AGXT (P21549) variants and mutations
AGXT (also known as P21549) is a human protein-coding gene encoding an alanine--glyoxylate aminotransferase protein. A peroxisomal enzyme that converts glyoxylate to glycine, helping prevent oxalate buildup. Biallelic variants cause primary hyperoxaluria type 1. This analysis covers 841 AGXT variants and mutations. Of these, 96% have computational variant effect predictions. Disease context includes primary hyperoxaluria type 1, primary hyperoxaluria, and alanine glyoxylate aminotransferase deficiency. Example AGXT variants include M1I, M1N, and M1T.
Variant analysis overview
- Gene: AGXT
- Protein: P21549
- UniProt accession: P21549
- Organism: Homo sapiens
- Variants analyzed: 841
- Variant scope: all variants
- Completed: 2026-10-09
Variant and mutation evidence
- Variant composition: 658 unspecified-consequence records; 110 missense variants; 80 synonymous variants; 11 frameshift variants; 3 splice-region variants; 3 stop-gained variants; 1 in-frame insertions; 4 substitution
- Prediction scores: 809 variants have prediction scores (96% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: primary hyperoxaluria type 1, primary hyperoxaluria, alanine glyoxylate aminotransferase deficiency, hereditary disease, Hyperoxaluria, nephrocalcinosis, nephrolithiasis, nephrotic syndrome, Abnormality of metabolism/homeostasis, cardiac arrhythmia, hepatocellular carcinoma, familial idiopathic steroid-resistant nephrotic syndrome.
Protein structure and variant hotspots
- Protein features: 1 binding sites; 6 post-translational modification sites.
- PTM context: 12 variants overlap post-translational modification sites.
- Experimental data: 383 protein positions have experimental scores. Source: AGXT complementation assay *1 B, AGXT complementation assay *2 b.
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.
Diseases linked to AGXT
Notable AGXT variants
Examples include M1I, M1N, M1T, A2T, A2A, S3P, S3C, H4L. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1I (p.Met1Ile), rs180177213, ClinGen CA275615, ClinVar RCV000186272, ESM-1b 1.00, AlphaMissense 0.34, Pathogenic, Primary hyperoxaluria, type I
- M1N (p.Met1Asn), rs180177194, ClinGen CA275812, ClinVar RCV000186379, ClinVar RCV001225511, ESM-1b 1.00, AlphaMissense 0.44, Pathogenic, not provided; Primary hyperoxaluria, type I
- M1T (p.Met1Thr), rs138584408, ClinGen CA275613, ClinVar RCV000186271, ClinVar RCV001061218, ESM-1b 1.00, AlphaMissense 0.26, Pathogenic/Likely pathogenic, AGXT-related disorder; Primary hyperoxaluria; not provided
- A2T (p.Ala2Thr), gnomAD 2-240868869-G-A, REVEL 0.45, ESM-1b 0.00
- A2A (p.Ala2Ala), rs1419329633, gnomAD 2-240868871-C-T, CADD 5.23
- S3P (p.Ser3Pro), Ensembl rs2058974789, ESM-1b 0.00, AlphaMissense 0.10
- S3C (p.Ser3Cys), gnomAD 2-240868873-C-G, REVEL 0.38, ESM-1b 0.00
- H4L (p.His4Leu), ExAC rs762363201, TOPMed rs762363201, gnomAD rs762363201, REVEL 0.29, ESM-1b 0.00
- H4Q (p.His4Gln), Ensembl rs1559567678, REVEL 0.16, ESM-1b 0.00
- H4N (p.His4Asn), gnomAD 2-240868875-C-A, REVEL 0.14, ESM-1b 0.00
- H4Y (p.His4Tyr), gnomAD 2-240868875-C-T, REVEL 0.24, ESM-1b 0.00
- K5R (p.Lys5Arg), 1000Genomes rs182819405, gnomAD rs182819405, REVEL 0.22, ESM-1b 0.00
- K5K (p.Lys5Lys), rs767860823, gnomAD 2-240868880-G-A, CADD 4.55
- L6M (p.Leu6Met), gnomAD rs1486834101, REVEL 0.34, ESM-1b 0.07
- L6P (p.Leu6Pro), gnomAD 2-240868882-T-C, REVEL 0.41, ESM-1b 0.00
- L7L (p.Leu7Leu), rs1455078510, gnomAD 2-240868886-G-C, CADD 3.44
- V8D (p.Val8Asp), rs2528738855, ClinGen CA2586971624, ClinVar RCV003468677, ESM-1b 0.00, AlphaMissense 0.41, Likely pathogenic, Primary hyperoxaluria, type I
- V8L (p.Val8Leu), rs796052057, TOPMed rs796052057, gnomAD rs796052057, ClinGen CA275617, REVEL 0.27, ESM-1b 0.00, Uncertain significance, not specified
- V8M (p.Val8Met), TOPMed rs796052057, gnomAD rs796052057, REVEL 0.29, ESM-1b 0.00, Uncertain significance, not specified
- V8V (p.Val8Val), gnomAD 2-240868889-G-A, CADD 1.88
- T9A (p.Thr9Ala), Ensembl rs1575707111, ESM-1b 0.00, AlphaMissense 0.06
- T9I (p.Thr9Ile), 1000Genomes rs115014558, ESP rs115014558, ExAC rs115014558, TOPMed rs115014558, REVEL 0.22, ESM-1b 0.00, Benign
- T9N (p.Thr9Asn), rs115014558, ClinGen CA275540, ClinVar RCV000186218, ClinVar RCV000314232, REVEL 0.26, ESM-1b 0.00, Benign/Likely benign, not specified; not provided; Primary hyperoxaluria, type I
- T9P (p.Thr9Pro), Ensembl rs1575707111, REVEL 0.25, ESM-1b 0.00
- T9S (p.Thr9Ser), 1000Genomes rs115014558, ESP rs115014558, ExAC rs115014558, TOPMed rs115014558, REVEL 0.16, ESM-1b 0.00, Benign
- T9T (p.Thr9Thr), rs180177188, gnomAD 2-240868892-C-A, CADD 0.15
- P10A (p.Pro10Ala), rs180177191, ClinGen CA2208964, ClinVar RCV000425921, ClinVar RCV001833537, REVEL 0.43, ESM-1b 0.97, Uncertain significance, not provided
- P10H (p.Pro10His), ExAC rs748087765, gnomAD rs748087765, ESM-1b 1.00, AlphaMissense 0.39
- P10L (p.Pro10Leu), ExAC rs748087765, gnomAD rs748087765, REVEL 0.44, ESM-1b 1.00
- P10S (p.Pro10Ser), rs180177191, ClinGen CA275619, ClinVar RCV000186274, 1000Genomes rs180177191, REVEL 0.42, ESM-1b 1.00, Pathogenic, Primary hyperoxaluria, type I
- P10T (p.Pro10Thr), 1000Genomes rs180177191, ESP rs180177191, ExAC rs180177191, TOPMed rs180177191, REVEL 0.47, ESM-1b 1.00, Uncertain significance, Primary hyperoxaluria, type I
- P11A (p.Pro11Ala), rs375712696, ClinGen CA2208966, NCI-TCGA Cosmic COSV1002, NCI-TCGA Cosmic COSV5675, REVEL 0.49, ESM-1b 1.00, Uncertain significance, Primary hyperoxaluria, type I
- P11H (p.Pro11His), rs34116584, ClinGen CA275544, ClinVar RCV000186220, ClinVar RCV000884267, REVEL 0.56, ESM-1b 1.00, Conflicting interpretations, Alanine glyoxylate aminotransferase deficiency; not provided; Primary hyperoxalu
- P11L (p.Pro11Leu), rs2106427293, ClinGen CA2740096543, ClinVar RCV003879411, ClinGen CA2499215811, REVEL 0.44, ESM-1b 1.00, Likely benign, not specified; not provided; Primary hyperoxaluria, type I
- P11R (p.Pro11Arg), rs34116584, ClinGen CA275621, ClinVar RCV000186275, ClinVar RCV001553704, REVEL 0.70, ESM-1b 1.00, Conflicting interpretations, AGXT-related disorder; Inborn genetic diseases; Primary hyperoxaluria
- P11S (p.Pro11Ser), rs375712696, ClinGen CA2208968, ClinVar RCV002958785, ClinVar RCV005356229, REVEL 0.52, ESM-1b 1.00, Uncertain significance, Alanine glyoxylate aminotransferase deficiency; not provided
- P11T (p.Pro11Thr), ESP rs375712696, ExAC rs375712696, TOPMed rs375712696, gnomAD rs375712696, REVEL 0.58, ESM-1b 1.00, Uncertain significance, in allele minor
- P11P (p.Pro11Pro), rs1318935887, gnomAD 2-240868898-C-T, CADD 0.24
- K12N (p.Lys12Asn), TOPMed rs1277875813, gnomAD rs1277875813, REVEL 0.26, ESM-1b 0.00
- K12Q (p.Lys12Gln), Ensembl rs2106427300, ESM-1b 0.00, AlphaMissense 0.09
- K12R (p.Lys12Arg), rs142969817, ClinGen CA275546, ClinVar RCV000186221, ClinVar RCV000881725, REVEL 0.20, ESM-1b 0.00, Conflicting interpretations, AGXT-related disorder; Inborn genetic diseases; not provided
- K12P (p.Lys12Pro), gnomAD 2-240868890-A-ACC, CADD 11.50
- A13P (p.Ala13Pro), rs2528738973, ClinGen CA351312764, ClinVar RCV003309067, ESM-1b 0.00, AlphaMissense 0.13, Uncertain significance, Inborn genetic diseases
- A13T (p.Ala13Thr), gnomAD 2-240868902-G-A, REVEL 0.32, ESM-1b 0.00
- A13A (p.Ala13Ala), rs530836808, gnomAD 2-240868904-C-T, CADD 8.87
- L14R (p.Leu14Arg), 1000Genomes rs552120667, ExAC rs552120667, gnomAD rs552120667, REVEL 0.78, ESM-1b 0.80
- L14L (p.Leu14Leu), rs2058975287, gnomAD 2-240868905-C-T, CADD 9.47
- L15I (p.Leu15Ile), ExAC rs768057159, gnomAD rs768057159, REVEL 0.30, ESM-1b 1.00
- L15L (p.Leu15Leu), rs1176113554, gnomAD 2-240868910-C-G, CADD 5.21
- K16K (p.Lys16Lys), rs571553505, gnomAD 2-240868913-G-A, CADD 6.16
- P17H (p.Pro17His), ExAC rs761064900, TOPMed rs761064900, gnomAD rs761064900, ESM-1b 1.00, AlphaMissense 0.21
- P17L (p.Pro17Leu), ExAC rs761064900, TOPMed rs761064900, gnomAD rs761064900, REVEL 0.66, ESM-1b 1.00
- P17S (p.Pro17Ser), ExAC rs773611094, gnomAD rs773611094, REVEL 0.59, ESM-1b 0.00
- P17T (p.Pro17Thr), ExAC rs773611094, gnomAD rs773611094, REVEL 0.68, ESM-1b 0.00
- L18F (p.Leu18Phe), rs2528739011, ClinGen CA351312842, ClinVar RCV003468708, ESM-1b 0.47, AlphaMissense 0.18, Uncertain significance, Primary hyperoxaluria, type I
- L18L (p.Leu18Leu), rs1057288575, gnomAD 2-240868919-C-T, CADD 0.90
- I20L (p.Ile20Leu), TOPMed rs1400902861, gnomAD rs1400902861, ESM-1b 0.45, AlphaMissense 0.08
- I20N (p.Ile20Asn), Ensembl rs895965609, ESM-1b 1.00, AlphaMissense 0.29
- I20V (p.Ile20Val), TOPMed rs1400902861, gnomAD rs1400902861, ESM-1b 0.00, AlphaMissense 0.08
- I20I (p.Ile20Ile), gnomAD 2-240868925-C-A, CADD 3.84
- P21S (p.Pro21Ser), TOPMed rs2058975411, ESM-1b 0.31, AlphaMissense 0.11
- P21L (p.Pro21Leu), gnomAD 2-240868927-C-T, REVEL 0.58, ESM-1b 1.00
- N22K (p.Asn22Lys), TOPMed rs2058975463, ESM-1b 0.00, AlphaMissense 0.10
- N22S (p.Asn22Ser), rs34885252, ClinGen CA275548, ClinVar RCV000186222, ClinVar RCV000280164, REVEL 0.22, ESM-1b 0.00, Benign/Likely benign, not specified; not provided; Primary hyperoxaluria, type I
- Q23* (p.Gln23Ter), rs1575707182, ClinGen CA351312936, ClinVar RCV000810788, Ensembl rs1575707182, Pathogenic
- Q23R (p.Gln23Arg), Ensembl rs2106427319, ESM-1b 0.00, AlphaMissense 0.05
- L24I (p.Leu24Ile), rs754037121, ClinGen CA2208974, ClinVar RCV001230740, ClinVar RCV001833997, REVEL 0.45, ESM-1b 0.00, Uncertain significance, Primary hyperoxaluria, type I; not provided
- L24V (p.Leu24Val), gnomAD 2-240868935-C-G, REVEL 0.48, ESM-1b 0.00
- L24L (p.Leu24Leu), rs900156149, gnomAD 2-240868937-C-G, CADD 0.18
- L25R (p.Leu25Arg), rs180177262, ClinGen CA275623, ClinVar RCV000186276, ExAC rs180177262, REVEL 0.91, ESM-1b 1.00, Pathogenic, Primary hyperoxaluria, type I
- L25L (p.Leu25Leu), gnomAD 2-240868940-G-C, CADD 1.25
- L26P (p.Leu26Pro), rs180177268, ClinGen CA275625, ClinVar RCV000186277, TOPMed rs180177268, ESM-1b 1.00, AlphaMissense 0.82, Pathogenic, Primary hyperoxaluria, type I
- L26L (p.Leu26Leu), rs2058975534, gnomAD 2-240868943-G-A, CADD 3.66
- G27E (p.Gly27Glu), rs765405040, ClinGen CA351313017, ClinVar RCV003468715, ESM-1b 1.00, AlphaMissense 0.63, Uncertain significance, Primary hyperoxaluria, type I
- G27V (p.Gly27Val), ExAC rs765405040, gnomAD rs765405040, REVEL 0.76, ESM-1b 1.00, Uncertain significance
- G27W (p.Gly27Trp), rs2528739107, ClinGen CA351313009, ClinVar RCV003448955, ESM-1b 1.00, AlphaMissense 0.81, Likely pathogenic, Primary hyperoxaluria, type I
- G27G (p.Gly27Gly), gnomAD 2-240868946-G-A, CADD 5.04
- P28S (p.Pro28Ser), rs376684240, ClinGen CA2208976, ClinVar RCV000670153, ESP rs376684240, REVEL 0.74, ESM-1b 0.31, Uncertain significance, Primary hyperoxaluria, type I
- P28A (p.Pro28Ala), gnomAD 2-240868947-C-G, REVEL 0.76, ESM-1b 0.44
- P30S (p.Pro30Ser), gnomAD 2-240868953-C-T, REVEL 0.71, ESM-1b 1.00
- S31F (p.Ser31Phe), gnomAD 2-240868957-C-T, REVEL 0.71, ESM-1b 1.00
- N32D (p.Asn32Asp), gnomAD 2-240868959-A-G, REVEL 0.75, ESM-1b 1.00
- N32H (p.Asn32His), gnomAD 2-240868959-A-C, REVEL 0.80, ESM-1b 1.00
- N32K (p.Asn32Lys), gnomAD 2-240868961-C-A, REVEL 0.60, ESM-1b 1.00
- N32N (p.Asn32Asn), rs1461964497, gnomAD 2-240868961-C-T, CADD 5.27
- L33P (p.Leu33Pro), TOPMed rs2058975609, REVEL 0.68, ESM-1b 0.85
- L33L (p.Leu33Leu), rs1181815243, gnomAD 2-240868964-G-C, CADD 4.54
- P34A (p.Pro34Ala), ExAC rs758388293, TOPMed rs758388293, gnomAD rs758388293, ESM-1b 0.00, AlphaMissense 0.12, Uncertain significance
- P34S (p.Pro34Ser), rs758388293, ClinGen CA2208977, ClinVar RCV002686152, ExAC rs758388293, REVEL 0.29, ESM-1b 0.00, Uncertain significance, not provided
- P34T (p.Pro34Thr), ExAC rs758388293, TOPMed rs758388293, gnomAD rs758388293, REVEL 0.26, ESM-1b 0.00, Uncertain significance
- P35H (p.Pro35His), ExAC rs779013628, TOPMed rs779013628, gnomAD rs779013628, REVEL 0.42, ESM-1b 1.00, Uncertain significance, Inborn genetic diseases
- P35L (p.Pro35Leu), ExAC rs779013628, TOPMed rs779013628, gnomAD rs779013628, REVEL 0.65, ESM-1b 1.00, Uncertain significance
- P35S (p.Pro35Ser), NCI-TCGA Cosmic COSV5675, TOPMed rs2058975630, REVEL 0.43, ESM-1b 0.30, Variant assessed as somatic; moderate impact.
- R36C (p.Arg36Cys), rs180177157, ClinGen CA274183, ClinVar RCV000169332, ClinVar RCV001054309, REVEL 0.78, ESM-1b 1.00, Pathogenic/Likely pathogenic, not provided; Primary hyperoxaluria, type I
- R36G (p.Arg36Gly), rs180177157, ClinGen CA351313112, ClinVar RCV002630271, REVEL 0.74, ESM-1b 1.00, Likely pathogenic, not provided
- R36H (p.Arg36His), rs180177162, ClinGen CA275627, ClinVar RCV000186278, ClinVar RCV001383728, REVEL 0.77, ESM-1b 1.00, Pathogenic/Likely pathogenic, AGXT-related disorder; Primary hyperoxaluria; not provided
- R36P (p.Arg36Pro), rs180177162, ClinGen CA351313118, ClinVar RCV003011885, REVEL 0.72, ESM-1b 1.00, Likely pathogenic, not provided
- I37V (p.Ile37Val), gnomAD 2-240868974-A-G, REVEL 0.18, ESM-1b 0.00
- I37N (p.Ile37Asn), gnomAD 2-240868975-T-A, REVEL 0.43, ESM-1b 1.00
- M38I (p.Met38Ile), gnomAD rs1234749250, REVEL 0.24, ESM-1b 0.11, Uncertain significance, AGXT-related disorder
- M38R (p.Met38Arg), ExAC rs780905277, TOPMed rs780905277, gnomAD rs780905277, REVEL 0.16, ESM-1b 0.00
- M38T (p.Met38Thr), ExAC rs780905277, TOPMed rs780905277, gnomAD rs780905277, REVEL 0.20, ESM-1b 0.00
- M38L (p.Met38Leu), gnomAD 2-240868977-A-T, REVEL 0.19, ESM-1b 0.00
- M38V (p.Met38Val), gnomAD 2-240868977-A-G, REVEL 0.14, ESM-1b 0.15
- A39E (p.Ala39Glu), gnomAD rs1305673661, REVEL 0.32, ESM-1b 0.00
- A40G (p.Ala40Gly), TOPMed rs1335566978, gnomAD rs1335566978, REVEL 0.61, ESM-1b 1.00
- A40T (p.Ala40Thr), TOPMed rs1235145069, gnomAD rs1235145069, REVEL 0.68, ESM-1b 1.00
- A40Q (p.Ala40Gln), rs180177166, gnomAD 2-240868980-G-GCA, CADD 23.00
- A40A (p.Ala40Ala), rs1333685290, gnomAD 2-240868985-C-T, CADD 0.13
- G41A (p.Gly41Ala), TOPMed rs180177168, gnomAD rs180177168, ESM-1b 0.00, AlphaMissense 0.10, Pathogenic, in HP1
- G41E (p.Gly41Glu), rs180177168, ClinGen CA275629, ClinVar RCV000186279, ClinVar RCV005089932, REVEL 0.79, ESM-1b 1.00, Conflicting interpretations, Primary hyperoxaluria; not provided
- G41R (p.Gly41Arg), rs121908523, ClinGen CA351313171, ClinVar RCV002664289, ClinVar RCV003466000, REVEL 0.75, ESM-1b 1.00, Pathogenic/Likely pathogenic, not provided; Primary hyperoxaluria, type I
- G41V (p.Gly41Val), rs180177168, ClinGen CA274216, ClinVar RCV000169364, ClinVar RCV001386862, REVEL 0.73, ESM-1b 1.00, Conflicting interpretations, not provided; Primary hyperoxaluria, type I
- G41G (p.Gly41Gly), rs769473982, gnomAD 2-240868988-G-C, CADD 0.12
- G42E (p.Gly42Glu), rs180177170, ClinGen CA275631, ClinVar RCV000186280, 1000Genomes rs180177170, REVEL 0.63, ESM-1b 1.00, Pathogenic, Primary hyperoxaluria, type I
- G42R (p.Gly42Arg), ExAC rs779515162, REVEL 0.38, ESM-1b 0.79, Uncertain significance, Primary hyperoxaluria, type I
- G42G (p.Gly42Gly), rs1251984525, gnomAD 2-240868991-G-A, CADD 1.09
- L43Q (p.Leu43Gln), rs768181954, ClinGen CA2208983, ClinVar RCV002076010, ExAC rs768181954, REVEL 0.22, ESM-1b 0.12, Likely benign, not provided
- L43R (p.Leu43Arg), ExAC rs768181954, TOPMed rs768181954, gnomAD rs768181954, REVEL 0.17, ESM-1b 0.00, Likely benign
- L43A (p.Leu43Ala), rs180177171, gnomAD 2-240868985-C-CG, CADD 23.60
- L43C (p.Leu43Cys), rs180177171, gnomAD 2-240868985-CG-C, CADD 23.10
- L43P (p.Leu43Pro), gnomAD 2-240868993-T-C, REVEL 0.50, ESM-1b 1.00
- L43L (p.Leu43Leu), gnomAD 2-240868994-G-A, CADD 2.68
- Q44* (p.Gln44Ter), rs180177172, ClinGen CA275633, ClinVar RCV000186281, Ensembl rs180177172, CADD 35.00, Pathogenic
- Q44Q (p.Gln44Gln), rs1443921633, gnomAD 2-240868997-G-A, CADD 2.51
- M45V (p.Met45Val), gnomAD 2-240868998-A-G, REVEL 0.20, ESM-1b 0.05
- M45T (p.Met45Thr), gnomAD 2-240868999-T-C, REVEL 0.26, ESM-1b 0.00
- I46T (p.Ile46Thr), ExAC rs773705695, gnomAD rs773705695, REVEL 0.58, ESM-1b 0.29
- I46M (p.Ile46Met), gnomAD 2-240869003-C-G, REVEL 0.48, ESM-1b 0.00
- I46I (p.Ile46Ile), rs200488482, gnomAD 2-240869003-C-T, CADD 0.31
- G47E (p.Gly47Glu), rs1171762321, ClinGen CA351313242, NCI-TCGA Cosmic COSV1002, ClinVar RCV003468678, REVEL 0.76, ESM-1b 1.00, Likely pathogenic, Primary hyperoxaluria, type I
- G47R (p.Gly47Arg), rs180177173, ClinGen CA275636, NCI-TCGA Cosmic COSV5675, ClinVar RCV000186282, REVEL 0.67, ESM-1b 1.00, Pathogenic/Likely pathogenic, not provided; Primary hyperoxaluria, type I
- G47V (p.Gly47Val), NCI-TCGA Cosmic COSV1002, gnomAD rs1171762321, REVEL 0.75, ESM-1b 1.00, Likely pathogenic, in HP1
- G47W (p.Gly47Trp), rs180177173, ClinGen CA351313239, ClinVar RCV002019332, ExAC rs180177173, ESM-1b 1.00, AlphaMissense 0.56, Likely pathogenic, not provided
- S48F (p.Ser48Phe), Ensembl rs1575707256, ESM-1b 0.00, AlphaMissense 0.20
- S48P (p.Ser48Pro), gnomAD rs1279674854, REVEL 0.33, ESM-1b 0.00
- S48S (p.Ser48Ser), rs776929752, gnomAD 2-240869009-C-T, CADD 6.03
- M49I (p.Met49Ile), Ensembl rs2058976092, REVEL 0.51, ESM-1b 0.02
- M49L (p.Met49Leu), rs74205173, ClinGen CA2208988, ClinVar RCV000665056, ClinVar RCV000885301, REVEL 0.31, ESM-1b 0.00, Benign/Likely benign, not specified; not provided; Primary hyperoxaluria, type I
- M49T (p.Met49Thr), TOPMed rs2058976084, ESM-1b 1.00, AlphaMissense 0.19
- M49V (p.Met49Val), 1000Genomes rs74205173, ExAC rs74205173, TOPMed rs74205173, gnomAD rs74205173, REVEL 0.58, ESM-1b 0.00, Benign
- M49R (p.Met49Arg), gnomAD 2-240869011-T-G, REVEL 0.73, ESM-1b 1.00
- D52H (p.Asp52His), gnomAD rs2058976103, REVEL 0.49, ESM-1b 0.27
- D52N (p.Asp52Asn), gnomAD 2-240869019-G-A, REVEL 0.32, ESM-1b 0.00
- D52D (p.Asp52Asp), rs765607242, gnomAD 2-240869021-T-C, CADD 6.67
- M53T (p.Met53Thr), gnomAD 2-240869023-T-C, REVEL 0.35, ESM-1b 0.78
- Y54H (p.Tyr54His), TOPMed rs1422349310, ESM-1b 1.00, AlphaMissense 0.19
- Q55H (p.Gln55His), gnomAD rs1395481866, REVEL 0.71, ESM-1b 0.00
- Q55Q (p.Gln55Gln), gnomAD 2-240869030-G-A, CADD 23.00
- I56N (p.Ile56Asn), rs180177180, ClinGen CA275638, ClinVar RCV000186283, ClinVar RCV003229816, REVEL 0.78, ESM-1b 1.00, Conflicting interpretations, Primary hyperoxaluria; not provided; Primary hyperoxaluria, type I
- I56S (p.Ile56Ser), ExAC rs180177180, TOPMed rs180177180, gnomAD rs180177180, REVEL 0.85, ESM-1b 1.00, Likely pathogenic
- I56V (p.Ile56Val), Ensembl rs2058977841, ESM-1b 0.00, AlphaMissense 0.11
- M57I (p.Met57Ile), gnomAD rs1258238960, REVEL 0.67, ESM-1b 0.82
- M57V (p.Met57Val), gnomAD rs868580226, REVEL 0.88, ESM-1b 0.96
- M57T (p.Met57Thr), gnomAD 2-240869174-T-C, REVEL 0.88, ESM-1b 1.00
- D58E (p.Asp58Glu), rs761756536, ClinGen CA68173735, ClinVar RCV001141969, ExAC rs761756536, REVEL 0.35, ESM-1b 0.00, Uncertain significance, Primary hyperoxaluria, type I
- D58G (p.Asp58Gly), gnomAD rs1373914192, REVEL 0.64, ESM-1b 1.00
- D58N (p.Asp58Asn), rs774651961, ClinGen CA2209029, ClinVar RCV001222536, ClinVar RCV001833929, REVEL 0.41, ESM-1b 0.00, Uncertain significance, not provided
- D58D (p.Asp58Asp), rs761756536, gnomAD 2-240869178-C-T, CADD 0.72
- E59* (p.Glu59Ter), rs767586362, ClinGen CA351313364, ClinVar RCV001939627, ExAC rs767586362, AlphaMissense 0.40, MetaLR 0.78, Pathogenic
- E59K (p.Glu59Lys), rs767586362, ClinGen CA275640, NCI-TCGA Cosmic COSV5675, ClinVar RCV000186284, REVEL 0.76, ESM-1b 1.00, Uncertain significance, not specified
- I60M (p.Ile60Met), TOPMed rs983369223, gnomAD rs983369223, REVEL 0.73, ESM-1b 1.00
- I60S (p.Ile60Ser), gnomAD 2-240869183-T-G, REVEL 0.94, ESM-1b 1.00
- I60I (p.Ile60Ile), rs983369223, gnomAD 2-240869184-C-T, CADD 10.90
- E62A (p.Glu62Ala), ExAC rs773078356, TOPMed rs773078356, gnomAD rs773078356, REVEL 0.26, ESM-1b 0.00, Uncertain significance, Primary hyperoxaluria, type I
- G63D (p.Gly63Asp), rs760666036, ClinGen CA2209032, ClinVar RCV002651631, ClinVar RCV003445215, REVEL 0.81, ESM-1b 1.00, Conflicting interpretations, Primary hyperoxaluria, type I; not provided
- G63R (p.Gly63Arg), rs180177181, ClinGen CA275642, ClinVar RCV000186285, ClinVar RCV004689661, ESM-1b 1.00, AlphaMissense 0.33, Pathogenic, Primary hyperoxaluria; Primary hyperoxaluria, type I
- G63S (p.Gly63Ser), Ensembl rs180177181, ESM-1b 1.00, AlphaMissense 0.33, Pathogenic
- G63G (p.Gly63Gly), rs1030478832, gnomAD 2-240869193-C-T, CADD 10.30
- I64F (p.Ile64Phe), rs2528739981, ClinGen CA351313398, ClinVar RCV003445263, ClinVar RCV003479520, ESM-1b 1.00, AlphaMissense 0.48, Conflicting interpretations, not specified; Primary hyperoxaluria, type I
- I64N (p.Ile64Asn), rs2528739984, ClinGen CA351313399, ClinVar RCV003445264, ESM-1b 1.00, AlphaMissense 0.72, Likely pathogenic, Primary hyperoxaluria, type I
- Q65K (p.Gln65Lys), TOPMed rs2058978010, gnomAD rs2058978010, REVEL 0.56, ESM-1b 0.00
- Q65* (p.Gln65Ter), gnomAD 2-240869197-C-T, CADD 39.00
- Q65Q (p.Gln65Gln), rs890310872, gnomAD 2-240869199-G-A, CADD 9.47
- Y66* (p.Tyr66Ter), rs121908521, ClinGen CA351313417, ClinVar RCV001263729, ExAC rs121908521, CADD 35.00, Pathogenic
- Y66Y (p.Tyr66Tyr), rs121908521, gnomAD 2-240869202-C-T, CADD 5.29
- V67M (p.Val67Met), ExAC rs753677855, TOPMed rs753677855, gnomAD rs753677855, REVEL 0.45, ESM-1b 1.00
- V67E (p.Val67Glu), gnomAD 2-240869204-T-A, REVEL 0.73, ESM-1b 1.00
- F68S (p.Phe68Ser), rs2106427539, ClinGen CA351313427, ClinVar RCV001816298, Ensembl rs2106427539, ESM-1b 1.00, AlphaMissense 0.86, Uncertain significance, not provided
- Q69* (p.Gln69Ter), rs180177182, ClinGen CA275644, ClinVar RCV000186286, Ensembl rs180177182, Pathogenic
Public AGXT analysis runs
- AGXT analysis run — AGXT (841 variants) — completed 2026-10-09