SLC47A1 (Q96FL8) variants and mutations
SLC47A1 (also known as Q96FL8) is a human protein-coding gene encoding a multidrug and toxin extrusion protein 1 protein. It uses proton gradients to secrete organic cations from renal and hepatic cells into urine or bile. Its activity influences elimination and drug interactions for compounds such as metformin. This analysis covers 918 SLC47A1 variants and mutations. Of these, 82% have computational variant effect predictions. Disease context includes neurodegenerative disease, brain aneurysm, and gout. Example SLC47A1 variants include E2Q, E2*, and E2K.
Variant analysis overview
- Gene: SLC47A1
- Protein: Q96FL8
- UniProt accession: Q96FL8
- Organism: Homo sapiens
- Variants analyzed: 918
- Variant scope: all variants
- Completed: 2026-08-21
Variant and mutation evidence
- Variant composition: 678 unspecified-consequence records; 10 stop-gained variants; 145 missense variants; 64 synonymous variants; 14 frameshift variants; 2 in-frame insertions; 3 splice-region variants; 3 substitution
- Prediction scores: 750 variants have prediction scores (82% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: neurodegenerative disease, brain aneurysm, gout, kidney failure, aneurysm, vitiligo, colorectal carcinoma, type 2 diabetes mellitus, Hypertryptophanemia, neonatal intrahepatic cholestasis due to citrin deficiency, maple syrup urine disease, chronic myelogenous leukemia, BCR-ABL1 positive.
Protein structure and variant hotspots
- Protein features: 13 transmembrane segments; 1 post-translational modification sites.
- Structural context: 364 variants have structural context.
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 SLC47A1 variants
Examples include E2Q, E2*, E2K, E2G, E2E, A3T, A3V, A3S. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- E2Q (p.Glu2Gln), TOPMed rs1915916207
- E2* (p.Glu2Ter), gnomAD 17-19533943-G-T, CADD 34.00
- E2K (p.Glu2Lys), gnomAD 17-19533943-G-A, REVEL 0.15, CADD 18.40
- E2G (p.Glu2Gly), gnomAD 17-19533944-A-G, REVEL 0.15, CADD 22.20
- E2E (p.Glu2Glu), rs2152311164, gnomAD 17-19533945-A-G, CADD 8.70
- A3T (p.Ala3Thr), ExAC rs754396350, TOPMed rs754396350, gnomAD rs754396350, REVEL 0.05, CADD 8.03
- A3V (p.Ala3Val), gnomAD rs1418027645, REVEL 0.04, CADD 3.87
- A3S (p.Ala3Ser), gnomAD 17-19533946-G-T, REVEL 0.07, CADD 5.09
- A3D (p.Ala3Asp), gnomAD 17-19533947-C-A, REVEL 0.06, CADD 2.42
- A3A (p.Ala3Ala), gnomAD 17-19533948-T-C, CADD 7.73
- P4H (p.Pro4His), gnomAD rs1157961028, REVEL 0.02, CADD 14.40
- P4S (p.Pro4Ser), Ensembl rs1198064639, REVEL 0.02, CADD 1.78
- P4A (p.Pro4Ala), gnomAD 17-19533949-C-G, REVEL 0.02, CADD 0.97
- P4T (p.Pro4Thr), gnomAD 17-19533949-C-A, REVEL 0.01, CADD 1.86
- P4R (p.Pro4Arg), gnomAD 17-19533950-C-G, REVEL 0.01, CADD 9.77
- P4P (p.Pro4Pro), gnomAD 17-19533951-T-C, CADD 5.70
- E5* (p.Glu5Ter), 1000Genomes rs912701678, TOPMed rs912701678, gnomAD rs912701678, CADD 27.00
- E5K (p.Glu5Lys), 1000Genomes rs912701678, TOPMed rs912701678, gnomAD rs912701678, REVEL 0.08, CADD 8.50
- E5G (p.Glu5Gly), gnomAD 17-19533953-A-G, REVEL 0.08, CADD 12.60
- E5V (p.Glu5Val), gnomAD 17-19533953-A-T, REVEL 0.05, CADD 11.10
- E5E (p.Glu5Glu), rs944316615, gnomAD 17-19533954-G-A, CADD 7.16
- E5D (p.Glu5Asp), gnomAD 17-19533954-G-T, REVEL 0.07, CADD 9.25
- E6G (p.Glu6Gly), TOPMed rs1915916610, gnomAD rs1915916610, REVEL 0.05, CADD 17.30
- E6K (p.Glu6Lys), ExAC rs762440633, TOPMed rs762440633, gnomAD rs762440633, REVEL 0.10, CADD 16.00
- E6* (p.Glu6Ter), gnomAD 17-19533955-G-T, CADD 33.00
- E6D (p.Glu6Asp), gnomAD 17-19533957-G-T, REVEL 0.05, CADD 8.17
- E6E (p.Glu6Glu), gnomAD 17-19533957-G-A, CADD 7.32
- P7S (p.Pro7Ser), gnomAD 17-19533958-C-T, REVEL 0.03, CADD 3.39
- P7T (p.Pro7Thr), gnomAD 17-19533958-C-A, REVEL 0.03, CADD 3.88
- P7R (p.Pro7Arg), gnomAD 17-19533959-C-G, REVEL 0.11, CADD 12.10
- P7L (p.Pro7Leu), gnomAD 17-19533959-C-T, REVEL 0.08, CADD 13.10
- P7H (p.Pro7His), gnomAD 17-19533959-C-A, REVEL 0.14, CADD 13.40
- P7P (p.Pro7Pro), rs1915916661, gnomAD 17-19533960-C-T, CADD 7.50
- A8E (p.Ala8Glu), ExAC rs751148502, TOPMed rs751148502, gnomAD rs751148502, REVEL 0.01, CADD 5.12
- A8T (p.Ala8Thr), ExAC rs763664282, TOPMed rs763664282, gnomAD rs763664282, REVEL 0.03, CADD 14.10
- A8S (p.Ala8Ser), gnomAD 17-19533961-G-T, REVEL 0.04, CADD 12.70
- A8P (p.Ala8Pro), gnomAD 17-19533961-G-C, REVEL 0.02, CADD 14.90
- A8V (p.Ala8Val), gnomAD 17-19533962-C-T, REVEL 0.01, CADD 6.57
- A8A (p.Ala8Ala), gnomAD 17-19533963-G-A, CADD 9.60
- P9L (p.Pro9Leu), TOPMed rs961377718, REVEL 0.05, CADD 15.90
- P9S (p.Pro9Ser), TOPMed rs1915916835, REVEL 0.02, CADD 16.00
- P9Q (p.Pro9Gln), gnomAD 17-19533963-GC-G, CADD 19.00
- P9T (p.Pro9Thr), gnomAD 17-19533964-C-A, REVEL 0.02, CADD 10.80
- P9P (p.Pro9Pro), rs756949058, gnomAD 17-19533966-A-G, CADD 4.72
- V10G (p.Val10Gly), ExAC rs750264871, TOPMed rs750264871, gnomAD rs750264871, REVEL 0.01, CADD 1.33
- V10L (p.Val10Leu), rs555657341, cosmic curated COSV54500, 1000Genomes rs555657341, ExAC rs555657341, REVEL 0.04, CADD 10.60, Benign
- V10M (p.Val10Met), 1000Genomes rs555657341, ExAC rs555657341, TOPMed rs555657341, gnomAD rs555657341, REVEL 0.03, CADD 13.20
- V10R (p.Val10Arg), gnomAD 17-19533966-AGTGC, CADD 21.50
- V10E (p.Val10Glu), gnomAD 17-19533968-T-A, REVEL 0.01, CADD 1.22
- V10A (p.Val10Ala), gnomAD 17-19533968-T-C, REVEL 0.02, CADD 0.22
- V10V (p.Val10Val), rs1354826404, gnomAD 17-19533969-G-T, CADD 6.13
- R11C (p.Arg11Cys), TOPMed rs1042708808, REVEL 0.08, CADD 21.30
- R11G (p.Arg11Gly), TOPMed rs1042708808
- R11H (p.Arg11His), Ensembl rs1915917347, REVEL 0.04, CADD 11.70
- R11S (p.Arg11Ser), gnomAD 17-19533970-C-A, REVEL 0.05, CADD 9.42
- R11L (p.Arg11Leu), gnomAD 17-19533971-G-T, REVEL 0.02, CADD 8.97
- R11R (p.Arg11Arg), rs755902763, gnomAD 17-19533972-C-T, CADD 8.48
- G12R (p.Gly12Arg), ExAC rs780125876, gnomAD rs780125876, REVEL 0.00, CADD 3.43
- G12* (p.Gly12Ter), gnomAD 17-19533973-G-T, CADD 26.60
- G12E (p.Gly12Glu), gnomAD 17-19533974-G-A, REVEL 0.01, CADD 1.39
- G12V (p.Gly12Val), gnomAD 17-19533974-G-T, REVEL 0.01, CADD 6.47
- G12G (p.Gly12Gly), gnomAD 17-19533975-A-C, CADD 7.76
- G13C (p.Gly13Cys), gnomAD 17-19533976-G-T, REVEL 0.05, CADD 15.00
- G13S (p.Gly13Ser), gnomAD 17-19533976-G-A, REVEL 0.00, CADD 6.88
- G13D (p.Gly13Asp), gnomAD 17-19533977-G-A, REVEL 0.01, CADD 9.71
- G13V (p.Gly13Val), gnomAD 17-19533977-G-T, REVEL 0.01, CADD 9.30
- G13G (p.Gly13Gly), gnomAD 17-19533978-C-A, CADD 7.54
- P14R (p.Pro14Arg), TOPMed rs1211450471, gnomAD rs1211450471, REVEL 0.01, CADD 4.18
- P14T (p.Pro14Thr), TOPMed rs1172816544, REVEL 0.01, CADD 8.03
- P14S (p.Pro14Ser), gnomAD 17-19533979-C-T, REVEL 0.03, CADD 9.16
- P14Q (p.Pro14Gln), gnomAD 17-19533980-C-A, REVEL 0.03, CADD 4.59
- P14L (p.Pro14Leu), gnomAD 17-19533980-C-T, REVEL 0.02, CADD 6.03
- P14P (p.Pro14Pro), rs1238649455, gnomAD 17-19533981-G-T, CADD 6.54
- E15K (p.Glu15Lys), gnomAD rs1479387747, REVEL 0.04, CADD 10.10
- E15* (p.Glu15Ter), gnomAD 17-19533982-G-T, CADD 33.00
- E15G (p.Glu15Gly), gnomAD 17-19533983-A-G, REVEL 0.00, CADD 7.42
- E15D (p.Glu15Asp), gnomAD 17-19533984-G-T, REVEL 0.02, CADD 7.21
- E15E (p.Glu15Glu), rs1477526593, gnomAD 17-19533984-G-A, CADD 7.06
- A16T (p.Ala16Thr), TOPMed rs1915917809, gnomAD rs1915917809, REVEL 0.01, CADD 6.53
- A16V (p.Ala16Val), cosmic curated COSV54499, TOPMed rs1177605964, gnomAD rs1177605964, REVEL 0.03, CADD 11.20
- A16S (p.Ala16Ser), gnomAD 17-19533985-G-T, REVEL 0.01, CADD 2.98
- A16D (p.Ala16Asp), gnomAD 17-19533986-C-A, REVEL 0.03, CADD 11.10
- A16A (p.Ala16Ala), gnomAD 17-19533987-C-A, CADD 8.06
- T17A (p.Thr17Ala), TOPMed rs2044249111, REVEL 0.01, CADD 1.22
- T17N (p.Thr17Asn), ExAC rs768787010, TOPMed rs768787010, gnomAD rs768787010, REVEL 0.01, CADD 0.08
- T17I (p.Thr17Ile), gnomAD 17-19533989-C-T, REVEL 0.01, CADD 0.54
- T17T (p.Thr17Thr), rs1441313284, gnomAD 17-19533990-C-T, CADD 8.48
- L18P (p.Leu18Pro), TOPMed rs1171452426, gnomAD rs1171452426, REVEL 0.01, CADD 12.90
- L18F (p.Leu18Phe), gnomAD 17-19533991-C-T, REVEL 0.03, CADD 7.91
- L18I (p.Leu18Ile), gnomAD 17-19533991-C-A, REVEL 0.01, CADD 0.89
- L18R (p.Leu18Arg), gnomAD 17-19533992-T-G, REVEL 0.02, CADD 10.30
- L18L (p.Leu18Leu), rs1057372810, gnomAD 17-19533993-T-G, CADD 5.66
- E19Q (p.Glu19Gln), ExAC rs779144949, gnomAD rs779144949, REVEL 0.05, CADD 13.30
- E19R (p.Glu19Arg), gnomAD 17-19533991-CT-C, CADD 17.80
- E19* (p.Glu19Ter), gnomAD 17-19533994-G-T, CADD 34.00
- E19K (p.Glu19Lys), gnomAD 17-19533994-G-A, REVEL 0.05, CADD 14.50
- E19V (p.Glu19Val), gnomAD 17-19533995-A-T, REVEL 0.02, CADD 12.00
- E19G (p.Glu19Gly), gnomAD 17-19533995-A-G, REVEL 0.01, CADD 12.60
- E19D (p.Glu19Asp), gnomAD 17-19533996-G-T, REVEL 0.08, CADD 11.10
- E19E (p.Glu19Glu), rs1915918397, gnomAD 17-19533996-G-A, CADD 7.60
- V20I (p.Val20Ile), TOPMed rs1915918483, REVEL 0.01, CADD 0.39
- V20F (p.Val20Phe), gnomAD 17-19533997-G-T, REVEL 0.00, CADD 0.39
- V20A (p.Val20Ala), gnomAD 17-19533998-T-C, REVEL 0.01, CADD 7.55
- V20V (p.Val20Val), gnomAD 17-19533999-C-A, CADD 8.29
- R21H (p.Arg21His), TOPMed rs895634071, gnomAD rs895634071, REVEL 0.01, CADD 4.51, Likely benign, not specified
- R21S (p.Arg21Ser), gnomAD 17-19534000-C-A, REVEL 0.04, CADD 17.10
- R21C (p.Arg21Cys), gnomAD 17-19534000-C-T, REVEL 0.03, CADD 17.10
- R21L (p.Arg21Leu), gnomAD 17-19534001-G-T, REVEL 0.00, CADD 4.35
- R21R (p.Arg21Arg), gnomAD 17-19534002-T-C, CADD 7.39
- G22E (p.Gly22Glu), ExAC rs748267094, TOPMed rs748267094, gnomAD rs748267094, REVEL 0.02, CADD 8.77
- G22W (p.Gly22Trp), gnomAD 17-19534003-G-T, REVEL 0.03, CADD 19.50
- G22R (p.Gly22Arg), gnomAD 17-19534003-G-A, REVEL 0.01, CADD 13.50
- G22V (p.Gly22Val), gnomAD 17-19534004-G-T, REVEL 0.02, CADD 13.40
- G22G (p.Gly22Gly), gnomAD 17-19534005-G-A, CADD 6.24
- S23L (p.Ser23Leu), TOPMed rs1915918788, REVEL 0.02, CADD 10.70
- S23P (p.Ser23Pro), gnomAD rs1915918719, REVEL 0.04, CADD 9.65
- S23W (p.Ser23Trp), gnomAD 17-19534007-C-G, REVEL 0.04, CADD 13.80
- S23* (p.Ser23Ter), gnomAD 17-19534007-C-A, CADD 33.00
- S23S (p.Ser23Ser), rs1013290688, gnomAD 17-19534008-G-T, CADD 6.19
- R24L (p.Arg24Leu), rs772367782, ClinGen CA8441919, ClinVar RCV004152811, ExAC rs772367782, REVEL 0.18, CADD 19.60, Uncertain significance, not specified
- R24S (p.Arg24Ser), gnomAD 17-19534009-C-A, REVEL 0.12, CADD 12.80
- R24C (p.Arg24Cys), gnomAD 17-19534009-C-T, REVEL 0.16, CADD 15.10
- R24H (p.Arg24His), gnomAD 17-19534010-G-A, REVEL 0.15, CADD 22.70
- R24R (p.Arg24Arg), gnomAD 17-19534011-C-A, CADD 9.14
- C25F (p.Cys25Phe), gnomAD 17-19534013-G-T, REVEL 0.02, CADD 7.56
- C25Y (p.Cys25Tyr), gnomAD 17-19534013-G-A, REVEL 0.01, CADD 5.05
- C25C (p.Cys25Cys), gnomAD 17-19534014-C-T, CADD 10.20
- C25* (p.Cys25Ter), gnomAD 17-19534014-C-A, CADD 33.00
- L26* (p.Leu26Ter), TOPMed rs1200085369, gnomAD rs1200085369, CADD 33.00
- L26L (p.Leu26Leu), rs2152311178, gnomAD 17-19534015-T-C, CADD 8.19
- L26M (p.Leu26Met), gnomAD 17-19534015-T-A, REVEL 0.05, CADD 10.70
- L26S (p.Leu26Ser), gnomAD 17-19534016-T-C, REVEL 0.03, CADD 13.30
- L26F (p.Leu26Phe), gnomAD 17-19534017-G-T, REVEL 0.05, CADD 13.10
- R27W (p.Arg27Trp), TOPMed rs1330917266, gnomAD rs1330917266, REVEL 0.07, CADD 23.20
- R27R (p.Arg27Arg), rs1330917266, gnomAD 17-19534018-C-A, CADD 10.20
- R27L (p.Arg27Leu), gnomAD 17-19534019-G-T, REVEL 0.03, CADD 9.09
- R27Q (p.Arg27Gln), gnomAD 17-19534019-G-A, REVEL 0.03, CADD 8.98
- R27P (p.Arg27Pro), gnomAD 17-19534019-G-C, REVEL 0.02, CADD 11.00
- L28M (p.Leu28Met), NCI-TCGA Cosmic COSV9956, cosmic curated COSV99564, REVEL 0.04, CADD 10.80, Variant assessed as somatic; moderate impact.
- L28L (p.Leu28Leu), gnomAD 17-19534021-C-T, CADD 9.00
- L28P (p.Leu28Pro), gnomAD 17-19534022-T-C, REVEL 0.12, CADD 16.90
- S29F (p.Ser29Phe), gnomAD rs1301627633, REVEL 0.02, CADD 16.90
- S29A (p.Ser29Ala), rs1272832115, gnomAD 17-19534018-C-CGG, CADD 21.70
- S29P (p.Ser29Pro), gnomAD 17-19534022-TG-T, CADD 22.70
- S29Y (p.Ser29Tyr), gnomAD 17-19534025-C-A, REVEL 0.05, CADD 16.40
- S29C (p.Ser29Cys), gnomAD 17-19534025-C-G, REVEL 0.05, CADD 20.60
- S29S (p.Ser29Ser), gnomAD 17-19534026-C-A, CADD 8.10
- A30S (p.Ala30Ser), gnomAD 17-19534027-G-T, REVEL 0.01, CADD 14.80
- A30T (p.Ala30Thr), gnomAD 17-19534027-G-A, REVEL 0.02, CADD 16.30
- A30V (p.Ala30Val), gnomAD 17-19534028-C-T, REVEL 0.01, CADD 7.42
- A30D (p.Ala30Asp), gnomAD 17-19534028-C-A, REVEL 0.01, CADD 5.16
- A30A (p.Ala30Ala), rs1220273399, gnomAD 17-19534029-C-T, CADD 11.60
- F31L (p.Phe31Leu), TOPMed rs1351069694, gnomAD rs1351069694, REVEL 0.03, CADD 18.90
- F31V (p.Phe31Val), gnomAD 17-19534030-T-G, REVEL 0.04, CADD 18.10
- F31S (p.Phe31Ser), gnomAD 17-19534031-T-C, REVEL 0.20, CADD 22.80
- F31F (p.Phe31Phe), gnomAD 17-19534032-C-T, CADD 12.10
- R32P (p.Arg32Pro), Ensembl rs1334319569, REVEL 0.22, CADD 23.10
- R32* (p.Arg32Ter), gnomAD 17-19534033-C-T, CADD 35.00
- R32G (p.Arg32Gly), gnomAD 17-19534033-C-G, REVEL 0.12, CADD 17.70
- R32R (p.Arg32Arg), gnomAD 17-19534033-C-A, CADD 13.60
- R32L (p.Arg32Leu), gnomAD 17-19534034-G-T, REVEL 0.03, CADD 19.60
- R32Q (p.Arg32Gln), gnomAD 17-19534034-G-A, REVEL 0.04, CADD 18.60
- E33K (p.Glu33Lys), rs771347017, ClinGen CA8441922, cosmic curated COSV54501, ClinVar RCV004244471, REVEL 0.07, CADD 17.30, Uncertain significance, not specified
- E33* (p.Glu33Ter), gnomAD 17-19534036-G-T, CADD 35.00
- E33G (p.Glu33Gly), gnomAD 17-19534037-A-G, REVEL 0.01, CADD 16.30
- E33D (p.Glu33Asp), gnomAD 17-19534038-A-T, REVEL 0.01, CADD 12.80
- E34Q (p.Glu34Gln), gnomAD 17-19534039-G-C, REVEL 0.25, CADD 26.60
- E34* (p.Glu34Ter), gnomAD 17-19534039-G-T, CADD 38.00
- E34K (p.Glu34Lys), gnomAD 17-19534039-G-A, REVEL 0.32, CADD 29.20
- E34G (p.Glu34Gly), gnomAD 17-19534040-A-G, REVEL 0.38, CADD 32.00
- E34D (p.Glu34Asp), gnomAD 17-19534041-G-T, REVEL 0.26, CADD 24.30
- E34E (p.Glu34Glu), gnomAD 17-19534041-G-A, CADD 13.60
- L35L (p.Leu35Leu), gnomAD 17-19534042-C-T, CADD 13.80
- L35V (p.Leu35Val), gnomAD 17-19534042-C-G, REVEL 0.11, CADD 16.20
- L35M (p.Leu35Met), gnomAD 17-19534042-C-A, REVEL 0.07, CADD 22.20
- L35Q (p.Leu35Gln), gnomAD 17-19534043-T-A, REVEL 0.26, CADD 24.50
- L35P (p.Leu35Pro), gnomAD 17-19534043-T-C, REVEL 0.29, CADD 25.20
- L35R (p.Leu35Arg), gnomAD 17-19534043-T-G, REVEL 0.26, CADD 25.00
- R36L (p.Arg36Leu), cosmic curated COSV10583, Ensembl rs866557628, REVEL 0.12, CADD 17.90
- R36W (p.Arg36Trp), 1000Genomes rs557911875, ExAC rs557911875, gnomAD rs557911875, REVEL 0.07, CADD 16.20
Public SLC47A1 analysis runs
- SLC47A1 analysis run — SLC47A1 (918 variants) — completed 2026-08-21