ABCA3 (Q99758) variants and mutations
ABCA3 (also known as Q99758) is a human protein-coding gene encoding a phospholipid-transporting ATPase protein. It transports phospholipids into lamellar bodies of alveolar type II cells, supporting pulmonary surfactant assembly and normal gas exchange. Biallelic loss-of-function variants can cause neonatal respiratory failure or childhood interstitial lung disease. This analysis covers 2,358 ABCA3 variants and mutations. Of these, 86% have computational variant effect predictions. Disease context includes Neonatal acute respiratory distress with surfactant metabolism deficiency, Congenital pulmonary alveolar proteinosis, and hereditary pulmonary alveolar proteinosis. Example ABCA3 variants include A2D, A2T, and A2V.
Variant analysis overview
- Gene: ABCA3
- Protein: Q99758
- UniProt accession: Q99758
- Organism: Homo sapiens
- Variants analyzed: 2358
- Variant scope: all variants
- Completed: 2026-08-20
Variant and mutation evidence
- Variant composition: 2,106 unspecified-consequence records; 2 stop lost; 1 stop retained variant; 110 synonymous variants; 114 missense variants; 5 stop-gained variants; 4 in-frame deletions; 10 frameshift variants; 3 splice-region variants; 2 substitution
- Prediction scores: 2,033 variants have prediction scores (86% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Neonatal acute respiratory distress with surfactant metabolism deficiency, Congenital pulmonary alveolar proteinosis, hereditary pulmonary alveolar proteinosis, newborn respiratory distress syndrome, Primary interstitial lung disease specific to childhood due to pulmonary surfact, neurodegenerative disease, idiopathic pulmonary fibrosis, interstitial lung disease, carbamoyl phosphate synthetase I deficiency disease, Loeys-Dietz syndrome, surfactant metabolism dysfunction, pulmonary, 1, lung disorder.
Protein structure and variant hotspots
- Protein features: 14 transmembrane segments; 2 domains; 2 binding sites; 6 post-translational modification sites.
- Structural context: 1,032 variants have structural context.
- 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, MaveDB, LitVar.
Notable ABCA3 variants
Examples include A2D, A2T, A2V, V3A, V3M, L4F, R5T, Q6R. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- A2D (p.Ala2Asp), rs148662935, ClinGen CA7841831, ClinVar RCV000913469, ClinVar RCV001257124, REVEL 0.37, CADD 22.40, Conflicting interpretations, Hereditary pulmonary alveolar proteinosis; not provided; Interstitial lung disea
- A2T (p.Ala2Thr), gnomAD rs1180809929, REVEL 0.34, CADD 21.50
- A2V (p.Ala2Val), 1000Genomes rs148662935, ESP rs148662935, ExAC rs148662935, TOPMed rs148662935, REVEL 0.27, CADD 21.30, Likely benign
- V3A (p.Val3Ala), TOPMed rs1175119413, gnomAD rs1175119413, REVEL 0.33, CADD 17.40
- V3M (p.Val3Met), ExAC rs773639935, TOPMed rs773639935, gnomAD rs773639935, REVEL 0.35, CADD 19.30
- L4F (p.Leu4Phe), ExAC rs748559393, TOPMed rs748559393, gnomAD rs748559393, REVEL 0.12, CADD 16.10
- R5T (p.Arg5Thr), gnomAD rs1245878632, REVEL 0.47, CADD 22.30
- Q6R (p.Gln6Arg), Ensembl rs2093734573
- L7P (p.Leu7Pro), Ensembl rs2093734563
- L7V (p.Leu7Val), TOPMed rs2093734570, REVEL 0.50, CADD 25.10
- A8V (p.Ala8Val), rs755333350, ClinGen CA7841826, NCI-TCGA Cosmic COSV5705, cosmic curated COSV57059, REVEL 0.18, CADD 6.01, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- L9H (p.Leu9His), Ensembl rs1596866784
- L10F (p.Leu10Phe), Ensembl rs2093734533, REVEL 0.79, CADD 25.20
- L11R (p.Leu11Arg), Ensembl rs2093734523
- L11V (p.Leu11Val), gnomAD rs1370672803, REVEL 0.66, CADD 25.20
- K13* (p.Lys13Ter), ESP rs376792674, ExAC rs376792674, gnomAD rs376792674
- N14K (p.Asn14Lys), rs2505678099, ClinGen CA394353301, ClinVar RCV003079202, Uncertain significance, not provided
- Y15H (p.Tyr15His), Ensembl rs974526109, REVEL 0.58, CADD 28.00
- T16A (p.Thr16Ala), ExAC rs778818945, gnomAD rs778818945, REVEL 0.16, CADD 23.40
- T16N (p.Thr16Asn), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- Q18H (p.Gln18His), TOPMed rs1379570761, gnomAD rs1379570761, REVEL 0.14, CADD 35.00
- R20L (p.Arg20Leu), rs201777730, ClinGen CA7841794, ClinVar RCV002284278, ClinVar RCV003560930, REVEL 0.93, CADD 25.40, Conflicting interpretations, Interstitial lung disease 2; Interstitial lung disease due to ABCA3 deficiency
- R20Q (p.Arg20Gln), rs201777730, ClinGen CA7841793, ClinVar RCV001532314, ExAC rs201777730, REVEL 0.88, CADD 25.70, Uncertain significance, not provided
- R20W (p.Arg20Trp), ESP rs145242436, ExAC rs145242436, TOPMed rs145242436, gnomAD rs145242436, REVEL 0.89, CADD 25.50
- K21E (p.Lys21Glu), gnomAD rs1325162461, REVEL 0.21, CADD 23.60
- V24L (p.Val24Leu), ExAC rs777247264, gnomAD rs777247264, REVEL 0.21, CADD 18.70
- T25K (p.Thr25Lys), ExAC rs769313907, TOPMed rs769313907, gnomAD rs769313907, REVEL 0.77, CADD 23.60, Uncertain significance
- T25M (p.Thr25Met), rs769313907, ClinGen CA7841791, NCI-TCGA Cosmic COSV5705, cosmic curated COSV57054, REVEL 0.57, CADD 24.80, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- L27P (p.Leu27Pro), rs2505677808, ClinGen CA394352984, ClinVar RCV002419487, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- L27V (p.Leu27Val), gnomAD rs756665799
- E28A (p.Glu28Ala), TOPMed rs1226605978, gnomAD rs1226605978, REVEL 0.65, CADD 27.40, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- E28D (p.Glu28Asp), TOPMed rs1596866633, gnomAD rs1596866633, Likely benign
- E28K (p.Glu28Lys), ExAC rs776002639, TOPMed rs776002639, gnomAD rs776002639, REVEL 0.69, CADD 26.80
- E28V (p.Glu28Val), TOPMed rs1226605978, gnomAD rs1226605978
- L29V (p.Leu29Val), ExAC rs772507862, gnomAD rs772507862, REVEL 0.03, CADD 18.90
- F30S (p.Phe30Ser), gnomAD rs1404114368, REVEL 0.18, CADD 23.00
- P32L (p.Pro32Leu), rs771082062, ClinGen CA7841785, ClinVar RCV002374352, ClinVar RCV003103593, REVEL 0.82, CADD 24.70, Uncertain significance, not provided; Hereditary pulmonary alveolar proteinosis
- L34P (p.Leu34Pro), Ensembl rs2093734170
- F35I (p.Phe35Ile), TOPMed rs2093734163
- I38T (p.Ile38Thr), TOPMed rs1287053712
- L39F (p.Leu39Phe), 1000Genomes rs200090198, ESP rs200090198, ExAC rs200090198, TOPMed rs200090198, REVEL 0.78, CADD 24.50, Uncertain significance, not provided
- L39I (p.Leu39Ile), rs200090198, ClinGen CA276853867, ClinVar RCV003230948, 1000Genomes rs200090198, REVEL 0.60, CADD 22.70, Uncertain significance, not specified
- L39V (p.Leu39Val), rs200090198, ClinGen CA7841782, ClinVar RCV002963411, 1000Genomes rs200090198, REVEL 0.88, CADD 22.70, Conflicting interpretations, not provided; Hereditary pulmonary alveolar proteinosis
- I40M (p.Ile40Met), TOPMed rs1447629085, REVEL 0.29, CADD 5.87
- I40T (p.Ile40Thr), gnomAD rs1462396228
- R43C (p.Arg43Cys), rs373617498, ClinGen CA7841780, cosmic curated COSV10006, ClinVar RCV002385293, REVEL 0.94, CADD 31.00, Pathogenic/Likely pathogenic, Hereditary pulmonary alveolar proteinosis; not provided; Interstitial lung disea
- R43H (p.Arg43His), rs754714105, ClinGen CA7841779, ClinVar RCV000221771, ClinVar RCV001804948, REVEL 0.95, CADD 27.60, Pathogenic/Likely pathogenic, Primary interstitial lung disease specific to childhood due to pulmonary surfact
- R43L (p.Arg43Leu), UniProt VAR 084240, Uncertain significance, in SMDP3
- R43P (p.Arg43Pro), ExAC rs754714105, TOPMed rs754714105, gnomAD rs754714105, Pathogenic, in SMDP3
- L44M (p.Leu44Met), TOPMed rs1318403355, gnomAD rs1318403355, REVEL 0.37, CADD 22.50
- L44V (p.Leu44Val), TOPMed rs1318403355, gnomAD rs1318403355, REVEL 0.23, CADD 16.00
- I46F (p.Ile46Phe), ExAC rs751290060, TOPMed rs751290060, gnomAD rs751290060, REVEL 0.20, CADD 22.40
- I46V (p.Ile46Val), ExAC rs751290060, TOPMed rs751290060, gnomAD rs751290060, REVEL 0.10, CADD 17.80
- Q47L (p.Gln47Leu), TOPMed rs997304312, gnomAD rs997304312, REVEL 0.49, CADD 21.60, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- Q47R (p.Gln47Arg), TOPMed rs997304312, gnomAD rs997304312, REVEL 0.42, CADD 19.40
- S48* (p.Ser48Ter), rs763721411, ClinGen CA394352621, ClinVar RCV003719059, CADD 37.00, Pathogenic
- S48L (p.Ser48Leu), cosmic curated COSV57062, ExAC rs763721411, TOPMed rs763721411, gnomAD rs763721411, REVEL 0.20, CADD 22.50, Uncertain significance
- S48P (p.Ser48Pro), ExAC rs765928416, gnomAD rs765928416
- S48W (p.Ser48Trp), ExAC rs763721411, TOPMed rs763721411, gnomAD rs763721411, REVEL 0.31, CADD 25.30, Uncertain significance
- N50S (p.Asn50Ser), ESP rs140778917, TOPMed rs140778917, gnomAD rs140778917, REVEL 0.04, CADD 18.50
- P52L (p.Pro52Leu), rs761278645, ClinGen CA7841773, ClinVar RCV002971431, ExAC rs761278645, REVEL 0.21, CADD 22.80, Uncertain significance, not provided
- P52R (p.Pro52Arg), ExAC rs761278645, TOPMed rs761278645, gnomAD rs761278645, Uncertain significance
- P52T (p.Pro52Thr), TOPMed rs2093734061
- N53K (p.Asn53Lys), NCI-TCGA Cosmic COSV5704, cosmic curated COSV57049, NCI-TCGA Cosmic COSV5705, Variant assessed as somatic; moderate impact.
- N53S (p.Asn53Ser), rs918921301, ClinGen CA276853835, ClinVar RCV002398388, gnomAD rs918921301, REVEL 0.06, CADD 19.60, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- A54P (p.Ala54Pro), rs147278907, ClinGen CA394352523, ClinVar RCV002394822, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- A54T (p.Ala54Thr), rs147278907, ClinGen CA7841771, cosmic curated COSV10738, ClinVar RCV000288211, REVEL 0.11, CADD 23.50, Conflicting interpretations, Hereditary pulmonary alveolar proteinosis; not provided; Interstitial lung disea
- A54V (p.Ala54Val), rs759790104, ClinGen CA7841770, ClinVar RCV001768290, ExAC rs759790104, REVEL 0.17, CADD 22.50, Uncertain significance, not provided
- T55P (p.Thr55Pro), Ensembl rs1596866546
- I56S (p.Ile56Ser), Ensembl rs2093734017, REVEL 0.10, CADD 20.30
- I56V (p.Ile56Val), ExAC rs774682550, gnomAD rs774682550, REVEL 0.02, CADD 1.12, Conflicting interpretations, Hereditary pulmonary alveolar proteinosis; not provided
- Y57C (p.Tyr57Cys), NCI-TCGA Cosmic COSV5704, cosmic curated COSV57049, NCI-TCGA Cosmic COSV5705, Ensembl rs1596866532, Variant assessed as somatic; moderate impact.
- Y57F (p.Tyr57Phe), NCI-TCGA Cosmic COSV5704, NCI-TCGA Cosmic COSV5705, cosmic curated COSV57056, Variant assessed as somatic; moderate impact.
- Y57S (p.Tyr57Ser), Ensembl rs1596866532
- P58L (p.Pro58Leu), ExAC rs749485914, TOPMed rs749485914, gnomAD rs749485914, REVEL 0.11, CADD 22.30, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- P58R (p.Pro58Arg), ExAC rs749485914, TOPMed rs749485914, gnomAD rs749485914, REVEL 0.18, CADD 21.50
- S61C (p.Ser61Cys), rs1457878698, ClinGen CA394352413, ClinVar RCV003213782, REVEL 0.19, CADD 22.80, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- S61F (p.Ser61Phe), rs1457878698, ClinGen CA394352411, ClinVar RCV004149325, TOPMed rs1457878698, REVEL 0.10, CADD 17.00, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- S61T (p.Ser61Thr), TOPMed rs2093733933, REVEL 0.05, CADD 14.50
- I62T (p.Ile62Thr), TOPMed rs1252444330, gnomAD rs1252444330, REVEL 0.33, CADD 24.20
- Q63L (p.Gln63Leu), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- Q63P (p.Gln63Pro), Ensembl rs2093733923
- E64A (p.Glu64Ala), rs886051834, ClinGen CA10647184, ClinVar RCV000389710, Ensembl rs886051834, Uncertain significance, Interstitial lung disease due to ABCA3 deficiency
- E64D (p.Glu64Asp), ExAC rs748137752, gnomAD rs748137752, REVEL 0.11, CADD 5.26
- E64K (p.Glu64Lys), rs2505677616, ClinGen CA394352379, ClinVar RCV003691559, Uncertain significance, not provided
- T70P (p.Thr70Pro), Ensembl rs1596866516
- P72L (p.Pro72Leu), rs865833156, NCI-TCGA Cosmic COSV5705, cosmic curated COSV57053, REVEL 0.49, CADD 16.80, Variant assessed as somatic; moderate impact.
- P72S (p.Pro72Ser), TOPMed rs1463443074, gnomAD rs1463443074, REVEL 0.28, CADD 18.60
- P73L (p.Pro73Leu), rs779862368, NCI-TCGA Cosmic COSV5705, cosmic curated COSV57050, ExAC rs779862368, REVEL 0.47, CADD 22.20, Variant assessed as somatic; moderate impact.
- P73S (p.Pro73Ser), cosmic curated COSV57061, ExAC rs746805427, gnomAD rs746805427, REVEL 0.38, CADD 21.70
- P73T (p.Pro73Thr), ExAC rs746805427, gnomAD rs746805427, REVEL 0.38, CADD 20.90
- P74S (p.Pro74Ser), TOPMed rs1314400451, gnomAD rs1314400451, REVEL 0.21, CADD 10.50
- W78L (p.Trp78Leu), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- W78S (p.Trp78Ser), rs2093733845, ClinGen CA394352168, ClinVar RCV001265593, Ensembl rs2093733845, Likely pathogenic, Interstitial lung disease due to ABCA3 deficiency
- E79D (p.Glu79Asp), gnomAD rs1447801490, REVEL 0.59, CADD 23.50
- E79K (p.Glu79Lys), rs1185200028, NCI-TCGA Cosmic COSV5705, cosmic curated COSV57056, TOPMed rs1185200028, REVEL 0.50, CADD 23.60, Variant assessed as somatic; moderate impact.
- E79Q (p.Glu79Gln), TOPMed rs1185200028, gnomAD rs1185200028, MetaLR 0.81, MetaSVM 0.84
- A81G (p.Ala81Gly), Ensembl rs1036188771
- P84L (p.Pro84Leu), NCI-TCGA Cosmic COSV1000, cosmic curated COSV10006, Ensembl rs2093733815, MetaLR 0.89, MetaSVM 0.98, Variant assessed as somatic; moderate impact.
- S85C (p.Ser85Cys), gnomAD rs1327300434, REVEL 0.53, CADD 25.10
- S85P (p.Ser85Pro), Ensembl rs2093733810
- H86Y (p.His86Tyr), TOPMed rs1391232187, gnomAD rs1391232187, REVEL 0.17, CADD 19.60
- D88E (p.Asp88Glu), ExAC rs756824803, TOPMed rs756824803, gnomAD rs756824803, REVEL 0.33, CADD 0.00, Likely benign
- D88N (p.Asp88Asn), Ensembl rs2093733800, REVEL 0.15, CADD 16.30
- A89S (p.Ala89Ser), rs150902383, NCI-TCGA Cosmic COSV1000, cosmic curated COSV10006, ESP rs150902383, REVEL 0.33, CADD 22.60, Uncertain significance
- A89T (p.Ala89Thr), rs150902383, ClinGen CA7841754, ClinVar RCV001121935, ESP rs150902383, REVEL 0.24, CADD 18.50, Uncertain significance, Interstitial lung disease due to ABCA3 deficiency
- K91N (p.Lys91Asn), TOPMed rs1382854589, gnomAD rs1382854589, REVEL 0.29, CADD 17.80
- K91R (p.Lys91Arg), ExAC rs760037090, TOPMed rs760037090, gnomAD rs760037090, REVEL 0.21, CADD 6.98
- T92A (p.Thr92Ala), ESP rs371562078, ExAC rs371562078, TOPMed rs371562078, gnomAD rs371562078, REVEL 0.17, CADD 5.89
- T92I (p.Thr92Ile), ExAC rs763094260, gnomAD rs763094260, REVEL 0.16, CADD 12.70
- T92S (p.Thr92Ser), ESP rs371562078, ExAC rs371562078, TOPMed rs371562078, gnomAD rs371562078, REVEL 0.11, CADD 5.09, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- V93I (p.Val93Ile), rs199840288, ClinGen CA7841748, ClinVar RCV002963410, 1000Genomes rs199840288, REVEL 0.71, CADD 0.01, Benign/Likely benign, not provided; Hereditary pulmonary alveolar proteinosis
- E95Q (p.Glu95Gln), TOPMed rs1339472381, gnomAD rs1339472381, REVEL 0.31, CADD 23.40
- V97A (p.Val97Ala), rs1267775571, ClinGen CA394351873, ClinVar RCV004154100, TOPMed rs1267775571, REVEL 0.16, CADD 7.57, Likely benign, Hereditary pulmonary alveolar proteinosis
- V97M (p.Val97Met), ExAC rs748192749, gnomAD rs748192749, REVEL 0.30, CADD 19.10
- R98C (p.Arg98Cys), rs746902527, ClinGen CA7841744, NCI-TCGA Cosmic COSV5705, cosmic curated COSV57052, REVEL 0.31, CADD 17.20, Uncertain significance, not provided; Hereditary pulmonary alveolar proteinosis
- R98H (p.Arg98His), 1000Genomes rs149050042, ExAC rs149050042, TOPMed rs149050042, gnomAD rs149050042, REVEL 0.29, CADD 11.60, Uncertain significance, not provided; Hereditary pulmonary alveolar proteinosis
- R98L (p.Arg98Leu), 1000Genomes rs149050042, ExAC rs149050042, TOPMed rs149050042, gnomAD rs149050042
- R99S (p.Arg99Ser), gnomAD rs1240908252, REVEL 0.27, CADD 9.61
- A100T (p.Ala100Thr), TOPMed rs2093733734
- L101F (p.Leu101Phe), TOPMed rs1352909711, gnomAD rs1352909711, REVEL 0.11, CADD 2.47, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- L101P (p.Leu101Pro), rs121909182, ClinGen CA119214, ClinVar RCV000008476, UniProt VAR 023497, Pathogenic, Interstitial lung disease due to ABCA3 deficiency
- N104D (p.Asn104Asp), gnomAD rs1477041077, REVEL 0.28, CADD 19.20
- N104S (p.Asn104Ser), TOPMed rs1227308104, MetaLR 0.46, MetaSVM -0.68
- M105I (p.Met105Ile), Ensembl rs868384970, MetaLR 0.34, MetaSVM -0.74
- R106* (p.Arg106Ter), rs1278044377, ClinGen CA394351658, NCI-TCGA Cosmic COSV5705, cosmic curated COSV57059, CADD 35.00, Pathogenic
- R106G (p.Arg106Gly), TOPMed rs1278044377, gnomAD rs1278044377, REVEL 0.54, CADD 19.70, Pathogenic
- R106Q (p.Arg106Gln), ESP rs371116381, ExAC rs371116381, TOPMed rs371116381, gnomAD rs371116381, REVEL 0.32, CADD 18.10
- V107A (p.Val107Ala), Ensembl rs1416764724, REVEL 0.19, CADD 16.20
- V107L (p.Val107Leu), cosmic curated COSV57058, Ensembl rs1567354581, REVEL 0.27, CADD 25.10
- R108C (p.Arg108Cys), NCI-TCGA Cosmic COSV5705, cosmic curated COSV57054, REVEL 0.47, CADD 25.30, Variant assessed as somatic; moderate impact.
- R108H (p.Arg108His), cosmic curated COSV10811, ExAC rs759505278, gnomAD rs759505278, REVEL 0.12, CADD 4.89
- G109R (p.Gly109Arg), NCI-TCGA Cosmic COSV1000, Variant assessed as somatic; moderate impact.
- G109S (p.Gly109Ser), rs770790607, NCI-TCGA Cosmic COSV1000, cosmic curated COSV10006, 1000Genomes rs770790607, REVEL 0.69, CADD 23.20, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- G109V (p.Gly109Val), Ensembl rs2141738679, MetaLR 0.89, MetaSVM 1.01
- F110L (p.Phe110Leu), gnomAD rs1411608435, REVEL 0.59, CADD 22.60
- P111R (p.Pro111Arg), ExAC rs749005692, TOPMed rs749005692, gnomAD rs749005692, REVEL 0.28, CADD 14.00
- P111S (p.Pro111Ser), NCI-TCGA Cosmic COSV1000, cosmic curated COSV10006, REVEL 0.14, CADD 8.81, Variant assessed as somatic; moderate impact.
- S112F (p.Ser112Phe), NCI-TCGA Cosmic COSV5705, cosmic curated COSV57050, REVEL 0.56, CADD 25.60, Variant assessed as somatic; moderate impact.
- S112T (p.Ser112Thr), Ensembl rs2093731293, REVEL 0.16, CADD 15.40
- E113K (p.Glu113Lys), TOPMed rs1445383505, gnomAD rs1445383505, REVEL 0.68, CADD 25.20
- K114N (p.Lys114Asn), rs2505675729, ClinGen CA394350743, ClinVar RCV004315343, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- D115E (p.Asp115Glu), ESP rs148377880, ExAC rs148377880, TOPMed rs148377880, gnomAD rs148377880, REVEL 0.30, CADD 15.50
- F116C (p.Phe116Cys), ExAC rs780516803, gnomAD rs780516803, REVEL 0.91, CADD 26.20
- F116S (p.Phe116Ser), ExAC rs780516803, gnomAD rs780516803
- F116Y (p.Phe116Tyr), ExAC rs780516803, gnomAD rs780516803
- E117Q (p.Glu117Gln), NCI-TCGA Cosmic COSV1000, cosmic curated COSV10006, MetaLR 0.80, MetaSVM 0.65, Variant assessed as somatic; moderate impact.
- D118Y (p.Asp118Tyr), Ensembl rs929553873, REVEL 0.49, CADD 22.80, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- Y119C (p.Tyr119Cys), 1000Genomes rs538323458, ExAC rs538323458, TOPMed rs538323458, gnomAD rs538323458, REVEL 0.73, CADD 25.30
- Y119S (p.Tyr119Ser), 1000Genomes rs538323458, ExAC rs538323458, TOPMed rs538323458, gnomAD rs538323458
- I120V (p.Ile120Val), rs1202457869, TOPMed rs1202457869, gnomAD rs1202457869, REVEL 0.18, CADD 6.93, Variant assessed as somatic; moderate impact.
- R121M (p.Arg121Met), gnomAD rs1207006823, MetaLR 0.67, MetaSVM -0.25
- R121S (p.Arg121Ser), ExAC rs779311575, TOPMed rs779311575, gnomAD rs779311575, REVEL 0.45, CADD 11.10
- Y122C (p.Tyr122Cys), ExAC rs757614663, gnomAD rs757614663, REVEL 0.49, CADD 22.40
- D123E (p.Asp123Glu), Ensembl rs753500876, REVEL 0.28, CADD 14.30
- D123H (p.Asp123His), ESP rs145087575, ExAC rs145087575, TOPMed rs145087575, gnomAD rs145087575, Likely benign
- D123N (p.Asp123Asn), rs145087575, ClinGen CA175149, cosmic curated COSV57053, ClinVar RCV000150116, REVEL 0.17, CADD 14.90, Conflicting interpretations, Hereditary pulmonary alveolar proteinosis; not specified; not provided
- N124D (p.Asn124Asp), ExAC rs201575440, TOPMed rs201575440, gnomAD rs201575440, REVEL 0.48, CADD 22.60
- N124H (p.Asn124His), ExAC rs201575440, TOPMed rs201575440, gnomAD rs201575440, REVEL 0.43, CADD 19.70
- N124S (p.Asn124Ser), rs142977595, ClinGen CA7841690, ClinVar RCV000612210, ClinVar RCV001121934, REVEL 0.43, CADD 17.90, Conflicting interpretations, Hereditary pulmonary alveolar proteinosis; not specified; not provided
- C125R (p.Cys125Arg), Ensembl rs2141738606
- C125W (p.Cys125Trp), Ensembl rs2141738602, REVEL 0.18, CADD 18.90
- S126A (p.Ser126Ala), Ensembl rs2093731134
- S126L (p.Ser126Leu), ESP rs377155167, ExAC rs377155167, TOPMed rs377155167, gnomAD rs377155167, REVEL 0.69, CADD 25.70
- S127A (p.Ser127Ala), ExAC rs774416182, gnomAD rs774416182
- S128G (p.Ser128Gly), rs762775158, ClinGen CA7841685, ClinVar RCV002355380, ExAC rs762775158, REVEL 0.21, CADD 17.50, Uncertain significance, Hereditary pulmonary alveolar proteinosis
- S128R (p.Ser128Arg), ExAC rs772785502, TOPMed rs772785502, gnomAD rs772785502, REVEL 0.41, CADD 1.96, Likely benign
- V129A (p.Val129Ala), ExAC rs747691941, gnomAD rs747691941, REVEL 0.76, CADD 24.60
- V129L (p.Val129Leu), 1000Genomes rs137924161, ESP rs137924161, ExAC rs137924161, TOPMed rs137924161, REVEL 0.63, CADD 23.20, Likely benign
- V129M (p.Val129Met), rs137924161, ClinGen CA7841683, cosmic curated COSV57048, ClinVar RCV000732369, REVEL 0.63, CADD 22.70, Uncertain significance, Hereditary pulmonary alveolar proteinosis; not specified; not provided
- A132S (p.Ala132Ser), TOPMed rs1029885956, gnomAD rs1029885956, REVEL 0.61, CADD 24.30
- A132T (p.Ala132Thr), cosmic curated COSV10964, TOPMed rs1029885956, gnomAD rs1029885956, REVEL 0.70, CADD 24.50
- V133M (p.Val133Met), rs201400258, ClinGen CA7841680, ClinVar RCV000293579, ClinVar RCV002356430, REVEL 0.52, CADD 15.50, Uncertain significance, Hereditary pulmonary alveolar proteinosis; Interstitial lung disease due to ABCA
- E136K (p.Glu136Lys), cosmic curated COSV10511, ExAC rs779362355, gnomAD rs779362355, REVEL 0.58, CADD 18.60
- H137Q (p.His137Gln), gnomAD rs1223902982, REVEL 0.46, CADD 21.60
- H137Y (p.His137Tyr), TOPMed rs999747794, REVEL 0.49, CADD 22.40
- P138A (p.Pro138Ala), rs369686350, ClinGen CA7841676, ClinVar RCV002333049, ClinVar RCV006470672, REVEL 0.22, CADD 0.01, Uncertain significance, Hereditary pulmonary alveolar proteinosis; not provided
- P138H (p.Pro138His), Ensembl rs2141738514, REVEL 0.21, CADD 9.59
- P138L (p.Pro138Leu), NCI-TCGA Cosmic COSV5705, cosmic curated COSV57051, Variant assessed as somatic; moderate impact.
- P138T (p.Pro138Thr), rs369686350, ClinGen CA276851992, ClinVar RCV002333047, 1000Genomes rs369686350, REVEL 0.17, CADD 0.02, Likely benign, Hereditary pulmonary alveolar proteinosis
Public ABCA3 analysis runs
- ABCA3 analysis run — ABCA3 (2,358 variants) — completed 2026-08-20