LRP2 (P98164) variants and mutations
LRP2 (also known as P98164) is a human protein-coding gene encoding a low-density lipoprotein receptor-related protein 2 protein. It mediates endocytic uptake of filtered proteins, vitamins, hormones, and other ligands in proximal renal tubules and several absorptive epithelia. Biallelic loss-of-function variants cause Donnai-Barrow syndrome with proteinuria, craniofacial abnormalities, and neurodevelopmental features. This analysis covers 5,813 LRP2 variants and mutations. Of these, 70% have computational variant effect predictions. Disease context includes Donnai-Barrow syndrome, Intellectual disability, and gout. Example LRP2 variants include R3C, R3H, and R3P.
Variant analysis overview
- Gene: LRP2
- Protein: P98164
- UniProt accession: P98164
- Organism: Homo sapiens
- Variants analyzed: 5813
- Variant scope: all variants
- Completed: 2026-08-22
Variant and mutation evidence
- Variant composition: 5,634 unspecified-consequence records; 1 stop retained variant; 77 synonymous variants; 84 missense variants; 6 frameshift variants; 5 in-frame deletions; 5 stop-gained variants; 1 in-frame insertions; 2 splice-region variants; 1 substitution
- Prediction scores: 4,064 variants have prediction scores (70% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Donnai-Barrow syndrome, Intellectual disability, gout, Hearing impairment, hereditary disease, intellectual disability, autosomal dominant 40, chronic kidney disease, hyperuricemia, disease of peritoneum, Retinal dystrophy, clear cell renal carcinoma, Stickler syndrome.
Protein structure and variant hotspots
- Protein features: 1 transmembrane segments; 42 domains; 11 binding sites; 46 post-translational modification sites.
- Structural context: 1,925 variants have structural context.
- PTM context: 66 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, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Notable LRP2 variants
Examples include R3C, R3H, R3P, G4R, G4W, P5L, P5R, A6E. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- R3C (p.Arg3Cys), gnomAD rs1397756574, CADD 24.20, PolyPhen-2 0.55
- R3H (p.Arg3His), TOPMed rs1172501525, gnomAD rs1172501525, CADD 23.30, PolyPhen-2 0.55
- R3P (p.Arg3Pro), TOPMed rs1172501525, gnomAD rs1172501525, CADD 22.40, PolyPhen-2 0.41
- G4R (p.Gly4Arg), rs781681275, ClinGen CA349256996, ClinVar RCV002630511, ExAC rs781681275, CADD 0.46, PolyPhen-2 0.00, Uncertain significance, not provided
- G4W (p.Gly4Trp), ExAC rs781681275, TOPMed rs781681275, gnomAD rs781681275, CADD 7.39, PolyPhen-2 0.00, Uncertain significance
- P5L (p.Pro5Leu), gnomAD rs1396944343, CADD 10.40, PolyPhen-2 0.00
- P5R (p.Pro5Arg), gnomAD rs1396944343
- A6E (p.Ala6Glu), rs878853100, ClinGen CA10581410, ClinVar RCV000224450, gnomAD rs878853100, CADD 13.80, PolyPhen-2 0.07, Uncertain significance, not provided
- V8M (p.Val8Met), rs747080240, ClinGen CA1956028, ClinVar RCV002023719, ClinVar RCV002486727, CADD 14.30, PolyPhen-2 0.28, Uncertain significance, Donnai-Barrow syndrome; not provided
- A9G (p.Ala9Gly), TOPMed rs1196519126, gnomAD rs1196519126, CADD 13.80, PolyPhen-2 0.18, Uncertain significance
- A9T (p.Ala9Thr), rs2105595174, ClinGen CA349256941, ClinVar RCV001966887, Ensembl rs2105595174, CADD 16.10, PolyPhen-2 0.08, Uncertain significance, not provided
- A9V (p.Ala9Val), rs1196519126, ClinGen CA349256931, cosmic curated COSV10802, ClinVar RCV004413137, CADD 13.00, PolyPhen-2 0.00, Uncertain significance, Inborn genetic diseases
- C10F (p.Cys10Phe), gnomAD rs1231417165, CADD 16.70, PolyPhen-2 0.00
- T11M (p.Thr11Met), gnomAD rs1266874181, CADD 15.50, PolyPhen-2 0.01
- T11P (p.Thr11Pro), gnomAD rs1686192550, CADD 14.00, PolyPhen-2 0.07
- L13F (p.Leu13Phe), TOPMed rs1255290148, gnomAD rs1255290148, CADD 20.60, PolyPhen-2 0.03
- V17F (p.Val17Phe), gnomAD rs1238825402, CADD 15.40, PolyPhen-2 0.00
- A18T (p.Ala18Thr), rs2105595106, ClinGen CA349256836, ClinVar RCV001947332, Ensembl rs2105595106, CADD 16.70, PolyPhen-2 0.01, Uncertain significance, not provided
- A18V (p.Ala18Val), rs1348031583, ClinGen CA349256830, ClinVar RCV002949731, TOPMed rs1348031583, CADD 14.00, PolyPhen-2 0.00, Uncertain significance, not provided
- C19Y (p.Cys19Tyr), gnomAD rs1280935446, CADD 18.50, PolyPhen-2 0.01
- L20Q (p.Leu20Gln), NCI-TCGA TCGA novel, CADD 16.70, PolyPhen-2 0.37, Variant assessed as somatic; moderate impact.
- L20R (p.Leu20Arg), ExAC rs755874795
- A21D (p.Ala21Asp), rs2105595067, ClinGen CA2573133668, ClinVar RCV001982219, ClinVar RCV005023481, Uncertain significance, Donnai-Barrow syndrome; not provided
- A21E (p.Ala21Glu), rs200858963, ClinGen CA1956023, ClinVar RCV003241157, ExAC rs200858963, CADD 13.40, PolyPhen-2 0.01, Uncertain significance, Inborn genetic diseases
- P22L (p.Pro22Leu), gnomAD rs867254167, CADD 12.40, PolyPhen-2 0.00, Uncertain significance, Donnai-Barrow syndrome
- P22Q (p.Pro22Gln), gnomAD rs867254167, CADD 9.71, PolyPhen-2 0.01, Uncertain significance
- P22S (p.Pro22Ser), rs759114383, ClinGen CA10611327, ClinVar RCV000309024, ExAC rs759114383, CADD 16.40, PolyPhen-2 0.01, Uncertain significance, Donnai-Barrow syndrome
- P22T (p.Pro22Thr), rs759114383, ClinGen CA1956022, ClinVar RCV003206404, ExAC rs759114383, CADD 17.10, PolyPhen-2 0.06, Uncertain significance, Inborn genetic diseases
- A23D (p.Ala23Asp), ExAC rs762617592, gnomAD rs762617592, CADD 21.90, PolyPhen-2 0.16
- A23S (p.Ala23Ser), ExAC rs766070722, gnomAD rs766070722, CADD 21.20, PolyPhen-2 0.06
- A23T (p.Ala23Thr), ExAC rs766070722, gnomAD rs766070722, CADD 22.50, PolyPhen-2 0.04
- S24G (p.Ser24Gly), ExAC rs772782805, gnomAD rs772782805, CADD 13.80, PolyPhen-2 0.00
- S24N (p.Ser24Asn), Ensembl rs1686190829, CADD 16.50, PolyPhen-2 0.00
- S24R (p.Ser24Arg), ExAC rs770065910, gnomAD rs770065910, NCI-TCGA TCGA novel, CADD 9.13, PolyPhen-2 0.00, Variant assessed as somatic; moderate impact.
- G25C (p.Gly25Cys), ExAC rs762223491, gnomAD rs762223491, CADD 22.20, PolyPhen-2 0.03
- Q26L (p.Gln26Leu), ExAC rs777070747, gnomAD rs777070747, CADD 22.70, PolyPhen-2 0.20
- Q26R (p.Gln26Arg), ExAC rs777070747, gnomAD rs777070747, CADD 17.60, PolyPhen-2 0.01
- E27D (p.Glu27Asp), ExAC rs772294760, TOPMed rs772294760, gnomAD rs772294760, CADD 16.00, PolyPhen-2 0.18
- E27Q (p.Glu27Gln), gnomAD rs1486585687, CADD 24.90, PolyPhen-2 0.20
- C28R (p.Cys28Arg), gnomAD rs1161067807, CADD 26.60, PolyPhen-2 1.00
- C28Y (p.Cys28Tyr), Ensembl rs927875898
- D29G (p.Asp29Gly), NCI-TCGA Cosmic COSV9979, cosmic curated COSV99790, Variant assessed as somatic; moderate impact.
- A31E (p.Ala31Glu), rs144829356, ClinGen CA59967238, ClinVar RCV001965244, 1000Genomes rs144829356, CADD 9.53, PolyPhen-2 0.00, Uncertain significance, not provided
- A31V (p.Ala31Val), rs144829356, ClinGen CA248700, ClinVar RCV000117554, ClinVar RCV000362234, CADD 16.00, PolyPhen-2 0.07, Benign/Likely benign, not specified; not provided; Donnai-Barrow syndrome
- H32Q (p.His32Gln), Ensembl rs2105516337, CADD 1.44, PolyPhen-2 0.01
- H32R (p.His32Arg), rs771153702, NCI-TCGA Cosmic COSV5556, cosmic curated COSV55565, ExAC rs771153702, CADD 14.70, PolyPhen-2 0.00, Variant assessed as somatic; moderate impact.
- H32Y (p.His32Tyr), rs950601446, NCI-TCGA Cosmic COSV9978, cosmic curated COSV99786, Ensembl rs950601446, AlphaMissense 0.08, MetaLR 0.63, Variant assessed as somatic; moderate impact.
- R34C (p.Arg34Cys), rs747942310, ClinGen CA1955990, NCI-TCGA Cosmic COSV5553, cosmic curated COSV55539, CADD 26.90, PolyPhen-2 0.96, Uncertain significance, not provided
- R34H (p.Arg34His), rs186568676, ClinGen CA1955989, cosmic curated COSV55541, NCI-TCGA Cosmic COSV9978, CADD 23.30, PolyPhen-2 0.92, Uncertain significance, Donnai-Barrow syndrome; not provided
- R34L (p.Arg34Leu), NCI-TCGA Cosmic COSV9978, cosmic curated COSV99787, CADD 17.20, PolyPhen-2 0.06, Variant assessed as somatic; moderate impact.
- G36E (p.Gly36Glu), gnomAD rs1684891571, CADD 0.96
- G38E (p.Gly38Glu), TOPMed rs1684891403
- G38R (p.Gly38Arg), TOPMed rs1684891492
- H39Y (p.His39Tyr), gnomAD rs1684891259, CADD 0.07, PolyPhen-2 0.00
- C40R (p.Cys40Arg), Ensembl rs1559073963, CADD 24.70, PolyPhen-2 1.00
- I41L (p.Ile41Leu), Ensembl rs1559073960
- P42A (p.Pro42Ala), Ensembl rs1559073954, CADD 9.28, PolyPhen-2 0.59
- P42L (p.Pro42Leu), NCI-TCGA Cosmic COSV5556, CADD 16.20, PolyPhen-2 0.83, Variant assessed as somatic; moderate impact.
- A43E (p.Ala43Glu), rs746960003, ClinGen CA1955987, ClinVar RCV001954328, ClinVar RCV005025540, CADD 0.01, PolyPhen-2 0.12, Uncertain significance, not provided; Donnai-Barrow syndrome
- A43T (p.Ala43Thr), TOPMed rs1684890956, gnomAD rs1684890956, CADD 0.23, PolyPhen-2 0.16
- D44N (p.Asp44Asn), TOPMed rs1028136133, gnomAD rs1028136133, CADD 0.01, PolyPhen-2 0.01
- W45R (p.Trp45Arg), gnomAD rs1453272607, CADD 24.90, PolyPhen-2 0.79
- R46T (p.Arg46Thr), ExAC rs757970183, gnomAD rs757970183, CADD 21.50, PolyPhen-2 0.86
- G49A (p.Gly49Ala), Ensembl rs778689139
- G49E (p.Gly49Glu), rs778689139, NCI-TCGA Cosmic COSV5555, cosmic curated COSV55551, Ensembl rs778689139, CADD 23.20, PolyPhen-2 0.92, Variant assessed as somatic; moderate impact.
- G49W (p.Gly49Trp), Ensembl rs1684890507
- T50S (p.Thr50Ser), rs114460450, ClinGen CA1955983, cosmic curated COSV10437, ClinVar RCV000305070, CADD 20.20, PolyPhen-2 0.57, Benign/Likely benign, not provided; Donnai-Barrow syndrome
- C53F (p.Cys53Phe), gnomAD rs1684890156, AlphaMissense 0.95, MetaLR 1.00
- C53Y (p.Cys53Tyr), rs1684890156, ClinGen CA349174603, ClinVar RCV002299052, AlphaMissense 0.95, MetaLR 1.00, Uncertain significance, not provided
- S54* (p.Ser54Ter), NCI-TCGA Cosmic COSV9978, cosmic curated COSV99787, Variant assessed as somatic; high impact.
- D56N (p.Asp56Asn), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- D56V (p.Asp56Val), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- A57G (p.Ala57Gly), 1000Genomes rs115350461, ESP rs115350461, ExAC rs115350461, TOPMed rs115350461, CADD 22.90, PolyPhen-2 0.13, Uncertain significance, Donnai-Barrow syndrome
- A57S (p.Ala57Ser), rs147295930, ClinGen CA1955980, ClinVar RCV001465374, ClinVar RCV001542320, CADD 0.00, PolyPhen-2 0.00, Conflicting interpretations, not provided; Donnai-Barrow syndrome
- A57T (p.Ala57Thr), rs147295930, NCI-TCGA Cosmic COSV5555, cosmic curated COSV55555, 1000Genomes rs147295930, CADD 0.00, PolyPhen-2 0.00, Uncertain significance
- A57V (p.Ala57Val), rs115350461, ClinGen CA1955978, cosmic curated COSV55549, ClinVar RCV000405564, CADD 22.60, PolyPhen-2 0.08, Conflicting interpretations, Donnai-Barrow syndrome; not provided
- I60S (p.Ile60Ser), Ensembl rs2105516169
- G61A (p.Gly61Ala), TOPMed rs925936001, gnomAD rs925936001, CADD 15.20, PolyPhen-2 0.91
- G61D (p.Gly61Asp), TOPMed rs925936001, gnomAD rs925936001, CADD 7.54, PolyPhen-2 0.13
- G61S (p.Gly61Ser), gnomAD rs1483233129, CADD 20.40, PolyPhen-2 0.91, Uncertain significance, Donnai-Barrow syndrome
- G61V (p.Gly61Val), TOPMed rs925936001, gnomAD rs925936001, CADD 19.60, PolyPhen-2 0.98
- A63D (p.Ala63Asp), ESP rs150829296, ExAC rs150829296, TOPMed rs150829296, gnomAD rs150829296, CADD 18.70, Uncertain significance
- A63T (p.Ala63Thr), rs759579869, ClinGen CA1955976, NCI-TCGA Cosmic COSV5556, cosmic curated COSV55566, CADD 16.80, PolyPhen-2 0.11, Uncertain significance, not provided
- A63V (p.Ala63Val), rs150829296, ClinGen CA1955957, cosmic curated COSV55563, ClinVar RCV002038455, CADD 22.80, PolyPhen-2 0.10, Uncertain significance, Inborn genetic diseases; not provided; Donnai-Barrow syndrome
- V64D (p.Val64Asp), ExAC rs762925787, gnomAD rs762925787, CADD 0.16, PolyPhen-2 0.01
- V64I (p.Val64Ile), rs766487772, ClinGen CA1955956, ClinVar RCV001997022, ExAC rs766487772, CADD 5.34, PolyPhen-2 0.02, Uncertain significance, not provided
- V65L (p.Val65Leu), rs1256042017, ClinGen CA349173977, ClinVar RCV002049366, ClinVar RCV006362614, CADD 0.01, PolyPhen-2 0.08, Uncertain significance, Inborn genetic diseases; not provided
- T66A (p.Thr66Ala), gnomAD rs1213030084, CADD 5.70, PolyPhen-2 0.17
- Q68R (p.Gln68Arg), rs2105513338, ClinGen CA349173938, ClinVar RCV001971725, Ensembl rs2105513338, CADD 0.16, PolyPhen-2 0.12, Uncertain significance, not provided
- Q69* (p.Gln69Ter), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- G70V (p.Gly70Val), TOPMed rs1016233199, CADD 5.97, PolyPhen-2 0.44
- K73N (p.Lys73Asn), ExAC rs773487420, TOPMed rs773487420, gnomAD rs773487420, CADD 7.50, PolyPhen-2 0.17
- K73R (p.Lys73Arg), Ensembl rs1574252636, CADD 0.13, PolyPhen-2 0.00
- K73T (p.Lys73Thr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- C74* (p.Cys74Ter), cosmic curated COSV55569, ESP rs376100403, ExAC rs376100403, TOPMed rs376100403
- C74F (p.Cys74Phe), cosmic curated COSV99791, gnomAD rs1260276729, CADD 23.60, PolyPhen-2 1.00
- Q75H (p.Gln75His), NCI-TCGA Cosmic COSV5555, cosmic curated COSV55553, Variant assessed as somatic; moderate impact.
- Q75P (p.Gln75Pro), Ensembl rs201683542
- S76G (p.Ser76Gly), gnomAD rs1318993740, CADD 7.02, PolyPhen-2 0.01
- S76N (p.Ser76Asn), Ensembl rs1684836920, CADD 0.04, PolyPhen-2 0.01
- E77V (p.Glu77Val), rs200113428, ClinGen CA1955952, ClinVar RCV002206077, ClinVar RCV005025693, CADD 13.90, PolyPhen-2 0.11, Conflicting interpretations, Donnai-Barrow syndrome; not provided
- G78A (p.Gly78Ala), rs546882372, ClinGen CA1955950, ClinVar RCV002994564, 1000Genomes rs546882372, CADD 17.00, PolyPhen-2 0.45, Uncertain significance, not provided
- G78E (p.Gly78Glu), rs546882372, ClinGen CA349173804, ClinVar RCV002958490, 1000Genomes rs546882372, CADD 14.30, PolyPhen-2 0.19, Uncertain significance, not provided
- Q79E (p.Gln79Glu), TOPMed rs1415388974, gnomAD rs1415388974, CADD 0.00, PolyPhen-2 0.00
- Q79H (p.Gln79His), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- Q79K (p.Gln79Lys), TOPMed rs1415388974, gnomAD rs1415388974, CADD 0.00, PolyPhen-2 0.06
- Q79R (p.Gln79Arg), ExAC rs778655445, TOPMed rs778655445, gnomAD rs778655445, CADD 0.02, PolyPhen-2 0.12
- C80G (p.Cys80Gly), Ensembl rs1684836219
- P82S (p.Pro82Ser), rs2528664586, ClinGen CA349173753, ClinVar RCV003035933, Uncertain significance, not provided
- N83D (p.Asn83Asp), ExAC rs770534351, TOPMed rs770534351, gnomAD rs770534351, CADD 1.06, PolyPhen-2 0.01
- N83S (p.Asn83Ser), rs2229263, ClinGen CA153570, cosmic curated COSV55541, ClinVar RCV000117519, CADD 0.03, PolyPhen-2 0.01, Benign, not provided; not specified; Donnai-Barrow syndrome
- N83Y (p.Asn83Tyr), ExAC rs770534351, TOPMed rs770534351, gnomAD rs770534351, CADD 5.38, PolyPhen-2 0.18
- S84C (p.Ser84Cys), NCI-TCGA Cosmic COSV5554, NCI-TCGA Cosmic COSV5556, cosmic curated COSV55563, Variant assessed as somatic; moderate impact.
- S84F (p.Ser84Phe), cosmic curated COSV55548, Ensembl rs1185362355, CADD 2.10, PolyPhen-2 0.04
- W85L (p.Trp85Leu), rs2528664497, ClinGen CA349173701, ClinVar RCV003001891, Uncertain significance, not provided
- W85R (p.Trp85Arg), TOPMed rs1684835636
- V86G (p.Val86Gly), ExAC rs777608905, gnomAD rs777608905, CADD 24.90, PolyPhen-2 0.88
- C87* (p.Cys87Ter), gnomAD rs1416229470, CADD 37.00
- C87G (p.Cys87Gly), NCI-TCGA Cosmic COSV9979, cosmic curated COSV99790, Variant assessed as somatic; moderate impact.
- Q89R (p.Gln89Arg), rs2105513194, ClinGen CA349173650, ClinVar RCV001973241, Ensembl rs2105513194, AlphaMissense 0.07, MetaLR 0.67, Uncertain significance, not provided
- D90N (p.Asp90Asn), TOPMed rs1684835252
- D90V (p.Asp90Val), rs2528664421, ClinGen CA349173631, ClinVar RCV002928150, Uncertain significance, not provided
- D90Y (p.Asp90Tyr), TOPMed rs1684835252, CADD 23.80, PolyPhen-2 0.88
- Q91E (p.Gln91Glu), Ensembl rs879193025, CADD 0.01, PolyPhen-2 0.00
- Q91R (p.Gln91Arg), TOPMed rs1179577930, gnomAD rs1179577930, CADD 5.14
- D94N (p.Asp94Asn), ExAC rs781716261, TOPMed rs781716261, gnomAD rs781716261, CADD 8.12, PolyPhen-2 0.01
- D95G (p.Asp95Gly), Ensembl rs1029524786
- G96D (p.Gly96Asp), cosmic curated COSV10505, gnomAD rs1203496853, CADD 24.20, PolyPhen-2 1.00
- G96S (p.Gly96Ser), rs1684834732, ClinGen CA349173526, ClinVar RCV002705233, Ensembl rs1684834732, AlphaMissense 0.11, MetaLR 0.92, Uncertain significance, not provided
- G96V (p.Gly96Val), gnomAD rs1203496853, CADD 24.10, PolyPhen-2 1.00
- S97L (p.Ser97Leu), NCI-TCGA Cosmic COSV9978, cosmic curated COSV99787, Variant assessed as somatic; moderate impact.
- S97T (p.Ser97Thr), rs1468975390, NCI-TCGA Cosmic COSV5556, cosmic curated COSV55560, TOPMed rs1468975390, AlphaMissense 0.13, MetaLR 0.92, Variant assessed as somatic; moderate impact.
- R100C (p.Arg100Cys), cosmic curated COSV55540, ESP rs138682237, ExAC rs138682237, TOPMed rs138682237, CADD 21.80, PolyPhen-2 0.04, Uncertain significance
- R100H (p.Arg100His), rs35642533, ClinGen CA1955940, ClinVar RCV001404180, ClinVar RCV003920885, CADD 0.18, PolyPhen-2 0.00, Conflicting interpretations, Inborn genetic diseases; not provided
- R100S (p.Arg100Ser), rs138682237, ClinGen CA1955941, ClinVar RCV001299301, ClinVar RCV003166681, CADD 18.10, PolyPhen-2 0.01, Uncertain significance, Inborn genetic diseases; not provided
- D102Y (p.Asp102Tyr), cosmic curated COSV99790, TOPMed rs1212764557, gnomAD rs1212764557, CADD 9.44, PolyPhen-2 0.07
- C103F (p.Cys103Phe), NCI-TCGA Cosmic COSV9979, cosmic curated COSV99790, Variant assessed as somatic; moderate impact.
- C103R (p.Cys103Arg), UniProt VAR 064727, Uncertain significance
- C103S (p.Cys103Ser), NCI-TCGA Cosmic COSV5558, NCI-TCGA Cosmic COSV9979, cosmic curated COSV99790, Variant assessed as somatic; moderate impact.
- S104L (p.Ser104Leu), gnomAD rs1396320167, CADD 18.40, PolyPhen-2 0.04, Uncertain significance, Donnai-Barrow syndrome
- Q105R (p.Gln105Arg), cosmic curated COSV55566, gnomAD rs1166656681, CADD 10.10, PolyPhen-2 0.00
- S106G (p.Ser106Gly), rs754114646, ClinGen CA1955917, ClinVar RCV001864498, ClinVar RCV005023332, CADD 7.54, PolyPhen-2 0.10, Uncertain significance, Inborn genetic diseases; Donnai-Barrow syndrome; not provided
- S106I (p.Ser106Ile), ExAC rs759417883, TOPMed rs759417883, gnomAD rs759417883, CADD 0.11, PolyPhen-2 0.01, Uncertain significance
- S106N (p.Ser106Asn), rs759417883, ClinGen CA1955915, ClinVar RCV002200980, ClinVar RCV004982934, CADD 0.02, PolyPhen-2 0.06, Conflicting interpretations, Donnai-Barrow syndrome; Inborn genetic diseases; not provided
- S106R (p.Ser106Arg), NCI-TCGA Cosmic COSV9978, cosmic curated COSV99789, Variant assessed as somatic; moderate impact.
- T107A (p.Thr107Ala), gnomAD rs1173133205, CADD 20.90, PolyPhen-2 0.98
- T107I (p.Thr107Ile), Ensembl rs1684448684, CADD 23.60, PolyPhen-2 0.99
- S109L (p.Ser109Leu), ExAC rs770710407, gnomAD rs770710407, CADD 23.10, PolyPhen-2 0.51
- S109P (p.Ser109Pro), rs2528617718, ClinGen CA349168753, ClinVar RCV002824570, Uncertain significance, not provided
- S110T (p.Ser110Thr), rs768641585, ClinGen CA59955878, ClinVar RCV002010126, Ensembl rs768641585, AlphaMissense 0.10, MetaLR 0.86, Uncertain significance, not provided
- H111R (p.His111Arg), ExAC rs773221527, gnomAD rs773221527, CADD 9.77, PolyPhen-2 0.00
- Q112H (p.Gln112His), rs2528617661, ClinGen CA349168675, ClinVar RCV003280211, CADD 21.50, PolyPhen-2 0.97, Uncertain significance, Inborn genetic diseases
- Q112P (p.Gln112Pro), rs769445177, ClinGen CA349168681, ClinVar RCV003044471, ExAC rs769445177, CADD 24.30, PolyPhen-2 0.96, Uncertain significance, not provided
- Q112R (p.Gln112Arg), rs769445177, ClinGen CA1955910, ClinVar RCV001869995, ExAC rs769445177, CADD 24.00, PolyPhen-2 0.84, Uncertain significance, not provided
- I113L (p.Ile113Leu), ExAC rs747650396, TOPMed rs747650396, gnomAD rs747650396, CADD 5.92, PolyPhen-2 0.00
- I113V (p.Ile113Val), ExAC rs747650396, TOPMed rs747650396, gnomAD rs747650396, CADD 5.55, PolyPhen-2 0.07
- T114P (p.Thr114Pro), gnomAD rs1559067605, CADD 18.00, PolyPhen-2 0.42
- C115* (p.Cys115Ter), rs1483364237, ClinGen CA349168617, ClinVar RCV002815649, NCI-TCGA TCGA novel, Pathogenic
- C115F (p.Cys115Phe), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- S116C (p.Ser116Cys), ExAC rs776383533, TOPMed rs776383533, gnomAD rs776383533, Uncertain significance
- S116F (p.Ser116Phe), rs776383533, ClinGen CA1955908, cosmic curated COSV10723, ClinVar RCV002014157, CADD 23.90, PolyPhen-2 0.91, Uncertain significance, not provided
- N117K (p.Asn117Lys), rs1275076469, ClinGen CA349168569, ClinVar RCV001973640, TOPMed rs1275076469, CADD 0.26, PolyPhen-2 0.28, Uncertain significance, not provided
- N117S (p.Asn117Ser), rs746620514, ClinGen CA1955906, ClinVar RCV001927634, ExAC rs746620514, CADD 0.22, PolyPhen-2 0.01, Uncertain significance, not provided
- N117Y (p.Asn117Tyr), ExAC rs768168854, TOPMed rs768168854, gnomAD rs768168854, CADD 21.50, PolyPhen-2 0.78
- G118V (p.Gly118Val), ExAC rs780310223, TOPMed rs780310223, gnomAD rs780310223, CADD 23.60, PolyPhen-2 1.00, Uncertain significance, Donnai-Barrow syndrome
- C120R (p.Cys120Arg), ExAC rs746387870, gnomAD rs746387870, CADD 25.50, PolyPhen-2 1.00
- I121T (p.Ile121Thr), Ensembl rs1684447240
- I121V (p.Ile121Val), TOPMed rs1344377370
- P122L (p.Pro122Leu), Ensembl rs1483297948
- P122S (p.Pro122Ser), NCI-TCGA Cosmic COSV9978, cosmic curated COSV99786, Variant assessed as somatic; moderate impact.
- P122T (p.Pro122Thr), NCI-TCGA Cosmic COSV9978, Variant assessed as somatic; moderate impact.
- S123C (p.Ser123Cys), NCI-TCGA Cosmic COSV9978, cosmic curated COSV99787, Variant assessed as somatic; moderate impact.
- S123G (p.Ser123Gly), ExAC rs779378631, TOPMed rs779378631, gnomAD rs779378631, CADD 0.01, PolyPhen-2 0.00
- S123N (p.Ser123Asn), rs1684446974, ClinGen CA349168474, cosmic curated COSV10584, ClinVar RCV002000328, CADD 0.38, PolyPhen-2 0.00, Uncertain significance, not provided
- S123R (p.Ser123Arg), rs757393374, ClinGen CA1955901, ClinVar RCV004413143, ExAC rs757393374, CADD 0.02, PolyPhen-2 0.00, Uncertain significance, Inborn genetic diseases
- E124D (p.Glu124Asp), Ensembl rs757263549, Likely benign
- Y125H (p.Tyr125His), TOPMed rs1684446711
- R126G (p.Arg126Gly), ExAC rs753886411, gnomAD rs753886411, CADD 24.50, PolyPhen-2 0.70
- C127W (p.Cys127Trp), rs2105492305, ClinGen CA349168413, ClinVar RCV003253353, Uncertain significance, Inborn genetic diseases
- D128N (p.Asp128Asn), cosmic curated COSV55544, ExAC rs756312774, TOPMed rs756312774, gnomAD rs756312774, CADD 23.90, PolyPhen-2 0.98
Public LRP2 analysis runs
- LRP2 analysis run — LRP2 (5,813 variants) — completed 2026-08-22