ClinGen CA33993109, ClinVar RCV001911460, ClinVar RCV002554354, REVEL 0.31, MetaLR 0.21, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- L9F (p.Leu9Phe), gnomAD rs1391299879, REVEL 0.36, MetaLR 0.30
- L9I (p.Leu9Ile), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- L9P (p.Leu9Pro), TOPMed rs1213412723, gnomAD rs1213412723, REVEL 0.71, MetaLR 0.55
- W10* (p.Trp10Ter), rs2102942512, ClinGen CA343685252, ClinVar RCV001909878, Ensembl rs2102942512, CADD 40.00, Pathogenic
- W10L (p.Trp10Leu), cosmic curated COSV10083
- W10S (p.Trp10Ser), TOPMed rs1261814657, gnomAD rs1261814657, REVEL 0.83, MetaLR 0.57
- N11D (p.Asn11Asp), Ensembl rs1572181710
- E12A (p.Glu12Ala), TOPMed rs1673584287, REVEL 0.60, MetaLR 0.52
- E12D (p.Glu12Asp), TOPMed rs1673584126, REVEL 0.45, MetaLR 0.47
- E12K (p.Glu12Lys), NCI-TCGA Cosmic COSV6231, cosmic curated COSV62314, Variant assessed as somatic; moderate impact.
- V14L (p.Val14Leu), ExAC rs763816212, TOPMed rs763816212, gnomAD rs763816212, REVEL 0.43, MetaLR 0.52
- L15P (p.Leu15Pro), gnomAD rs1379367905, REVEL 0.53, MetaLR 0.34
- A16V (p.Ala16Val), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- A17E (p.Ala17Glu), cosmic curated COSV10083, 1000Genomes rs201589700, ExAC rs201589700, TOPMed rs201589700, REVEL 0.63, MetaLR 0.53
- A17T (p.Ala17Thr), rs758057222, ClinGen CA1285071, ClinVar RCV000642278, ClinVar RCV005672443, REVEL 0.45, MetaLR 0.52, Uncertain significance, Inborn genetic diseases; Granulomatous disease, chronic, autosomal recessive, cy
- A17V (p.Ala17Val), 1000Genomes rs201589700, ExAC rs201589700, TOPMed rs201589700, gnomAD rs201589700, REVEL 0.35, MetaLR 0.36
- D18E (p.Asp18Glu), TOPMed rs969698184, gnomAD rs969698184, REVEL 0.15, MetaLR 0.40, Uncertain significance, Inborn genetic diseases
- D18Y (p.Asp18Tyr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- K19E (p.Lys19Glu), Ensembl rs1673582296, REVEL 0.11, MetaLR 0.27
- D21E (p.Asp21Glu), TOPMed rs1673581472, gnomAD rs1673581472, REVEL 0.41, MetaLR 0.20
- D21Y (p.Asp21Tyr), ExAC rs773175637, gnomAD rs773175637, REVEL 0.79, MetaLR 0.56
- W22* (p.Trp22Ter), rs2528039666, ClinGen CA343684958, ClinVar RCV002671990, Pathogenic
- W22R (p.Trp22Arg), rs1673581250, ClinGen CA343684969, ClinVar RCV001050845, gnomAD rs1673581250, REVEL 0.80, MetaLR 0.54, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- K23M (p.Lys23Met), rs767533151, ClinGen CA1285066, ClinVar RCV002766342, ExAC rs767533151, REVEL 0.28, MetaLR 0.36, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- G24E (p.Gly24Glu), cosmic curated COSV62315
- A25D (p.Ala25Asp), ExAC rs761962182, gnomAD rs761962182, REVEL 0.93, MetaLR 0.77
- D27G (p.Asp27Gly), gnomAD rs1413816919, REVEL 0.07, MetaLR 0.22
- S30N (p.Ser30Asn), 1000Genomes rs544745512, ExAC rs544745512, gnomAD rs544745512, REVEL 0.12, MetaLR 0.26, Uncertain significance, Inborn genetic diseases; not provided
- A31G (p.Ala31Gly), cosmic curated COSV10652
- A31T (p.Ala31Thr), cosmic curated COSV62315, TOPMed rs1477543413
- A31V (p.Ala31Val), NCI-TCGA Cosmic COSV1008, cosmic curated COSV10083, Variant assessed as somatic; moderate impact.
- V32I (p.Val32Ile), rs201869337, ClinGen CA1285061, cosmic curated COSV62314, ClinVar RCV001038440, REVEL 0.14, MetaLR 0.17, Uncertain significance, Inborn genetic diseases; Granulomatous disease, chronic, autosomal recessive, cy
- Q33L (p.Gln33Leu), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- D34G (p.Asp34Gly), rs745752489, ClinGen CA1285059, ClinVar RCV002995921, ExAC rs745752489, REVEL 0.44, MetaLR 0.43, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- D34N (p.Asp34Asn), NCI-TCGA TCGA novel, MetaLR 0.15, MetaSVM -1.02, Variant assessed as somatic; moderate impact.
- P35S (p.Pro35Ser), ESP rs368781381, ExAC rs368781381, gnomAD rs368781381, REVEL 0.65, MetaLR 0.52
- P35T (p.Pro35Thr), ESP rs368781381, ExAC rs368781381, gnomAD rs368781381, REVEL 0.63, MetaLR 0.57
- H36R (p.His36Arg), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- H36T (p.His36Thr), NCI-TCGA TCGA novel, MetaLR 0.15, MetaSVM -1.01, Variant assessed as somatic; high impact.
- S37F (p.Ser37Phe), cosmic curated COSV62314, MetaLR 0.61, MetaSVM 0.58
- R38L (p.Arg38Leu), cosmic curated COSV62316, MetaLR 0.53, MetaSVM -0.15
- R38Q (p.Arg38Gln), rs147415774, ClinGen CA1285055, ClinVar RCV000313929, ClinVar RCV001085219, REVEL 0.59, MetaLR 0.53, Conflicting interpretations, not specified; not provided; Granulomatous disease, chronic, autosomal recessive
- R38W (p.Arg38Trp), rs200824291, ClinGen CA1285056, cosmic curated COSV62315, ClinVar RCV000794385, REVEL 0.61, MetaLR 0.54, Uncertain significance, Inborn genetic diseases; Granulomatous disease, chronic, autosomal recessive, cy
- C40G (p.Cys40Gly), TOPMed rs979104686, MetaLR 0.50, MetaSVM -0.11
- C40R (p.Cys40Arg), TOPMed rs979104686, REVEL 0.66, MetaLR 0.52
- N42S (p.Asn42Ser), rs137854514, ClinGen CA145205, ClinVar RCV000059357, UniProt VAR 065002, AlphaMissense 0.34, MetaLR 0.43, not provided, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- I43V (p.Ile43Val), TOPMed rs1673576220, REVEL 0.09, MetaLR 0.21, Uncertain significance, Inborn genetic diseases
- G44C (p.Gly44Cys), rs137854510, ClinGen CA145209, ClinVar RCV000059359, ClinVar RCV000430894, AlphaMissense 0.98, MetaLR 0.72, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- G44R (p.Gly44Arg), rs137854510, ClinGen CA145207, ClinVar RCV000059358, UniProt VAR 065004, AlphaMissense 0.98, MetaLR 0.72, not provided, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- M46I (p.Met46Ile), rs1673575856, ClinGen CA343684313, ClinVar RCV001307894, Ensembl rs1673575856, AlphaMissense 0.18, MetaLR 0.09, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- Y47C (p.Tyr47Cys), cosmic curated COSV10083, MetaLR 0.30, MetaSVM -0.66
- T48A (p.Thr48Ala), TOPMed rs1673575726, REVEL 0.03, MetaLR 0.10
- I49N (p.Ile49Asn), TOPMed rs1673575574, gnomAD rs1673575574, REVEL 0.33, MetaLR 0.48
- N52K (p.Asn52Lys), ExAC rs752384353, TOPMed rs752384353, gnomAD rs752384353, REVEL 0.11, MetaLR 0.15, Likely benign
- M53I (p.Met53Ile), cosmic curated COSV10468, MetaLR 0.04, MetaSVM -0.96
- M53V (p.Met53Val), rs993538958, ClinGen CA33992941, ClinVar RCV001219158, TOPMed rs993538958, REVEL 0.05, MetaLR 0.10, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- K58* (p.Lys58Ter), rs898012170, ClinGen CA33992939, ClinVar RCV003603318, TOPMed rs898012170, CADD 40.00, Pathogenic, in CGD2
- K58N (p.Lys58Asn), cosmic curated COSV62316, MetaLR 0.23, MetaSVM -0.94
- K58R (p.Lys58Arg), rs2528038922, ClinGen CA343684056, ClinVar RCV002586633, REVEL 0.25, MetaLR 0.40, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- A59D (p.Ala59Asp), TOPMed rs1673383491, MetaLR 0.45, MetaSVM -0.01
- A59P (p.Ala59Pro), 1000Genomes rs545984071, ExAC rs545984071, gnomAD rs545984071, REVEL 0.52, MetaLR 0.45, Uncertain significance
- A59T (p.Ala59Thr), rs545984071, ClinGen CA1285036, ClinVar RCV001907238, 1000Genomes rs545984071, REVEL 0.33, MetaLR 0.45, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- F60L (p.Phe60Leu), TOPMed rs1673383330, MetaLR 0.44, MetaSVM -0.02
- T61A (p.Thr61Ala), TOPMed rs1673383001
- T61I (p.Thr61Ile), NCI-TCGA Cosmic COSV6231, cosmic curated COSV62316, MetaLR 0.27, MetaSVM -0.74, Variant assessed as somatic; moderate impact.
- R62K (p.Arg62Lys), Ensembl rs2102934545, MetaLR 0.08, MetaSVM -1.07
- S63G (p.Ser63Gly), TOPMed rs1317264911, gnomAD rs1317264911
- S63R (p.Ser63Arg), TOPMed rs1317264911, gnomAD rs1317264911, REVEL 0.39, MetaLR 0.42
- S63T (p.Ser63Thr), Ensembl rs2102934525, MetaLR 0.20, MetaSVM -0.89
- I64L (p.Ile64Leu), Ensembl rs1558107073, MetaLR 0.40, MetaSVM -0.57
- N65D (p.Asn65Asp), Ensembl rs111532709, MetaLR 0.11, MetaSVM -1.02
- N65S (p.Asn65Ser), rs778546412, ClinGen CA1285034, ClinVar RCV000801293, ExAC rs778546412, REVEL 0.05, MetaLR 0.09, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- R66* (p.Arg66Ter), rs750782115, ClinGen CA1285032, NCI-TCGA Cosmic COSV6231, cosmic curated COSV62314, CADD 36.00, Pathogenic
- R66G (p.Arg66Gly), ExAC rs750782115, TOPMed rs750782115, gnomAD rs750782115, REVEL 0.15, MetaLR 0.18, Pathogenic
- R66L (p.Arg66Leu), 1000Genomes rs142803799, ESP rs142803799, ExAC rs142803799, TOPMed rs142803799, REVEL 0.14, MetaLR 0.10, Uncertain significance
- R66Q (p.Arg66Gln), rs142803799, ClinGen CA1285030, cosmic curated COSV62315, ClinVar RCV000933372, REVEL 0.03, MetaLR 0.10, Conflicting interpretations, Inborn genetic diseases; Granulomatous disease, chronic, autosomal recessive, cy
- D67G (p.Asp67Gly), rs1673381111, ClinGen CA343683399, ClinVar RCV001299845, Ensembl rs1673381111, AlphaMissense 0.95, MetaLR 0.48, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- D67Y (p.Asp67Tyr), rs2102934452, ClinGen CA343683409, ClinVar RCV001367005, Ensembl rs2102934452, AlphaMissense 0.98, MetaLR 0.50, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- H69L (p.His69Leu), TOPMed rs1448318570, gnomAD rs1448318570, REVEL 0.48, MetaLR 0.42
- H69N (p.His69Asn), Ensembl rs1673380587, REVEL 0.37, MetaLR 0.37
- H69R (p.His69Arg), cosmic curated COSV10528, TOPMed rs1448318570, gnomAD rs1448318570, REVEL 0.51, MetaLR 0.42
- L70S (p.Leu70Ser), Ensembl rs895330372, REVEL 0.30, MetaLR 0.29
- A71S (p.Ala71Ser), rs2102934403, ClinGen CA343683320, ClinVar RCV001997319, Ensembl rs2102934403, REVEL 0.34, MetaLR 0.43, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- V72A (p.Val72Ala), gnomAD rs1328721147, REVEL 0.40, MetaLR 0.42
- A73P (p.Ala73Pro), cosmic curated COSV62315
- Y74C (p.Tyr74Cys), ExAC rs763140210, TOPMed rs763140210, gnomAD rs763140210, REVEL 0.89, MetaLR 0.64
- Y74D (p.Tyr74Asp), gnomAD rs1673379582, REVEL 0.92, MetaLR 0.64
- Y74S (p.Tyr74Ser), ExAC rs763140210, TOPMed rs763140210, gnomAD rs763140210, MetaLR 0.64, MetaSVM 0.39
- F75V (p.Phe75Val), NCI-TCGA Cosmic COSV6231, cosmic curated COSV62315, MetaLR 0.33, MetaSVM -0.28, Variant assessed as somatic; moderate impact.
- R77* (p.Arg77Ter), rs752901695, ClinGen CA1285026, NCI-TCGA Cosmic COSV6231, cosmic curated COSV62315, CADD 38.00, Pathogenic, in CGD2
- R77L (p.Arg77Leu), ExAC rs119103275, TOPMed rs119103275, gnomAD rs119103275, REVEL 0.42, MetaLR 0.37, Uncertain significance, in CGD2
- R77Q (p.Arg77Gln), rs119103275, ClinGen CA115435, cosmic curated COSV62316, ClinVar RCV000002335, REVEL 0.48, MetaLR 0.40, Uncertain significance, not specified; Granulomatous disease, chronic, autosomal recessive, cytochrome b
- G78E (p.Gly78Glu), rs137854519, ClinGen CA145211, cosmic curated COSV62315, ClinVar RCV000059360, REVEL 0.70, MetaLR 0.54, not provided, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- G78R (p.Gly78Arg), Ensembl rs1558107011
- M79I (p.Met79Ile), cosmic curated COSV10468, ExAC rs770674754, gnomAD rs770674754, REVEL 0.07, MetaLR 0.09
- M79L (p.Met79Leu), ExAC rs137854512, TOPMed rs137854512, gnomAD rs137854512, REVEL 0.10, MetaLR 0.10
- M79T (p.Met79Thr), gnomAD rs1412099566, MetaLR 0.10, MetaSVM -1.01
- M79V (p.Met79Val), rs137854512, ClinGen CA219767, ClinVar RCV000059361, UniProt VAR 065006, REVEL 0.13, MetaLR 0.07, not provided
- L80F (p.Leu80Phe), TOPMed rs1345007682
- Y81* (p.Tyr81Ter), ESP rs143178891, ExAC rs143178891, TOPMed rs143178891, gnomAD rs143178891, CADD 40.00, Likely benign
- Y82* (p.Tyr82Ter), rs2528021632, ClinGen CA343683020, ClinVar RCV003605052, CADD 37.00, Pathogenic
- Y82N (p.Tyr82Asn), rs201003183, ClinGen CA1285022, ClinVar RCV000809135, ClinVar RCV002538047, REVEL 0.23, MetaLR 0.23, Uncertain significance, Inborn genetic diseases; Granulomatous disease, chronic, autosomal recessive, cy
- T84I (p.Thr84Ile), ExAC rs779088549, TOPMed rs779088549, gnomAD rs779088549, REVEL 0.04, MetaLR 0.11
- E85D (p.Glu85Asp), TOPMed rs1457361434, gnomAD rs1457361434, REVEL 0.13, MetaLR 0.25
- E85K (p.Glu85Lys), NCI-TCGA Cosmic COSV1008, cosmic curated COSV10083, Variant assessed as somatic; moderate impact.
- Y87* (p.Tyr87Ter), Ensembl rs999877155
- Y87H (p.Tyr87His), rs940390623, ClinGen CA343679739, ClinVar RCV002824716, AlphaMissense 0.25, MetaLR 0.37, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- Y87N (p.Tyr87Asn), rs940390623, ClinGen CA33985411, ClinVar RCV003065698, TOPMed rs940390623, REVEL 0.39, AlphaMissense 0.25, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- D88N (p.Asp88Asn), NCI-TCGA Cosmic COSV6231, cosmic curated COSV62316, TOPMed rs1672861388, Variant assessed as somatic; moderate impact.
- D88Y (p.Asp88Tyr), cosmic curated COSV62316
- A90T (p.Ala90Thr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- A90V (p.Ala90Val), rs1439247206, ClinGen CA343679652, ClinVar RCV000812884, gnomAD rs1439247206, REVEL 0.63, MetaLR 0.86, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- I91M (p.Ile91Met), NCI-TCGA Cosmic COSV6231, cosmic curated COSV62314, MetaLR 0.15, MetaSVM -0.96, Variant assessed as somatic; moderate impact.
- I91V (p.Ile91Val), gnomAD rs1558101170, REVEL 0.07, MetaLR 0.15, Uncertain significance, Inborn genetic diseases
- K92R (p.Lys92Arg), gnomAD rs1178973806, REVEL 0.12, MetaLR 0.26
- D93E (p.Asp93Glu), rs137854507, cosmic curated COSV62316, ClinGen CA145213, ClinVar RCV000059362, AlphaMissense 0.93, MetaLR 0.41, not provided, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- D93Y (p.Asp93Tyr), cosmic curated COSV10820, NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact., in CGD2
- L94F (p.Leu94Phe), rs2102912563, ClinGen CA343679556, ClinVar RCV002027444, Ensembl rs2102912563, AlphaMissense 0.09, MetaLR 0.07, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- K95Q (p.Lys95Gln), gnomAD rs1222090455, REVEL 0.28, MetaLR 0.31
- K95T (p.Lys95Thr), rs765461476, ClinGen CA1285010, ClinVar RCV004473529, ExAC rs765461476, REVEL 0.47, MetaLR 0.34, Uncertain significance, Inborn genetic diseases
- E96K (p.Glu96Lys), NCI-TCGA Cosmic COSV6231, cosmic curated COSV62315, Variant assessed as somatic; moderate impact., in CGD2
- A97D (p.Ala97Asp), rs755222977, ClinGen CA343679471, ClinVar RCV003989926, ExAC rs755222977, AlphaMissense 0.29, MetaLR 0.60, Conflicting interpretations, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- A97G (p.Ala97Gly), rs755222977, ClinGen CA1285009, ClinVar RCV001326426, ExAC rs755222977, REVEL 0.64, AlphaMissense 0.29, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- A97P (p.Ala97Pro), rs1558101108, ClinGen CA343679476, ClinVar RCV002030953, TOPMed rs1558101108, AlphaMissense 0.99, MetaLR 0.61, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- A97T (p.Ala97Thr), rs1558101108, ClinGen CA343679484, ClinVar RCV002697478, TOPMed rs1558101108, AlphaMissense 0.99, MetaLR 0.61, Uncertain significance, Inborn genetic diseases
- L98S (p.Leu98Ser), ExAC rs754041676, TOPMed rs754041676, gnomAD rs754041676, REVEL 0.72, MetaLR 0.53
- I99M (p.Ile99Met), TOPMed rs1229246306, gnomAD rs1229246306, REVEL 0.04, MetaLR 0.11
- I99T (p.Ile99Thr), ExAC rs766146068, REVEL 0.07, MetaLR 0.07
- Q100* (p.Gln100Ter), rs119103276, ClinGen CA115430, cosmic curated COSV62314, ClinVar RCV000002332, CADD 36.00, Pathogenic
- Q100E (p.Gln100Glu), rs119103276, ClinGen CA1285006, ClinVar RCV000913787, 1000Genomes rs119103276, REVEL 0.08, MetaLR 0.22, Conflicting interpretations, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- Q100H (p.Gln100His), ExAC rs773131016, TOPMed rs773131016, gnomAD rs773131016, REVEL 0.42, MetaLR 0.42, Likely benign
- Q100K (p.Gln100Lys), rs119103276, ClinGen CA343679384, ClinVar RCV001886123, 1000Genomes rs119103276, REVEL 0.19, MetaLR 0.40, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- R102* (p.Arg102Ter), rs374402066, ClinGen CA212789, ClinVar RCV000002329, ESP rs374402066, CADD 39.00, Pathogenic, in CGD2
- R102L (p.Arg102Leu), ExAC rs137854515, TOPMed rs137854515, gnomAD rs137854515, REVEL 0.68, MetaLR 0.63, Uncertain significance, in CGD2
- R102P (p.Arg102Pro), rs137854515, ClinGen CA145215, NCI-TCGA Cosmic COSV1008, cosmic curated COSV10083, REVEL 0.74, MetaLR 0.55, not provided, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- R102Q (p.Arg102Gln), rs137854515, ClinGen CA1285003, ClinVar RCV001320606, ClinVar RCV004720854, REVEL 0.66, MetaLR 0.63, Uncertain significance, not provided; Granulomatous disease, chronic, autosomal recessive, cytochrome b
- G103E (p.Gly103Glu), ExAC rs748898061, gnomAD rs748898061, REVEL 0.63, MetaLR 0.57
- G103R (p.Gly103Arg), ExAC rs768193963, TOPMed rs768193963, gnomAD rs768193963, REVEL 0.63, MetaLR 0.60, Uncertain significance, Inborn genetic diseases
- G103V (p.Gly103Val), NCI-TCGA Cosmic COSV6231, cosmic curated COSV62315, MetaLR 0.63, MetaSVM 0.38, Variant assessed as somatic; moderate impact.
- N104H (p.Asn104His), gnomAD rs1157170264, REVEL 0.57, MetaLR 0.48
- N104K (p.Asn104Lys), rs2102912417, ClinGen CA343679251, ClinVar RCV001996352, Ensembl rs2102912417, AlphaMissense 0.87, MetaLR 0.54, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- N104S (p.Asn104Ser), rs2102912424, ClinGen CA343679263, ClinVar RCV002041372, Ensembl rs2102912424, AlphaMissense 0.40, MetaLR 0.47, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- I107T (p.Ile107Thr), Ensembl rs1672856480, REVEL 0.80, MetaLR 0.59
- I107V (p.Ile107Val), rs1672856679, ClinGen CA343679177, ClinVar RCV001046167, Ensembl rs1672856679, REVEL 0.37, MetaLR 0.36, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- D108N (p.Asp108Asn), gnomAD rs749367579, REVEL 0.47, MetaLR 0.48
- D108V (p.Asp108Val), rs137854509, ClinGen CA145217, ClinVar RCV000059364, ClinVar RCV001559780, AlphaMissense 0.97, MetaLR 0.54, Uncertain significance, not specified; not provided
- D108Y (p.Asp108Tyr), NCI-TCGA Cosmic COSV6231, cosmic curated COSV62316, Variant assessed as somatic; moderate impact., in CGD2
- Y109F (p.Tyr109Phe), NCI-TCGA TCGA novel, MetaLR 0.61, MetaSVM 0.03, Variant assessed as somatic; moderate impact.
- K110N (p.Lys110Asn), TOPMed rs1672855755, gnomAD rs1672855755, MetaLR 0.45, MetaSVM -0.37, Likely benign
- I111T (p.Ile111Thr), ExAC rs771262057, gnomAD rs771262057, REVEL 0.29, MetaLR 0.44
- L112P (p.Leu112Pro), NCI-TCGA TCGA novel, REVEL 0.68, MetaLR 0.34, Variant assessed as somatic; moderate impact.
- G113E (p.Gly113Glu), rs200286542, ClinGen CA1284998, ClinVar RCV003051723, 1000Genomes rs200286542, REVEL 0.74, MetaLR 0.69, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- G113W (p.Gly113Trp), cosmic curated COSV62315
- L114I (p.Leu114Ile), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- Q115* (p.Gln115Ter), rs2527976811, NCI-TCGA Cosmic COSV6231, cosmic curated COSV62316, ClinGen CA343678915, Pathogenic
- Q115H (p.Gln115His), rs2527976784, NCI-TCGA TCGA novel, ClinGen CA343678908, ClinVar RCV002792607, REVEL 0.21, MetaLR 0.43, Uncertain significance, Inborn genetic diseases
- Q115P (p.Gln115Pro), cosmic curated COSV10970, gnomAD rs1672854950, REVEL 0.15, MetaLR 0.24
- F116S (p.Phe116Ser), TOPMed rs1672854639, gnomAD rs1672854639, REVEL 0.70, MetaLR 0.53
- F116V (p.Phe116Val), TOPMed rs1672854807, REVEL 0.63, MetaLR 0.52
- L118M (p.Leu118Met), gnomAD rs1490800202, REVEL 0.55, MetaLR 0.58
- F119C (p.Phe119Cys), NCI-TCGA TCGA novel, MetaLR 0.45, MetaSVM -0.51, Variant assessed as somatic; moderate impact.
- A120V (p.Ala120Val), rs1553258487, ClinGen CA343678763, ClinVar RCV000553435, Ensembl rs1553258487, REVEL 0.24, MetaLR 0.35, Uncertain significance, Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type
- C121Y (p.Cys121Tyr), NCI-TCGA TCGA novel, TOPMed rs1672853724, REVEL 0.60, MetaLR 0.45, Variant assessed as somatic; moderate impact.
- E122D (p.Glu122Asp), TOPMed rs1182112229, REVEL 0.35, MetaLR 0.44
- E122Q (p.Glu122Gln), cosmic curated COSV10468, MetaLR 0.44, MetaSVM 0.10
- V123M (p.Val123Met), NCI-TCGA TCGA novel, REVEL 0.43, MetaLR 0.48, Variant assessed as somatic; moderate impact.
- L124S (p.Leu124Ser), TOPMed rs1672717395
Public NCF2 analysis runs
- NCF2 analysis run — NCF2 (898 variants) — completed 2026-08-22