CLDN10 (Claudin-10) variants and mutations
CLDN10 (also known as Claudin-10) is a human protein-coding gene encoding a claudin-10 protein. Its annotated function is forms paracellular channels: polymerizes in tight junction strands with cation- and anion-selective channels through the strands, conveying epithelial permeability in a process known as paracellular tight junction permeability. It is annotated at the cell junction, tight junction. This analysis covers 509 CLDN10 variants and mutations. Of these, 84% have computational variant effect predictions. Disease context includes helix rolling, Abnormality of the skeletal system, and nephrolithiasis. Example CLDN10 variants include M1T, A2T, and A2V.
Variant analysis overview
- Gene: CLDN10
- Protein: Claudin-10
- UniProt accession: P78369
- Organism: Homo sapiens
- Variants analyzed: 509
- Variant scope: all variants
- Completed: 2026-08-27
Variant and mutation evidence
- Variant composition: 256 unspecified-consequence records; 132 missense variants; 86 synonymous variants; 20 frameshift variants; 8 stop-gained variants; 3 in-frame insertions; 4 splice-region variants
- Prediction scores: 427 variants have prediction scores (84% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: helix rolling, Abnormality of the skeletal system, nephrolithiasis, diabetes mellitus, alcohol drinking, urolithiasis, polyarteritis nodosa, hereditary disease, gout, bladder calculus, Hypokalemia, Hypomagnesemia.
Protein structure and variant hotspots
- Protein features: 4 transmembrane segments.
- Structural context: 179 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, AlphaFold DB, gnomAD constraint, Open Targets, MaveDB, LitVar.
Notable CLDN10 variants
Examples include M1T, A2T, A2V, S3R, S3F, S3S, S3I, T4M. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1T (p.Met1Thr), rs930701747, ClinGen CA388477628, ClinVar RCV000505532, MetaLR 0.90, MetaSVM 0.90, Pathogenic, HELIX syndrome
- A2T (p.Ala2Thr), ExAC rs773126278, TOPMed rs773126278, gnomAD rs773126278, REVEL 0.41, CADD 22.80
- A2V (p.Ala2Val), gnomAD 13-95552758-C-T, REVEL 0.26, MetaLR 0.61
- S3R (p.Ser3Arg), ExAC rs760775984, TOPMed rs760775984, gnomAD rs760775984, REVEL 0.26, CADD 16.70
- S3F (p.Ser3Phe), rs1188289218, gnomAD 13-95433838-C-T, CADD 21.70
- S3S (p.Ser3Ser), rs1367995645, gnomAD 13-95433839-C-T, CADD 11.00
- S3I (p.Ser3Ile), gnomAD 13-95552761-G-T, REVEL 0.36, MetaLR 0.67
- T4M (p.Thr4Met), gnomAD rs1304603274, REVEL 0.24, CADD 21.10
- T4T (p.Thr4Thr), rs144714087, gnomAD 13-95552765-G-T, CADD 9.96
- A5P (p.Ala5Pro), gnomAD rs1329246552, REVEL 0.72, CADD 25.60
- A5T (p.Ala5Thr), NCI-TCGA Cosmic COSV1001, REVEL 0.40, CADD 22.70, Variant assessed as somatic; moderate impact.
- A5V (p.Ala5Val), rs759786238, gnomAD 13-95433844-C-T, CADD 17.60
- A5G (p.Ala5Gly), rs759786238, gnomAD 13-95433844-C-G, CADD 19.60
- A5A (p.Ala5Ala), gnomAD 13-95433845-G-A, CADD 1.42
- S6A (p.Ser6Ala), gnomAD rs1212447250, REVEL 0.20, CADD 21.10
- S6L (p.Ser6Leu), rs1395670392, gnomAD rs1395670392, REVEL 0.23, CADD 19.90, Variant assessed as somatic; moderate impact.
- S6P (p.Ser6Pro), gnomAD rs1212447250
- S6S (p.Ser6Ser), rs2043582477, gnomAD 13-95552771-G-A, CADD 14.70
- E7D (p.Glu7Asp), NCI-TCGA Cosmic COSV1001, Variant assessed as somatic; moderate impact.
- E7K (p.Glu7Lys), rs1416896307, gnomAD 13-95433912-G-A, MetaLR 0.63, MetaSVM 0.15
- I8T (p.Ile8Thr), TOPMed rs1313268780, gnomAD rs1313268780, REVEL 0.84, CADD 29.70
- I8V (p.Ile8Val), rs1419542422, gnomAD 13-95433849-A-G, CADD 23.60
- I8F (p.Ile8Phe), gnomAD 13-95433849-A-T, CADD 27.30
- I8L (p.Ile8Leu), rs1419542422, gnomAD 13-95433849-A-C, CADD 24.20
- I8M (p.Ile8Met), rs1240150629, gnomAD 13-95433851-C-G, CADD 24.00
- I8I (p.Ile8Ile), rs2043582539, gnomAD 13-95552777-C-A, CADD 14.10
- I9V (p.Ile9Val), gnomAD 13-95552778-A-G, REVEL 0.20, MetaLR 0.29
- I9I (p.Ile9Ile), gnomAD 13-95552780-C-T, CADD 14.00
- A10T (p.Ala10Thr), rs753799088, NCI-TCGA Cosmic COSV5482, ExAC rs753799088, gnomAD rs753799088, REVEL 0.92, CADD 31.00, Variant assessed as somatic; moderate impact.
- A10V (p.Ala10Val), NCI-TCGA Cosmic COSV1001, REVEL 0.92, CADD 26.90, Variant assessed as somatic; moderate impact.
- A10A (p.Ala10Ala), gnomAD 13-95433857-T-C, CADD 12.60
- A10S (p.Ala10Ser), gnomAD 13-95433882-GGA-G, CADD 31.00
- A10G (p.Ala10Gly), rs369938854, gnomAD 13-95433886-C-G, CADD 23.90
- A10D (p.Ala10Asp), gnomAD 13-95433895-C-A, CADD 22.60
- F11S (p.Phe11Ser), gnomAD 13-95433880-T-C, CADD 25.40
- F11F (p.Phe11Phe), gnomAD 13-95433881-T-C, CADD 9.60
- F11V (p.Phe11Val), gnomAD 13-95552784-T-G, REVEL 0.85, MetaLR 0.76
- M12I (p.Met12Ile), gnomAD rs1285793191, REVEL 0.12, CADD 19.30
- M12T (p.Met12Thr), rs759535516, ClinGen CA7020095, ClinVar RCV004444299, ExAC rs759535516, REVEL 0.24, CADD 21.10, Uncertain significance, Inborn genetic diseases
- M12V (p.Met12Val), rs1438067157, NCI-TCGA Cosmic COSV5482, TOPMed rs1438067157, REVEL 0.23, CADD 7.22, Variant assessed as somatic; moderate impact.
- V13A (p.Val13Ala), Ensembl rs2138642472
- V13I (p.Val13Ile), ExAC rs764942392, TOPMed rs764942392, gnomAD rs764942392, REVEL 0.31, CADD 22.30
- V13L (p.Val13Leu), NCI-TCGA Cosmic COSV1001, Variant assessed as somatic; moderate impact.
- V13M (p.Val13Met), gnomAD 13-95433861-G-A, CADD 21.80
- V13E (p.Val13Glu), gnomAD 13-95433862-T-A, CADD 28.30
- V13V (p.Val13Val), rs2042236746, gnomAD 13-95433863-G-A, CADD 11.40
- V13C (p.Val13Cys), gnomAD 13-95433868-G-GT, CADD 32.00
- S14F (p.Ser14Phe), rs1377754819, gnomAD 13-95433865-C-T, CADD 11.80
- S14S (p.Ser14Ser), gnomAD 13-95433866-T-C, CADD 5.85
- I15P (p.Ile15Pro), gnomAD 13-95552790-G-GTC, CADD 31.00
- I15I (p.Ile15Ile), rs2043582844, gnomAD 13-95552798-C-T, CADD 14.50
- S16L (p.Ser16Leu), NCI-TCGA Cosmic COSV5482, Variant assessed as somatic; moderate impact.
- S16A (p.Ser16Ala), gnomAD 13-95552799-T-G, REVEL 0.31, MetaLR 0.54
- S16S (p.Ser16Ser), rs757992913, gnomAD 13-95552801-A-G, CADD 5.50
- G17V (p.Gly17Val), NCI-TCGA Cosmic COSV1001, Variant assessed as somatic; moderate impact.
- G17C (p.Gly17Cys), rs2042236831, gnomAD 13-95433867-G-T, CADD 23.20
- G17* (p.Gly17Ter), rs2042236887, gnomAD 13-95433873-G-T, CADD 38.00
- G17A (p.Gly17Ala), rs2042236927, gnomAD 13-95433874-G-C, CADD 18.50
- G17G (p.Gly17Gly), rs757224911, gnomAD 13-95433878-G-A, CADD 7.72
- W18L (p.Trp18Leu), Ensembl rs1594606952
- W18C (p.Trp18Cys), gnomAD 13-95433852-TGG-T, CADD 23.50
- W18G (p.Trp18Gly), gnomAD 13-95552805-T-G, REVEL 0.84, MetaLR 0.84
- V19G (p.Val19Gly), Ensembl rs1014516986
- V19I (p.Val19Ile), ExAC rs763834792, TOPMed rs763834792, gnomAD rs763834792
- V19L (p.Val19Leu), ExAC rs763834792, TOPMed rs763834792, gnomAD rs763834792, REVEL 0.44, CADD 21.30
- V19V (p.Val19Val), gnomAD 13-95552810-A-G, CADD 13.30
- L20P (p.Leu20Pro), ExAC rs756783148, gnomAD rs756783148
- L20V (p.Leu20Val), 1000Genomes rs534072709, ExAC rs534072709, gnomAD rs534072709, REVEL 0.70, CADD 23.50
- L20R (p.Leu20Arg), rs1301464172, gnomAD 13-95433859-T-G, CADD 29.40
- L20L (p.Leu20Leu), rs374417711, gnomAD 13-95433890-C-T, CADD 0.48
- V21A (p.Val21Ala), rs1157773336, ClinGen CA388478027, ClinVar RCV002759868, TOPMed rs1157773336, REVEL 0.48, CADD 24.50, Uncertain significance, Inborn genetic diseases
- V21T (p.Val21Thr), gnomAD 13-95552809-T-TAC, CADD 30.00
- V21V (p.Val21Val), gnomAD 13-95552816-G-A, CADD 13.20
- S22T (p.Ser22Thr), gnomAD 13-95552817-T-A, REVEL 0.54, MetaLR 0.62
- S22F (p.Ser22Phe), gnomAD 13-95552818-C-T, REVEL 0.55, MetaLR 0.54
- S23C (p.Ser23Cys), Ensembl rs2043583276
- S23F (p.Ser23Phe), gnomAD 13-95433907-C-T, MetaLR 0.78, MetaSVM 0.63
- S23Y (p.Ser23Tyr), gnomAD 13-95433907-C-A, MetaLR 0.80, MetaSVM 0.72
- p.Ser23dup, rs2043583228, gnomAD 13-95552816-G-GTC, CADD 21.00
- T24A (p.Thr24Ala), rs779968361, gnomAD 13-95433900-A-G, CADD 21.80
- T24N (p.Thr24Asn), rs2042237219, gnomAD 13-95433901-C-A, MetaLR 0.71, MetaSVM 0.43
- T24T (p.Thr24Thr), rs748827025, gnomAD 13-95433902-C-T, CADD 0.51
- T24M (p.Thr24Met), rs768312342, gnomAD 13-95433904-C-T, MetaLR 0.58, MetaSVM -0.32
- L25L (p.Leu25Leu), gnomAD 13-95552826-C-T, CADD 12.70
- P26T (p.Pro26Thr), ESP rs370647506, ExAC rs370647506, TOPMed rs370647506, gnomAD rs370647506, REVEL 0.49, CADD 22.50
- P26L (p.Pro26Leu), gnomAD 13-95552830-C-T, REVEL 0.49, MetaLR 0.55
- T27A (p.Thr27Ala), NCI-TCGA Cosmic COSV5482, REVEL 0.47, CADD 23.90, Variant assessed as somatic; moderate impact.
- T27I (p.Thr27Ile), gnomAD 13-95552833-C-T, REVEL 0.62, MetaLR 0.56
- T27T (p.Thr27Thr), gnomAD 13-95552834-C-T, CADD 14.10
- D28H (p.Asp28His), gnomAD rs1184988312, REVEL 0.82, CADD 28.80
- D28N (p.Asp28Asn), gnomAD rs1184988312
- D28T (p.Asp28Thr), gnomAD 13-95552834-CG-C, CADD 32.00
- Y29C (p.Tyr29Cys), NCI-TCGA Cosmic COSV5482, Variant assessed as somatic; moderate impact.
- Y29H (p.Tyr29His), gnomAD 13-95552838-T-C, REVEL 0.71, MetaLR 0.72
- Y29Y (p.Tyr29Tyr), rs2043583461, gnomAD 13-95552840-C-T, CADD 13.20
- W30P (p.Trp30Pro), gnomAD 13-95433911-TGAGT, CADD 29.30
- W30* (p.Trp30Ter), gnomAD 13-95552842-G-A, CADD 43.00
- K31E (p.Lys31Glu), ExAC rs779373596, gnomAD rs779373596, REVEL 0.87, CADD 32.00
- K31K (p.Lys31Lys), rs2042237476, gnomAD 13-95433920-A-G, CADD 5.01
- K31R (p.Lys31Arg), gnomAD 13-95552845-A-G, REVEL 0.51, MetaLR 0.54
- K31N (p.Lys31Asn), gnomAD 13-95552846-G-C, REVEL 0.65, MetaLR 0.83
- V32G (p.Val32Gly), Ensembl rs1441863688
- V32L (p.Val32Leu), NCI-TCGA Cosmic COSV5482, Variant assessed as somatic; moderate impact.
- V32M (p.Val32Met), gnomAD 13-95552847-G-A, REVEL 0.86, MetaLR 0.81
- V32V (p.Val32Val), rs1355343088, gnomAD 13-95552849-G-A, CADD 16.30
- S33A (p.Ser33Ala), Ensembl rs1594607014
- S33L (p.Ser33Leu), rs765511486, gnomAD 13-95433940-C-T, MetaLR 0.66, MetaSVM 0.30
- S33* (p.Ser33Ter), rs765511486, gnomAD 13-95433940-C-A, CADD 37.00
- S33S (p.Ser33Ser), rs149372773, gnomAD 13-95433941-G-A, CADD 8.04
- S33C (p.Ser33Cys), gnomAD 13-95552851-C-G, REVEL 0.88, MetaLR 0.89
- T34A (p.Thr34Ala), TOPMed rs932217780, gnomAD rs932217780, REVEL 0.23, CADD 23.90
- T34N (p.Thr34Asn), gnomAD rs1334933998, REVEL 0.30, CADD 23.50
- T34S (p.Thr34Ser), rs1163975093, gnomAD 13-95433924-A-T, MetaLR 0.38, MetaSVM -0.53
- T34T (p.Thr34Thr), gnomAD 13-95433926-C-T, CADD 3.96
- T34M (p.Thr34Met), rs1419354135, gnomAD 13-95433928-C-T, MetaLR 0.77, MetaSVM 0.69
- I35M (p.Ile35Met), ExAC rs748553948, TOPMed rs748553948, gnomAD rs748553948, REVEL 0.48, CADD 23.20
- D36E (p.Asp36Glu), ExAC rs773460504, gnomAD rs773460504
- D36G (p.Asp36Gly), ExAC rs772363407, gnomAD rs772363407, REVEL 0.41, CADD 23.30
- G37C (p.Gly37Cys), TOPMed rs1405417875, gnomAD rs1405417875, REVEL 0.88, CADD 32.00
- G37D (p.Gly37Asp), rs1371711623, NCI-TCGA Cosmic COSV5482, gnomAD rs1371711623, REVEL 0.85, CADD 29.70, Variant assessed as somatic; moderate impact.
- G37S (p.Gly37Ser), NCI-TCGA Cosmic COSV5482, REVEL 0.64, CADD 23.00, Variant assessed as somatic; moderate impact.
- G37V (p.Gly37Val), gnomAD rs1371711623
- G37R (p.Gly37Arg), gnomAD 13-95552862-G-C, REVEL 0.88, MetaLR 0.85
- T38A (p.Thr38Ala), gnomAD rs1221419822, REVEL 0.48, CADD 23.10
- T38K (p.Thr38Lys), gnomAD rs1280008667, REVEL 0.76, CADD 27.20
- T38M (p.Thr38Met), gnomAD rs1280008667, REVEL 0.79, CADD 26.90
- p.Thr39dup, rs2042237855, gnomAD 13-95433946-T-TAA, CADD 20.20
- T38P (p.Thr38Pro), rs199739747, gnomAD 13-95433948-A-C, MetaLR 0.89, MetaSVM 0.97
- T38T (p.Thr38Thr), gnomAD 13-95433950-A-G, CADD 1.50
- V39V (p.Val39Val), rs2043584118, gnomAD 13-95552870-C-T, CADD 14.70
- I40V (p.Ile40Val), gnomAD 13-95433945-A-G, MetaLR 0.80, MetaSVM 0.51
- I40M (p.Ile40Met), gnomAD 13-95433947-A-G, MetaLR 0.86, MetaSVM 0.75
- I40I (p.Ile40Ile), rs2043584161, gnomAD 13-95552873-C-T, CADD 15.30
- T41S (p.Thr41Ser), gnomAD 13-95433955-C-G, MetaLR 0.59, MetaSVM -0.09
- T41I (p.Thr41Ile), gnomAD 13-95433955-C-T, MetaLR 0.61, MetaSVM 0.07
- T41T (p.Thr41Thr), gnomAD 13-95433956-T-G, CADD 9.18
- T42T (p.Thr42Thr), gnomAD 13-95552879-C-T, CADD 12.50
- A43S (p.Ala43Ser), rs747253181, ClinGen CA7020109, ClinVar RCV004444298, ExAC rs747253181, REVEL 0.47, CADD 23.20, Uncertain significance, Inborn genetic diseases
- A43V (p.Ala43Val), ExAC rs771037194, gnomAD rs771037194, REVEL 0.64, CADD 28.40
- A43T (p.Ala43Thr), rs1487772163, gnomAD 13-95433933-G-A, MetaLR 0.76, MetaSVM 0.63
- A43A (p.Ala43Ala), rs1439350594, gnomAD 13-95433935-C-T, CADD 0.79
- T44I (p.Thr44Ile), ExAC rs776695497, TOPMed rs776695497, gnomAD rs776695497, REVEL 0.69, CADD 26.50
- T44T (p.Thr44Thr), gnomAD 13-95552885-C-T, CADD 14.90
- Y45D (p.Tyr45Asp), gnomAD 13-95433963-T-G, MetaLR 0.74, MetaSVM 0.61
- Y45F (p.Tyr45Phe), gnomAD 13-95552887-A-T, REVEL 0.17, MetaLR 0.36
- Y45Y (p.Tyr45Tyr), gnomAD 13-95552888-T-C, CADD 13.80
- Y45* (p.Tyr45Ter), gnomAD 13-95552888-T-A, CADD 37.00
- W46* (p.Trp46Ter), rs2501666796, ClinGen CA388478713, ClinVar RCV003319566, CADD 38.00, Pathogenic
- W46R (p.Trp46Arg), rs1379745136, gnomAD 13-95433957-T-A, MetaLR 0.70, MetaSVM 0.27
- W46S (p.Trp46Ser), rs1487018586, gnomAD 13-95433958-G-C, MetaLR 0.44, MetaSVM -0.37
- W46P (p.Trp46Pro), rs2043584361, gnomAD 13-95552888-TTGGG, CADD 33.00
- A47A (p.Ala47Ala), gnomAD 13-95552894-C-T, CADD 16.10
- N48H (p.Asn48His), rs2501666805, ClinGen CA388478746, ClinVar RCV004555308, Likely pathogenic, HELIX syndrome
- N48K (p.Asn48Lys), rs759408749, ExAC rs759408749, gnomAD rs759408749, ClinGen CA388478762, REVEL 0.83, CADD 26.50, Pathogenic, HELIX syndrome
- N48S (p.Asn48Ser), gnomAD rs1177632600, REVEL 0.54, CADD 26.80, Uncertain significance, Inborn genetic diseases
- N48T (p.Asn48Thr), gnomAD rs1177632600, REVEL 0.66, CADD 29.70, Uncertain significance, in HELIX
- N48D (p.Asn48Asp), rs747687660, gnomAD 13-95433909-A-G, MetaLR 0.40, MetaSVM -0.47
- N48N (p.Asn48Asn), gnomAD 13-95433911-T-C, CADD 1.54
- N48I (p.Asn48Ile), gnomAD 13-95433982-A-T, MetaLR 0.57, MetaSVM -0.06
- L49P (p.Leu49Pro), TOPMed rs1405643229, gnomAD rs1405643229, REVEL 0.88, CADD 32.00
- L49L (p.Leu49Leu), gnomAD 13-95433972-C-T, CADD 11.00
- L49V (p.Leu49Val), gnomAD 13-95433972-C-G, MetaLR 0.91, MetaSVM 1.03
- W50* (p.Trp50Ter), Ensembl rs868569022
- W50P (p.Trp50Pro), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- W50R (p.Trp50Arg), TOPMed rs2043584595, gnomAD rs2043584595, REVEL 0.92, CADD 32.00
- W50G (p.Trp50Gly), gnomAD 13-95552901-T-G, REVEL 0.91, MetaLR 0.97
- A52V (p.Ala52Val), gnomAD rs1191682747, REVEL 0.23, CADD 23.60
- A52S (p.Ala52Ser), rs751873803, gnomAD 13-95433987-G-T, MetaLR 0.59, MetaSVM 0.19
- A52T (p.Ala52Thr), gnomAD 13-95433987-G-A, MetaLR 0.52, MetaSVM -0.00
- A52E (p.Ala52Glu), gnomAD 13-95433988-C-A, MetaLR 0.69, MetaSVM 0.49
- A52A (p.Ala52Ala), rs767766614, gnomAD 13-95433998-G-C, CADD 4.84
- C53G (p.Cys53Gly), NCI-TCGA Cosmic COSV5482, Variant assessed as somatic; moderate impact.
- C53Y (p.Cys53Tyr), gnomAD 13-95433985-G-A, MetaLR 0.96, MetaSVM 1.10
- C53* (p.Cys53Ter), gnomAD 13-95433986-C-A, CADD 36.00
- C53C (p.Cys53Cys), rs762701437, gnomAD 13-95552912-C-T, CADD 14.80
- V54I (p.Val54Ile), Ensembl rs2043584768, REVEL 0.50, CADD 23.20
- V54F (p.Val54Phe), gnomAD 13-95552913-G-T, REVEL 0.85, MetaLR 0.75
- V54V (p.Val54Val), gnomAD 13-95552915-T-G, CADD 6.96
- T55S (p.Thr55Ser), ExAC rs763856292, gnomAD rs763856292, REVEL 0.51, CADD 22.70
- T55A (p.Thr55Ala), gnomAD 13-95552916-A-G, REVEL 0.61, MetaLR 0.75
Public CLDN10 analysis runs
- CLDN10 analysis run — CLDN10 (509 variants) — completed 2026-08-27