General Structure Information
| PDB ID | 3fby |
| HGNC Gene Label(s) | COMP |
| Structure Name | the crystal structure of the signature domain of cartilage oligomeric matrix protein. |
| Resolution | 3.15Å |
| Reference | AUTH K.TAN,M.DUQUETTE,A.JOACHIMIAK,J.LAWLERTITL THE CRYSTAL STRUCTURE OF THE SIGNATURE DOMAIN OF CARTILAGETITL 2 OLIGOMERIC MATRIX PROTEIN: IMPLICATIONS FOR COLLAGEN,TITL 3 GLYCOSAMINOGLYCAN AND INTEGRIN BINDING.REF FASEB J. V. 23 2490 2009REFN ISSN 0892-6638PMID 19276170DOI 10.1096/FJ.08-128090 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 533 |
| Number Of SNVs | 124 |
| Number Of Permutations | 25650 |
| Optimal Distance Threshold | 9.0 |
| K Statistic | 0.022 |
| p-value | 0.065 |
ClinVar
| Number Of Residues | 533 |
| Number Of SNVs | 17 |
| Number Of Permutations | 3288 |
| Optimal Distance Threshold | 14.0 |
| K Statistic | 0.191 |
| p-value | 0.006 |
COSMIC
| Number Of Residues | 533 |
| Number Of SNVs | 9 |
| Number Of Permutations | 2824 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.083 |
| p-value | 0.949 |
Ripley’s K Analysis Plots
ExACClinVarCOSMIC
Variant Set Comparisons
ClinVar vs. ExAC
| Number Of ExAC SNVs | 124 |
| Number Of ClinVar SNVs | 17 |
| Optimal Distance Threshold | 14.0 |
| K Statistic | 0.121 |
| p-value | 0.001 |
Cosmic vs. ExAC
| Number Of ExAC SNVs | 124 |
| Number Of COSMIC SNVs | 9 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.071 |
| p-value | 0.833 |
Pathogenic Proximity Analysis
ClinVar PathProx Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:18899470 | rs374210489 | D>E | A:231 | (-44.80, 55.39, 1.47) |
| 19:18899463 | rs557483957 | P>S | A:234 | (-41.23, 48.41, 3.47) |
| 19:18899449 | H>Q | A:238 | (-50.84, 37.74, 2.17) | |
| 19:18899424 | rs537695502 | R>G | A:247 | (-55.24, 62.27, 2.94) |
| 19:18899317 | V>I | A:257 | (-60.43, 40.13, -5.47) | |
| 19:18899286 | G>D | A:267 | (-57.79, 33.84, 2.42) | |
| 19:18899278 | T>A | A:270 | (-65.09, 31.04, -2.70) | |
| 19:18899254 | E>K | A:278 | (-60.53, 27.71, 5.95) | |
| 19:18899244 | R>H | A:281 | (-54.10, 31.32, 13.80) | |
| 19:18899242 | C>S | A:282 | (-56.44, 36.84, 12.99) | |
| 19:18899238 | P>R | A:283 | (-58.20, 38.80, 15.97) | |
| 19:18899236 | rs145895692 | E>K | A:284 | (-59.75, 40.55, 12.83) |
| 19:18899115 | T>N | A:294 | (-70.76, 28.69, -1.08) | |
| 19:18899110 | P>A | A:296 | (-73.08, 34.92, -0.58) | |
| 19:18899095 | rs377504596 | E>Q | A:301 | (-76.49, 37.01, 9.33) |
| 19:18899088 | V>A | A:303 | (-80.28, 33.20, 14.77) | |
| 19:18899067 | D>V | A:310 | (-79.20, 32.34, 8.67) | |
| 19:18899059 | D>Y | A:313 | (-79.40, 26.55, 8.44) | |
| 19:18899055 | rs370913967 | P>L | A:314 | (-81.54, 23.91, 6.91) |
| 19:18899037 | G>E | A:320 | (-88.07, 22.29, 13.32) | |
| 19:18899035 | V>F | A:321 | (-90.02, 24.35, 11.16) | |
| 19:18899032 | P>S | A:322 | (-88.31, 23.35, 7.97) | |
| 19:18899028 | rs367812050 | N>S | A:323 | (-86.47, 27.31, 6.35) |
| 19:18898419 | T>M | A:339 | (-104.22, 35.06, 13.23) | |
| 19:18898414 | E>K | A:341 | (-104.33, 33.44, 6.97) | |
| 19:18898404 | rs571146259 | W>S | A:344 | (-94.21, 37.07, 7.51) |
| 19:18898399 | D>Y | A:346 | (-98.64, 35.43, 14.96) | |
| 19:18898395 | A>E | A:347 | (-93.92, 35.24, 16.10) | |
| 19:18898381 | rs142274526 | R>W | A:352 | (-102.39, 38.82, 16.22) |
| 19:18898363 | D>H | A:358 | (-94.82, 44.76, 3.45) | |
| 19:18898335 | R>Q | A:367 | (-98.43, 49.65, 16.79) | |
| 19:18898336 | COSM4075740 | R>W | A:367 | (-98.43, 49.65, 16.79) |
| 19:18898333 | G>S | A:368 | (-97.14, 48.46, 11.71) | |
| 19:18898326 | A>V | A:370 | (-101.41, 48.37, 9.12) | |
| 19:18898317 | D>G | A:373 | (-102.28, 54.93, 15.74) | |
| 19:18898318 | COSM438985 | D>N | A:373 | (-102.28, 54.93, 15.74) |
| 19:18897440 | rs61739916 | N>D | A:386 | (-100.37, 67.43, 6.93) |
| 19:18897433 | P>L | A:388 | (-99.45, 60.73, 7.11) | |
| 19:18897428 | rs151050419 | V>I | A:390 | (-93.52, 62.49, 6.69) |
| 19:18897411 | Q>H | A:395 | (-98.78, 69.64, 10.69) | |
| 19:18897404 | S>G | A:398 | (-96.89, 76.81, 3.07) | |
| 19:18897397 | G>V | A:400 | (-103.37, 74.80, 1.57) | |
| 19:18897398 | rs200422116 | G>S | A:400 | (-103.37, 74.80, 1.57) |
| 19:18897379 | A>G | A:406 | (-92.85, 67.56, 4.84) | |
| 19:18897380 | A>T | A:406 | (-92.85, 67.56, 4.84) | |
| 19:18897370 | N>S | A:409 | (-94.80, 67.49, -4.91) | |
| 19:18897347 | D>N | A:417 | (-104.06, 66.90, -7.71) | |
| 19:18897342 | rs375908187 | Q>H | A:418 | (-99.83, 65.84, -5.50) |
| 19:18897344 | Q>E | A:418 | (-99.83, 65.84, -5.50) | |
| 19:18897070 | A>V | A:429 | (-96.93, 73.33, -10.94) | |
| 19:18896951 | G>A | A:438 | (-77.42, 67.09, -15.50) | |
| 19:18896939 | Q>R | A:442 | (-85.83, 71.51, -11.72) | |
| 19:18896930 | R>P | A:445 | (-86.84, 71.87, -6.54) | |
| 19:18896912 | rs530668887 | V>G | A:451 | (-72.12, 72.90, -10.86) |
| 19:18896909 | P>L | A:452 | (-72.41, 69.37, -11.86) | |
| 19:18896888 | S>L | A:459 | (-71.86, 73.00, 4.72) | |
| 19:18896889 | S>P | A:459 | (-71.86, 73.00, 4.72) | |
| 19:18896876 | G>A | A:463 | (-78.07, 77.96, -0.21) | |
| 19:18896865 | A>S | A:467 | (-69.86, 73.63, -6.05) | |
| 19:18896858 | COSM993159 | D>V | A:469 | (-69.83, 78.39, -1.88) |
| 19:18896831 | P>H | A:478 | (-61.51, 81.91, 1.41) | |
| 19:18896822 | R>Q | A:481 | (-55.05, 81.05, 0.99) | |
| 19:18896823 | R>W | A:481 | (-55.05, 81.05, 0.99) | |
| 19:18896811 | rs191645921 | R>G | A:485 | (-63.66, 72.86, 2.44) |
| 19:18896801 | P>H | A:488 | (-65.67, 76.73, 11.64) | |
| 19:18896795 | P>L | A:490 | (-61.52, 81.91, 11.79) | |
| 19:18896793 | rs541996591 | G>S | A:491 | (-57.35, 81.43, 12.23) |
| 19:18896781 | A>T | A:495 | (-52.15, 71.44, 17.48) | |
| 19:18896776 | rs143714206 | D>E | A:496 | (-50.62, 70.25, 14.37) |
| 19:18896777 | D>G | A:496 | (-50.62, 70.25, 14.37) | |
| 19:18896778 | D>Y | A:496 | (-50.62, 70.25, 14.37) | |
| 19:18896655 | rs554998204 | G>V | A:499 | (-52.28, 71.64, 7.20) |
| 19:18896627 | F>L | A:508 | (-62.18, 67.85, 5.89) | |
| 19:18896616 | K>R | A:512 | (-69.35, 61.77, 15.35) | |
| 19:18896617 | K>Q | A:512 | (-69.35, 61.77, 15.35) | |
| 19:18896603 | rs535198633 CD972154 |
K>N | A:516 | (-60.01, 54.60, 7.66) |
| 19:18896596 | V>M | A:519 | (-67.79, 56.65, 2.70) | |
| 19:18896583 | N>S | A:523 | (-70.65, 64.70, 3.22) | |
| 19:18896561 | D>E | A:530 | (-76.61, 52.13, 4.79) | |
| 19:18896562 | D>G | A:530 | (-76.61, 52.13, 4.79) | |
| 19:18896554 | A>T | A:533 | (-82.68, 53.31, 2.99) | |
| 19:18896544 | rs377451339 | T>I | A:536 | (-89.14, 50.97, -4.44) |
| 19:18896532 | D>V | A:540 | (-94.17, 47.05, -16.03) | |
| 19:18896533 | D>Y | A:540 | (-94.17, 47.05, -16.03) | |
| 19:18896517 | rs200870935 COSM3712861 |
A>V | A:545 | (-96.26, 39.00, -13.34) |
| 19:18896518 | A>T | A:545 | (-96.26, 39.00, -13.34) | |
| 19:18896512 | I>V | A:547 | (-94.73, 39.28, -9.27) | |
| 19:18896501 | rs373498615 | N>K | A:550 | (-89.11, 40.83, -2.30) |
| 19:18896352 | R>K | A:558 | (-72.20, 46.11, 3.54) | |
| 19:18896334 | rs376678596 | M>T | A:564 | (-89.61, 37.07, -5.97) |
| 19:18896327 | S>R | A:566 | (-90.07, 39.82, -10.90) | |
| 19:18896329 | S>G | A:566 | (-90.07, 39.82, -10.90) | |
| 19:18896323 | rs577011338 | P>T | A:568 | (-89.29, 45.09, -13.89) |
| 19:18896320 | G>S | A:569 | (-86.65, 46.74, -10.63) | |
| 19:18895851 | T>M | A:590 | (-80.75, 29.60, -8.11) | |
| 19:18895849 | V>I | A:591 | (-80.36, 26.38, -10.55) | |
| 19:18895795 | F>L | A:609 | (-81.70, 54.55, -15.05) | |
| 19:18895791 | Y>F | A:610 | (-76.01, 55.77, -16.45) | |
| 19:18895776 | K>R | A:615 | (-79.71, 36.96, -19.51) | |
| 19:18895770 | M>T | A:617 | (-79.63, 32.06, -21.48) | |
| 19:18895771 | M>L | A:617 | (-79.63, 32.06, -21.48) | |
| 19:18895726 | rs144170209 | E>K | A:632 | (-77.41, 39.04, -26.20) |
| 19:18895164 | S>T | A:642 | (-87.32, 57.29, -20.98) | |
| 19:18895155 | COSM993158 | G>S | A:645 | (-91.34, 55.53, -18.69) |
| 19:18895149 | G>R | A:647 | (-93.19, 50.60, -19.16) | |
| 19:18895143 | rs375484943 | Q>E | A:649 | (-91.76, 51.11, -24.91) |
| 19:18895137 | rs556356731 COSM993157 |
R>W | A:651 | (-91.42, 45.81, -20.82) |
| 19:18895134 | N>D | A:652 | (-89.53, 45.33, -24.32) | |
| 19:18895109 | rs150534218 | T>R | A:660 | (-84.59, 51.53, -27.79) |
| 19:18895100 | rs141708238 | Q>L | A:663 | (-86.53, 54.25, -24.13) |
| 19:18895094 | COSM438983 | R>Q | A:665 | (-77.62, 55.16, -25.31) |
| 19:18895095 | rs370202476 | R>W | A:665 | (-77.62, 55.16, -25.31) |
| 19:18895082 | K>T | A:669 | (-71.61, 43.65, -25.21) | |
| 19:18895073 | COSM3712860 | R>Q | A:672 | (-66.71, 37.04, -22.31) |
| 19:18895068 | V>M | A:674 | (-70.46, 34.93, -21.15) | |
| 19:18895052 | K>R | A:679 | (-75.37, 28.26, -7.14) | |
| 19:18895043 | Y>C | A:682 | (-69.65, 36.49, -11.01) | |
| 19:18895022 | R>Q | A:689 | (-65.43, 59.81, -11.76) | |
| 19:18895023 | R>G | A:689 | (-65.43, 59.81, -11.76) | |
| 19:18895007 | rs146374758 | Y>S | A:694 | (-64.38, 57.67, -16.42) |
| 19:18895005 | I>V | A:695 | (-68.39, 55.28, -17.34) | |
| 19:18894001 | V>A | A:697 | (-67.13, 48.60, -15.53) | |
| 19:18893999 | R>G | A:698 | (-62.90, 47.04, -13.59) | |
| 19:18893996 | F>V | A:699 | (-67.63, 42.69, -13.98) | |
| 19:18893977 | L>P | A:705 | (-60.33, 40.78, -14.86) | |
| 19:18893969 | COSM4075738 | D>N | A:708 | (-62.66, 46.18, -18.81) |
| 19:18893960 | V>M | A:711 | (-62.89, 54.68, -21.02) | |
| 19:18893957 | V>L | A:712 | (-67.34, 54.60, -21.22) | |
| 19:18893945 | T>A | A:716 | (-76.96, 61.16, -20.12) | |
| 19:18893938 | rs149551600 | R>Q | A:718 | (-72.94, 65.49, -16.12) |
| 19:18893929 | R>H | A:721 | (-80.44, 57.77, -6.16) | |
| 19:18893930 | R>C | A:721 | (-80.44, 57.77, -6.16) | |
| 19:18893921 | rs372951104 | V>I | A:724 | (-79.98, 47.08, -7.27) |
| 19:18893912 | rs374459827 | F>L | A:727 | (-86.52, 41.87, -15.98) |
| 19:18893905 | Q>R | A:729 | (-83.81, 35.83, -11.51) | |
| 19:18893887 | A>G | A:735 | (-72.79, 41.12, -1.40) | |
| 19:18893878 | R>H | A:738 | (-68.03, 48.49, 0.67) | |
| 19:18893872 | rs138174876 | R>H | A:740 | (-65.61, 54.53, -2.33) |
| 19:18893873 | R>C | A:740 | (-65.61, 54.53, -2.33) | |
| 19:18893754 | Y>H | A:749 | (-60.22, 61.32, -19.35) | |
| 19:18893745 | H>Y | A:752 | (-59.57, 57.79, -24.23) | |
| 19:18893736 | rs140511415 | R>W | A:755 | (-54.29, 56.29, -27.08) |
| 19:18893732 | rs61752496 | Q>R | A:756 | (-58.01, 60.17, -29.95) |
[+] ClinVar Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:18898453 | rs137852653 | C>R | A:328 | (-91.35, 32.42, 11.36) |
| 19:18898411 | rs137852652 | D>Y | A:342 | (-99.84, 37.07, 6.78) |
| 19:18898393 | rs137852656 | C>R | A:348 | (-92.87, 37.41, 13.15) |
| 19:18896906 | rs28936668 | N>S | A:453 | (-74.53, 69.57, -7.37) |
| 19:18896861 | rs137852651 | C>Y | A:468 | (-70.48, 77.20, -6.10) |
| 19:18896850 | rs137852650 | D>Y | A:472 | (-68.19, 75.93, 1.55) |
| 19:18896846 | rs28936669 | D>G | A:473 | (-67.40, 77.17, 6.34) |
| 19:18896582 | rs137852654 | N>K | A:523 | (-70.65, 64.70, 3.22) |
| 19:18896565 | rs312262903 | T>I | A:529 | (-72.08, 51.55, 2.99) |
| 19:18896486 | rs397515511 | N>K | A:555 | (-74.38, 43.28, 6.41) |
| 19:18895873 | rs312262899 | E>K | A:583 | (-67.12, 47.81, -4.43) |
| 19:18895866 | rs312262900 | T>M | A:585 | (-70.85, 40.38, -4.81) |
| 19:18895860 | rs312262901 | H>R | A:587 | (-74.36, 34.62, -5.98) |
| 19:18895807 | rs397515512 | D>N | A:605 | (-85.42, 59.75, -12.92) |
| 19:18895046 | rs397515513 | S>C | A:681 | (-69.40, 34.76, -7.17) |
| 19:18893938 | rs149551600 | R>Q | A:718 | (-72.94, 65.49, -16.12) |
| 19:18893939 | rs28936368 | R>W | A:718 | (-72.94, 65.49, -16.12) |
| 19:18893935 | rs137852655 | G>D | A:719 | (-75.38, 62.02, -11.61) |
| 19:18893936 | rs312262904 | G>S | A:719 | (-75.38, 62.02, -11.61) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 19:18899080 | COSM1712063 | D>N | A:306 | (-75.50, 26.51, 14.53) |
| 19:18897416 | COSM1680808 | D>Y | A:394 | (-94.66, 71.87, 12.21) |
| 19:18896895 | COSM137168 | E>K | A:457 | (-73.03, 69.19, -1.31) |
| 19:18896840 | COSM310278 | D>V | A:475 | (-64.91, 80.80, 8.40) |
| 19:18896517 | COSM3712861 | A>V | A:545 | (-96.26, 39.00, -13.34) |
| 19:18895749 | COSM3100443 | A>G | A:624 | (-94.23, 41.17, -28.97) |
| 19:18895741 | COSM4591709 | F>L | A:627 | (-90.04, 46.31, -28.91) |
| 19:18895737 | COSM4591196 | R>P | A:628 | (-89.18, 40.40, -31.41) |
| 19:18895073 | COSM3712860 | R>Q | A:672 | (-66.71, 37.04, -22.31) |