COL2A1 (Collagen alpha-1(II) chain) variants and mutations
COL2A1 (also known as Collagen alpha-1(II) chain) is a human protein-coding gene encoding a collagen alpha-1(II) chain protein. It provides the principal fibrillar collagen framework of cartilage and is also important in the vitreous and inner ear. Pathogenic variants cause a broad type II collagenopathy spectrum including Stickler syndrome, spondyloepiphyseal dysplasia, and severe skeletal dysplasias. This analysis covers 2,467 COL2A1 variants and mutations. Of these, 74% have computational variant effect predictions. Disease context includes spondyloepiphyseal dysplasia congenita, Stickler syndrome type 1, and achondrogenesis type II. Example COL2A1 variants include M1L, M1V, and R3C.
Variant analysis overview
- Gene: COL2A1
- Protein: Collagen alpha-1(II) chain
- UniProt accession: P02458
- Organism: Homo sapiens
- Variants analyzed: 2467
- Variant scope: all variants
- Completed: 2026-08-22
Variant and mutation evidence
- Variant composition: 2,194 unspecified-consequence records; 1 stop retained variant; 2 in-frame insertions; 150 synonymous variants; 111 missense variants; 4 splice-region variants; 3 frameshift variants; 5 in-frame deletions; 1 protein altering variant; 1 stop-gained variants; 1 substitution
- Prediction scores: 1,820 variants have prediction scores (74% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: spondyloepiphyseal dysplasia congenita, Stickler syndrome type 1, achondrogenesis type II, Kniest dysplasia, platyspondylic dysplasia, Torrance type, spondyloepimetaphyseal dysplasia, Strudwick type, Achondrogenesis type 2, spondyloperipheral dysplasia, familial avascular necrosis of femoral head, spondyloepiphyseal dysplasia, Stanescu type, Stickler syndrome, Stickler syndrome, type I, nonsyndromic ocular.
Protein structure and variant hotspots
- Protein features: 2 domains; 5 binding sites; 38 post-translational modification sites.
- Structural context: 624 variants have structural context.
- PTM context: 48 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, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Notable COL2A1 variants
Examples include M1L, M1V, R3C, R3G, R3H, R3L, R3S, L4P. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1L (p.Met1Leu), rs2136652928, ClinGen CA384528520, ClinVar RCV003049846, MetaLR 0.56, MetaSVM 0.04, Pathogenic, not provided
- M1V (p.Met1Val), rs2136652928, ClinGen CA384528522, ClinVar RCV001387776, ClinVar RCV005005921, MetaLR 0.56, MetaSVM 0.04, Pathogenic, not provided; Multiple epiphyseal dysplasia, Beighton type; Spondyloepiphyseal d
- R3C (p.Arg3Cys), TOPMed rs898585011, gnomAD rs898585011, REVEL 0.47, CADD 24.30, Likely benign
- R3G (p.Arg3Gly), rs898585011, ClinGen CA384528476, ClinVar RCV001324415, TOPMed rs898585011, REVEL 0.26, CADD 23.10, Likely benign, not provided
- R3H (p.Arg3His), ESP rs372229776, gnomAD rs372229776, REVEL 0.20, CADD 22.40, Likely benign
- R3L (p.Arg3Leu), rs372229776, ClinGen CA236497908, ClinVar RCV001317703, ESP rs372229776, REVEL 0.35, CADD 22.10, Likely benign, not provided
- R3S (p.Arg3Ser), rs898585011, ClinGen CA236497909, ClinVar RCV003665208, TOPMed rs898585011, REVEL 0.39, CADD 22.50, Uncertain significance, not provided
- L4P (p.Leu4Pro), rs1335702587, ClinGen CA384528450, ClinVar RCV001240505, TOPMed rs1335702587, REVEL 0.46, CADD 24.70, Uncertain significance, not provided
- G5A (p.Gly5Ala), rs557340983, ClinGen CA236497899, ClinVar RCV001774296, 1000Genomes rs557340983, REVEL 0.21, CADD 18.60, Conflicting interpretations, not provided
- G5R (p.Gly5Arg), TOPMed rs1275888661, gnomAD rs1275888661, REVEL 0.35, CADD 21.80, Uncertain significance, not provided
- A6D (p.Ala6Asp), rs369359592, ClinGen CA6536122, ClinVar RCV000283912, ClinVar RCV000896145, REVEL 0.29, CADD 21.70, Benign/Likely benign, Connective tissue disorder; not provided; Stickler syndrome type 1
- A6T (p.Ala6Thr), gnomAD rs1283945940, REVEL 0.19, CADD 18.10
- A6V (p.Ala6Val), 1000Genomes rs369359592, ExAC rs369359592, TOPMed rs369359592, gnomAD rs369359592, REVEL 0.27, CADD 22.30, Benign
- P7L (p.Pro7Leu), gnomAD rs1314340565
- P7S (p.Pro7Ser), gnomAD rs1340689824, REVEL 0.18, CADD 15.00
- Q8K (p.Gln8Lys), gnomAD rs1369890473, REVEL 0.20, CADD 19.50
- Q8L (p.Gln8Leu), gnomAD rs1940371665, REVEL 0.26, CADD 18.60, Uncertain significance, not provided
- Q8R (p.Gln8Arg), gnomAD rs1940371665, REVEL 0.18, CADD 13.20
- T9* (p.Thr9Ter), rs1131691546, ClinGen CA645369519, ClinVar RCV000493711, Pathogenic
- T9A (p.Thr9Ala), 1000Genomes rs3803183, ESP rs3803183, ExAC rs3803183, TOPMed rs3803183, Benign
- T9M (p.Thr9Met), cosmic curated COSV10047, 1000Genomes rs557946588, TOPMed rs557946588, Uncertain significance
- T9R (p.Thr9Arg), rs557946588, ClinVar RCV004577117, 1000Genomes rs557946588, TOPMed rs557946588, REVEL 0.46, CADD 20.30, Uncertain significance, Stickler syndrome type 1
- T9S (p.Thr9Ser), rs3803183, ClinGen CA147293, cosmic curated COSV61527, ClinVar RCV000079725, REVEL 0.21, CADD 18.40, Benign, not specified; not provided; Type 2 collagenopathy
- T9W (p.Thr9Trp), rs1131691546, ClinGen CA1139662593, ClinVar RCV001244285, Uncertain significance, not provided
- L10Q (p.Leu10Gln), gnomAD rs1363528151
- L12P (p.Leu12Pro), rs2136652710, ClinGen CA384528329, ClinVar RCV001754481, Ensembl rs2136652710, REVEL 0.75, CADD 32.00, Uncertain significance, not provided
- L13P (p.Leu13Pro), gnomAD rs1162410146, REVEL 0.75, CADD 32.00
- L13R (p.Leu13Arg), gnomAD rs1162410146, REVEL 0.70, CADD 32.00
- T14S (p.Thr14Ser), rs1940370196, ClinGen CA384528312, ClinVar RCV001247688, Ensembl rs1940370196, AlphaMissense 0.09, MetaLR 0.36, Uncertain significance, not provided
- V17A (p.Val17Ala), NCI-TCGA Cosmic COSV1004, cosmic curated COSV10047, Uncertain significance, not provided
- V17I (p.Val17Ile), 1000Genomes rs1370410549, gnomAD rs1370410549, REVEL 0.17, CADD 18.50
- V20I (p.Val20Ile), TOPMed rs911368398, REVEL 0.29, CADD 23.70
- L21F (p.Leu21Phe), rs11168349, ClinGen CA236497872, ClinVar RCV003053622, Ensembl rs11168349, REVEL 0.30, CADD 23.00, Uncertain significance, not provided
- R22P (p.Arg22Pro), TOPMed rs1565702485, REVEL 0.58, CADD 22.60, Likely benign, not provided
- Q24K (p.Gln24Lys), rs2540194078, ClinGen CA384528202, ClinVar RCV004437395, REVEL 0.29, CADD 23.30, Uncertain significance, Inborn genetic diseases
- Q24R (p.Gln24Arg), gnomAD rs1472271077, REVEL 0.31, CADD 23.30
- G25A (p.Gly25Ala), rs1940368906, ClinGen CA384528180, ClinVar RCV001894948, TOPMed rs1940368906, AlphaMissense 0.09, MetaLR 0.44, Uncertain significance, not provided
- G25S (p.Gly25Ser), rs1940369024, ClinGen CA384528187, ClinVar RCV001347380, TOPMed rs1940369024, AlphaMissense 0.08, MetaLR 0.49, Uncertain significance, not provided
- Q26* (p.Gln26Ter), rs2540194058, ClinGen CA384528173, ClinVar RCV002842009, CADD 42.00, Pathogenic
- Q26R (p.Gln26Arg), TOPMed rs1940368675, REVEL 0.17, CADD 21.80, Uncertain significance, Inborn genetic diseases
- D27M (p.Asp27Met), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- Q29* (p.Gln29Ter), rs1940368506, ClinGen CA384528134, ClinVar RCV001090712, Ensembl rs1940368506, CADD 39.00, Pathogenic
- Q29E (p.Gln29Glu), Ensembl rs1940368506, Pathogenic
- Q29P (p.Gln29Pro), gnomAD rs1190060899, REVEL 0.22, CADD 23.10
- A31T (p.Ala31Thr), rs2540187936, ClinGen CA384526851, ClinVar RCV003544976, Uncertain significance, not provided
- G32S (p.Gly32Ser), rs779475416, ClinGen CA6536094, ClinVar RCV003238537, ExAC rs779475416, REVEL 0.23, CADD 20.40, Uncertain significance, not provided
- S33R (p.Ser33Arg), Ensembl rs2136637563
- C34* (p.Cys34Ter), rs2136637552, ClinGen CA384526775, ClinVar RCV003046197, AlphaMissense 0.99, MetaLR 0.98, Pathogenic
- C34R (p.Cys34Arg), rs2540187904, ClinGen CA384526788, ClinVar RCV003120486, Pathogenic/Likely pathogenic, Stickler syndrome, type I, nonsyndromic ocular; not provided
- C34W (p.Cys34Trp), rs2136637552, ClinGen CA384526772, ClinVar RCV001995990, Ensembl rs2136637552, AlphaMissense 0.99, MetaLR 0.98, Uncertain significance, not provided
- Q36K (p.Gln36Lys), NCI-TCGA Cosmic COSV6153, Variant assessed as somatic; moderate impact.
- G38A (p.Gly38Ala), TOPMed rs1010211097, Uncertain significance, not provided
- G38E (p.Gly38Glu), rs1010211097, ClinGen CA384526724, ClinVar RCV003063856, AlphaMissense 0.23, MetaLR 0.48, Uncertain significance, not provided
- G38R (p.Gly38Arg), rs765855138, ClinGen CA6536091, ClinVar RCV001235397, ExAC rs765855138, REVEL 0.56, CADD 24.80, Conflicting interpretations, not provided
- G38V (p.Gly38Val), NCI-TCGA Cosmic COSV6152, Variant assessed as somatic; moderate impact.
- G38W (p.Gly38Trp), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- Q39* (p.Gln39Ter), rs1940161368, ClinGen CA384526708, ClinVar RCV001213799, ClinVar RCV001266759, Pathogenic
- R40K (p.Arg40Lys), rs2136637469, ClinGen CA384526685, ClinVar RCV001876802, Ensembl rs2136637469, AlphaMissense 0.08, MetaLR 0.20, Uncertain significance, not provided
- Y41* (p.Tyr41Ter), rs1226870134, ClinGen CA384526646, ClinVar RCV003062507, Pathogenic
- Y41D (p.Tyr41Asp), Ensembl rs1592239128, REVEL 0.87, CADD 28.10
- Y41H (p.Tyr41His), rs1592239128, ClinGen CA384526662, ClinVar RCV002464907, REVEL 0.45, CADD 24.40, Uncertain significance, not provided
- Y41S (p.Tyr41Ser), gnomAD rs1299510101
- N42K (p.Asn42Lys), rs1940160586, ClinGen CA384526623, ClinVar RCV003852842, TOPMed rs1940160586, AlphaMissense 0.13, MetaLR 0.13, Uncertain significance, not provided
- D43H (p.Asp43His), rs2540187816, ClinGen CA384526617, ClinVar RCV003860805, Uncertain significance, not provided
- D43N (p.Asp43Asn), NCI-TCGA Cosmic COSV6152, Variant assessed as somatic; moderate impact.
- D45E (p.Asp45Glu), rs375778172, ClinGen CA384526555, ClinVar RCV002716389, 1000Genomes rs375778172, REVEL 0.07, CADD 19.10, Uncertain significance, not provided
- D45Y (p.Asp45Tyr), rs202145830, ClinGen CA236495038, ClinVar RCV003879830, gnomAD rs202145830, REVEL 0.47, CADD 28.80, Likely benign, not provided
- V46A (p.Val46Ala), TOPMed rs1940159813, REVEL 0.62, CADD 27.50, Uncertain significance, Inborn genetic diseases
- W47* (p.Trp47Ter), rs121912896, ClinGen CA127181, NCI-TCGA Cosmic COSV6153, ClinVar RCV000018944, Pathogenic
- W47R (p.Trp47Arg), rs1064793352, ClinGen CA16619531, ClinVar RCV000483696, Ensembl rs1064793352, REVEL 0.93, CADD 31.00, Conflicting interpretations, not provided
- W47S (p.Trp47Ser), rs2540187780, ClinGen CA384526537, ClinVar RCV003570181, Uncertain significance, not provided
- K48N (p.Lys48Asn), gnomAD rs1940159051, REVEL 0.43, CADD 24.40
- P49L (p.Pro49Leu), rs774081386, ClinGen CA6536086, ClinVar RCV003323196, ExAC rs774081386, REVEL 0.66, CADD 25.20, Conflicting interpretations, not provided
- E50K (p.Glu50Lys), NCI-TCGA TCGA novel, REVEL 0.26, CADD 22.80, Variant assessed as somatic; moderate impact.
- P51S (p.Pro51Ser), rs945234297, ClinGen CA236494993, ClinVar RCV001232295, TOPMed rs945234297, REVEL 0.08, CADD 22.00, Conflicting interpretations, not provided
- C52* (p.Cys52Ter), rs1246771678, ClinGen CA384526460, ClinVar RCV000659383, ClinVar RCV001387827, Pathogenic
- R53G (p.Arg53Gly), rs776744207, ClinGen CA6536084, ClinVar RCV001297636, ClinVar RCV005802096, REVEL 0.45, CADD 24.30, Conflicting interpretations, Inborn genetic diseases; not provided
- R53Q (p.Arg53Gln), rs370821294, ClinGen CA6536082, ClinVar RCV001251954, ClinVar RCV001309564, REVEL 0.12, CADD 15.60, Likely benign, not specified; not provided
- R53W (p.Arg53Trp), rs776744207, ClinGen CA6536083, ClinVar RCV001041293, ExAC rs776744207, REVEL 0.54, CADD 29.20, Likely benign, not provided
- I54F (p.Ile54Phe), rs1940157670, ClinGen CA384526447, ClinVar RCV002259488, TOPMed rs1940157670, AlphaMissense 0.28, MetaLR 0.27, Uncertain significance, not provided
- I54V (p.Ile54Val), TOPMed rs1940157670, Uncertain significance, Inborn genetic diseases
- C55Y (p.Cys55Tyr), rs2540187702, ClinGen CA384526424, ClinVar RCV002296531, Uncertain significance, not provided
- V56I (p.Val56Ile), rs1940157547, ClinGen CA384526414, ClinVar RCV002009663, gnomAD rs1940157547, REVEL 0.15, CADD 21.70, Uncertain significance, not provided
- V56L (p.Val56Leu), gnomAD rs1940157547, REVEL 0.16, CADD 22.30, Uncertain significance
- C57* (p.Cys57Ter), Ensembl rs2136637244, Pathogenic, in STL1O
- C57Y (p.Cys57Tyr), rs121912898, ClinGen CA127185, ClinVar RCV000018946, UniProt VAR 063891, REVEL 0.97, CADD 26.90, Pathogenic, Stickler syndrome, type I, nonsyndromic ocular
- D58H (p.Asp58His), TOPMed rs1940157187
- T59A (p.Thr59Ala), rs376641474, ClinGen CA6536081, ClinVar RCV001772731, ESP rs376641474, REVEL 0.06, CADD 19.70, Conflicting interpretations, not provided
- G60A (p.Gly60Ala), rs2540187654, ClinGen CA384526327, ClinVar RCV003005164, Uncertain significance, not provided
- G60R (p.Gly60Arg), rs773434184, ClinGen CA6536080, ClinVar RCV003551021, ExAC rs773434184, REVEL 0.77, CADD 27.70, Likely benign, not provided
- V62I (p.Val62Ile), ExAC rs748537902, TOPMed rs748537902, REVEL 0.21, CADD 14.90
- V62L (p.Val62Leu), ExAC rs748537902, TOPMed rs748537902, REVEL 0.37, CADD 20.70
- C64* (p.Cys64Ter), rs121912897, ClinGen CA127183, ClinVar RCV000018945, ClinVar RCV000657640, Pathogenic
- D65N (p.Asp65Asn), rs1940156255, ClinGen CA384526262, NCI-TCGA Cosmic COSV6153, ClinVar RCV001046146, REVEL 0.55, CADD 27.20, Conflicting interpretations, not provided; MASS syndrome
- D66G (p.Asp66Gly), NCI-TCGA Cosmic COSV6152, REVEL 0.27, CADD 24.10, Variant assessed as somatic; moderate impact.
- D66N (p.Asp66Asn), rs976006680, ClinGen CA236494906, NCI-TCGA Cosmic COSV6153, ClinVar RCV001325892, REVEL 0.18, CADD 23.70, Conflicting interpretations, not provided
- D66Y (p.Asp66Tyr), TOPMed rs976006680, gnomAD rs976006680, Uncertain significance
- I67L (p.Ile67Leu), rs2540187598, ClinGen CA384526222, ClinVar RCV004534359, ClinVar RCV006473108, REVEL 0.16, CADD 20.80, Uncertain significance, not provided; COL2A1-related disorder
- I68M (p.Ile68Met), rs2136637135, ClinGen CA384526197, ClinVar RCV003574259, Uncertain significance, not provided
- C69R (p.Cys69Arg), rs749799023, ClinGen CA6536075, ClinVar RCV002996317, ExAC rs749799023, REVEL 0.98, CADD 29.70, Uncertain significance, not provided
- E70G (p.Glu70Gly), rs2540187583, ClinGen CA384526173, ClinVar RCV003706747, Uncertain significance, not provided
- D71N (p.Asp71Asn), rs943372344, ClinGen CA236494891, ClinVar RCV001902613, ClinVar RCV004975772, REVEL 0.18, CADD 24.30, Uncertain significance, not provided; Inborn genetic diseases
- V72L (p.Val72Leu), ExAC rs755705390, TOPMed rs755705390, gnomAD rs755705390, REVEL 0.06, CADD 0.22, Uncertain significance, Inborn genetic diseases
- V72M (p.Val72Met), rs755705390, ClinGen CA6536074, ClinVar RCV001230757, ExAC rs755705390, REVEL 0.04, CADD 4.16, Conflicting interpretations, not specified; not provided
- D74E (p.Asp74Glu), rs527800991, ClinGen CA384526103, ClinVar RCV002937290, Uncertain significance, not provided
- D74G (p.Asp74Gly), ExAC rs750031645, TOPMed rs750031645, gnomAD rs750031645, REVEL 0.26, CADD 23.40
- D74V (p.Asp74Val), ExAC rs750031645, TOPMed rs750031645, gnomAD rs750031645
- C75* (p.Cys75Ter), rs2540187525, ClinGen CA384526088, ClinVar RCV002825503, Pathogenic
- C75F (p.Cys75Phe), rs2136637051, ClinGen CA384526090, ClinVar RCV001364844, Ensembl rs2136637051, AlphaMissense 0.96, MetaLR 0.93, Likely pathogenic, not provided
- C75S (p.Cys75Ser), ExAC rs767276172, gnomAD rs767276172, REVEL 0.91, CADD 26.70
- L76F (p.Leu76Phe), gnomAD rs1940154691, REVEL 0.15, CADD 23.60
- S77G (p.Ser77Gly), Ensembl rs1940154402
- S77N (p.Ser77Asn), rs2540187508, ClinGen CA384526065, ClinVar RCV003710417, Uncertain significance, not provided
- P78L (p.Pro78Leu), rs952199404, ClinGen CA236494877, ClinVar RCV003820051, TOPMed rs952199404, REVEL 0.46, CADD 23.10, Uncertain significance, not provided
- E79D (p.Glu79Asp), rs757029242, ClinGen CA6536071, ClinVar RCV002036595, ExAC rs757029242, REVEL 0.14, CADD 17.90, Likely benign, not provided
- P81L (p.Pro81Leu), NCI-TCGA Cosmic COSV6153, Variant assessed as somatic; moderate impact.
- P81R (p.Pro81Arg), rs1940153785, ClinGen CA384526000, NCI-TCGA Cosmic COSV6153, ClinVar RCV003680414, REVEL 0.35, CADD 23.60, Uncertain significance, not provided
- P81S (p.Pro81Ser), gnomAD rs1292156036, REVEL 0.23, CADD 23.40
- F82L (p.Phe82Leu), rs142161948, ClinGen CA384525984, ClinVar RCV002958932, Uncertain significance, not provided
- F82V (p.Phe82Val), rs2136636961, ClinGen CA384525993, ClinVar RCV002002856, Ensembl rs2136636961, AlphaMissense 0.14, MetaLR 0.24, Uncertain significance, not provided
- G83A (p.Gly83Ala), rs2540187429, ClinGen CA384525967, ClinVar RCV002300453, Uncertain significance, not provided
- G83R (p.Gly83Arg), rs762911032, ClinGen CA6536068, ClinVar RCV001238519, ClinVar RCV005540336, REVEL 0.84, CADD 28.20, Conflicting interpretations, not provided; Inborn genetic diseases
- E84G (p.Glu84Gly), rs2540187413, ClinGen CA384525949, ClinVar RCV002791595, Uncertain significance, not provided
- E84K (p.Glu84Lys), rs2540187418, ClinGen CA384525958, ClinVar RCV003542555, REVEL 0.69, CADD 28.00, Uncertain significance, not provided
- C86* (p.Cys86Ter), rs794727261, ClinGen CA302808, ClinVar RCV000255165, ClinVar RCV000762897, Pathogenic
- I88F (p.Ile88Phe), rs760745824, ClinGen CA6536066, ClinVar RCV003546300, ExAC rs760745824, REVEL 0.39, CADD 22.30, Benign, not provided
- I88V (p.Ile88Val), rs760745824, ClinGen CA6536065, ClinVar RCV001921095, ClinVar RCV004529047, REVEL 0.11, CADD 10.60, Conflicting interpretations, Inborn genetic diseases; not provided; COL2A1-related disorder
- C89* (p.Cys89Ter), rs2136636832, ClinGen CA384525872, NCI-TCGA Cosmic COSV6152, ClinVar RCV001960525, Pathogenic
- C89F (p.Cys89Phe), NCI-TCGA Cosmic COSV6153, Uncertain significance, not provided
- C89Y (p.Cys89Tyr), Ensembl rs1940152571, REVEL 0.94, CADD 27.30
- P90A (p.Pro90Ala), Ensembl rs1592238883
- P90L (p.Pro90Leu), ExAC rs773342588, TOPMed rs773342588, gnomAD rs773342588, REVEL 0.24, CADD 23.00, Uncertain significance, Inborn genetic diseases
- T91A (p.Thr91Ala), rs1252498034, ClinGen CA384525846, ClinVar RCV002041192, TOPMed rs1252498034, REVEL 0.08, CADD 16.00, Conflicting interpretations, not provided
- D92A (p.Asp92Ala), Ensembl rs1592238847
- D92H (p.Asp92His), rs2540187330, ClinGen CA384525833, ClinVar RCV003685466, Uncertain significance, not provided
- L93F (p.Leu93Phe), NCI-TCGA Cosmic COSV1004, Variant assessed as somatic; moderate impact.
- L93I (p.Leu93Ile), TOPMed rs1940151567, gnomAD rs1940151567, REVEL 0.19, CADD 21.90
- L93R (p.Leu93Arg), rs2540187306, ClinGen CA384525795, ClinVar RCV004536703, Uncertain significance, COL2A1-related disorder
- A94P (p.Ala94Pro), ExAC rs768931460, TOPMed rs768931460, gnomAD rs768931460, Likely benign
- A94S (p.Ala94Ser), ExAC rs768931460, TOPMed rs768931460, gnomAD rs768931460, REVEL 0.26, CADD 3.66, Likely benign
- A94T (p.Ala94Thr), rs768931460, ClinGen CA6536060, ClinVar RCV001896702, ExAC rs768931460, REVEL 0.21, CADD 7.42, Likely benign, not provided
- A94V (p.Ala94Val), rs1224104246, ClinGen CA384525777, ClinVar RCV001903815, TOPMed rs1224104246, REVEL 0.18, CADD 22.30, Likely benign, not provided
- A96T (p.Ala96Thr), NCI-TCGA Cosmic COSV6153, Variant assessed as somatic; moderate impact.
- Q99* (p.Gln99Ter), cosmic curated COSV10816, Ensembl rs2136630375
- P100L (p.Pro100Leu), ExAC rs763903953, gnomAD rs763903953, REVEL 0.29, CADD 22.50, Uncertain significance
- P100R (p.Pro100Arg), rs763903953, ClinGen CA6536051, ClinVar RCV002041606, ExAC rs763903953, REVEL 0.30, CADD 15.80, Uncertain significance, not provided
- G101R (p.Gly101Arg), TOPMed rs1217575381, gnomAD rs1217575381, REVEL 0.52, CADD 22.70
- G101V (p.Gly101Val), rs557218250, ClinGen CA6536049, ClinVar RCV001054505, ClinVar RCV005540251, REVEL 0.54, CADD 23.20, Likely benign, not provided; Inborn genetic diseases
- G104* (p.Gly104Ter), rs764210489, ClinGen CA384525441, ClinVar RCV000732165, ExAC rs764210489, AlphaMissense 0.91, MetaLR 0.97, Pathogenic
- G104E (p.Gly104Glu), cosmic curated COSV10742, TOPMed rs1015202999, gnomAD rs1015202999, REVEL 0.91, CADD 32.00
- G104R (p.Gly104Arg), rs764210489, ClinGen CA6536019, ClinVar RCV000485870, ExAC rs764210489, REVEL 0.91, AlphaMissense 0.91, Uncertain significance, not provided
- Q105* (p.Gln105Ter), rs2540182818, ClinGen CA384525428, ClinVar RCV002863500, Pathogenic
- Q105H (p.Gln105His), NCI-TCGA Cosmic COSV1004, cosmic curated COSV10047, cosmic curated COSV10464, Variant assessed as somatic; moderate impact.
- K106E (p.Lys106Glu), NCI-TCGA Cosmic COSV6152, cosmic curated COSV61527, Variant assessed as somatic; moderate impact.
- G107A (p.Gly107Ala), rs1940054684, ClinGen CA384525386, ClinVar RCV001315103, Ensembl rs1940054684, AlphaMissense 0.71, MetaLR 0.97, Uncertain significance, not provided
- E108* (p.Glu108Ter), NCI-TCGA TCGA novel, Variant assessed as somatic; high impact.
- P109L (p.Pro109Leu), rs140120720, ClinGen CA384525359, ClinVar RCV002995038, AlphaMissense 0.41, MetaLR 0.93, Uncertain significance, not provided
- P109R (p.Pro109Arg), rs140120720, ClinGen CA6536016, ClinVar RCV001699642, ESP rs140120720, REVEL 0.69, AlphaMissense 0.41, Uncertain significance, not provided
- P109S (p.Pro109Ser), ESP rs373195482, ExAC rs373195482, gnomAD rs373195482, REVEL 0.66, CADD 25.70
- G110R (p.Gly110Arg), TOPMed rs959921134, gnomAD rs959921134, REVEL 0.87, CADD 33.00, Uncertain significance, not provided
- D111E (p.Asp111Glu), ExAC rs760076089, TOPMed rs760076089, gnomAD rs760076089, REVEL 0.29, CADD 17.90, Likely benign
- D111N (p.Asp111Asn), gnomAD rs1260264802, REVEL 0.41, CADD 23.20
- D111Y (p.Asp111Tyr), gnomAD rs1260264802
- I112T (p.Ile112Thr), rs2540182746, ClinGen CA384525320, ClinVar RCV002296586, NCI-TCGA TCGA novel, Uncertain significance, not provided
- I112V (p.Ile112Val), rs777293765, ClinGen CA6536014, ClinVar RCV003043051, ExAC rs777293765, REVEL 0.20, CADD 18.50, Likely benign, not provided
- D114E (p.Asp114Glu), gnomAD rs1341039824, REVEL 0.30, CADD 20.30
- D114G (p.Asp114Gly), ExAC rs746493017, gnomAD rs746493017, REVEL 0.54, CADD 31.00
- D114N (p.Asp114Asn), rs1940053470, ClinGen CA384525294, cosmic curated COSV10742, ClinVar RCV002006663, REVEL 0.40, CADD 23.90, Uncertain significance, not provided
- I115V (p.Ile115Val), rs1329462343, ClinGen CA384525230, ClinVar RCV003546369, TOPMed rs1329462343, REVEL 0.22, CADD 11.90, Uncertain significance, not provided
- V116A (p.Val116Ala), rs779950053, ClinGen CA6535982, ClinVar RCV002265491, ClinVar RCV005542741, REVEL 0.29, CADD 20.30, Uncertain significance, not provided; Inborn genetic diseases
- V116L (p.Val116Leu), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- G117A (p.Gly117Ala), rs201192882, ClinGen CA6535980, ClinVar RCV000522522, 1000Genomes rs201192882, REVEL 0.89, CADD 26.00, Conflicting interpretations, Inborn genetic diseases; not provided
- G117R (p.Gly117Arg), NCI-TCGA Cosmic COSV1004, cosmic curated COSV10047, ExAC rs755974820, gnomAD rs755974820, REVEL 0.94, CADD 27.40, Variant assessed as somatic; moderate impact.
- P118L (p.Pro118Leu), rs777669076, ClinGen CA6535979, ClinVar RCV003141684, ExAC rs777669076, REVEL 0.66, CADD 22.60, Conflicting interpretations, not provided
- K119R (p.Lys119Arg), ExAC rs758569692, gnomAD rs758569692, REVEL 0.20, CADD 16.60
- P121L (p.Pro121Leu), TOPMed rs987213463
- P121S (p.Pro121Ser), Ensembl rs2136628343
- P124L (p.Pro124Leu), ExAC rs754127735, TOPMed rs754127735, gnomAD rs754127735, REVEL 0.47, CADD 24.40, Uncertain significance
- P124R (p.Pro124Arg), rs754127735, ClinGen CA6535975, ClinVar RCV004531833, ExAC rs754127735, REVEL 0.80, CADD 28.00, Uncertain significance, COL2A1-related disorder
- Q125R (p.Gln125Arg), NCI-TCGA Cosmic COSV6153, cosmic curated COSV61535, Variant assessed as somatic; moderate impact.
Public COL2A1 analysis runs
- COL2A1 analysis run — COL2A1 (2,467 variants) — completed 2026-08-22