General Structure Information
| PDB ID | 3bdl |
| HGNC Gene Label(s) | SND1 |
| Structure Name | crystal structure of a truncated human tudor-sn |
| Resolution | 1.9Å |
| Reference | AUTH C.L.LI,W.Z.YANG,Y.P.CHEN,H.S.YUANTITL STRUCTURAL AND FUNCTIONAL INSIGHTS INTO HUMANTITL 2 TUDOR-SN, A KEY COMPONENT LINKING RNA INTERFERENCETITL 3 AND EDITING.REF NUCLEIC ACIDS RES. V. 36 3579 2008REFN ISSN 0305-1048PMID 18453631DOI 10.1093/NAR/GKN236 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 536 |
| Number Of SNVs | 115 |
| Number Of Permutations | 30237 |
| Optimal Distance Threshold | 6.0 |
| K Statistic | 0.01 |
| p-value | 0.443 |
COSMIC
| Number Of Residues | 536 |
| Number Of SNVs | 7 |
| Number Of Permutations | 3537 |
| Optimal Distance Threshold | 27.0 |
| K Statistic | 0.19 |
| p-value | 0.571 |
Ripley’s K Analysis Plots
ExACCOSMIC
Variant Set Comparisons
Cosmic vs. ExAC
| Number Of ExAC SNVs | 115 |
| Number Of COSMIC SNVs | 7 |
| Optimal Distance Threshold | 45.0 |
| K Statistic | 0.208 |
| p-value | 0.683 |
Pathogenic Proximity Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 7:127347682 | D>G | A:315 | (7.92, -45.16, -3.58) | |
| 7:127347689 | COSM331531 | Q>H | A:317 | (14.45, -44.77, -3.44) |
| 7:127361371 | V>L | A:332 | (7.64, -29.40, -7.45) | |
| 7:127361372 | rs202087140 | V>A | A:332 | (7.64, -29.40, -7.45) |
| 7:127361381 | rs568517395 | L>Q | A:335 | (6.36, -38.74, -10.20) |
| 7:127361386 | S>P | A:337 | (2.93, -41.45, -12.52) | |
| 7:127361392 | D>N | A:339 | (1.49, -38.04, -9.96) | |
| 7:127361396 | Y>C | A:340 | (2.54, -33.08, -10.64) | |
| 7:127361401 | T>A | A:342 | (6.00, -31.06, -2.56) | |
| 7:127361404 | I>V | A:343 | (10.00, -32.86, -2.05) | |
| 7:127361419 | I>V | A:348 | (17.68, -28.01, 5.59) | |
| 7:127361423 | R>Q | A:349 | (15.76, -24.89, 9.75) | |
| 7:127361429 | COSM1177808 | P>L | A:351 | (16.21, -18.52, 4.72) |
| 7:127361440 | rs567804903 | G>W | A:355 | (12.33, -12.95, 15.29) |
| 7:127447538 | D>N | A:360 | (9.26, -2.36, 7.60) | |
| 7:127447548 | rs199626178 COSM1226966 |
K>R | A:363 | (-0.09, -4.72, 4.73) |
| 7:127447557 | COSM1447862 | R>H | A:366 | (8.31, -8.43, -2.13) |
| 7:127447559 | COSM3877895 | P>T | A:367 | (9.23, -13.41, 0.93) |
| 7:127447580 | rs189206929 | M>V | A:374 | (15.31, -16.62, -0.12) |
| 7:127447590 | rs201531475 | A>G | A:377 | (18.70, -19.71, -2.78) |
| 7:127447592 | R>W | A:378 | (14.58, -18.89, -6.53) | |
| 7:127447593 | R>Q | A:378 | (14.58, -18.89, -6.53) | |
| 7:127447605 | rs374865628 | R>Q | A:382 | (16.21, -20.93, -11.43) |
| 7:127484381 | rs554481013 | N>S | A:391 | (18.36, -38.92, -7.78) |
| 7:127484387 | rs200994299 | T>M | A:393 | (15.96, -40.65, -0.72) |
| 7:127484389 | V>M | A:394 | (12.24, -40.20, 1.67) | |
| 7:127484398 | I>V | A:397 | (7.18, -37.76, 7.00) | |
| 7:127484465 | T>I | A:419 | (21.09, -36.06, -5.60) | |
| 7:127527980 | K>E | A:432 | (26.92, -21.81, -1.01) | |
| 7:127528026 | R>K | A:447 | (18.74, -37.32, 12.00) | |
| 7:127528038 | rs542618933 | Y>F | A:451 | (23.11, -34.51, 10.23) |
| 7:127528046 | L>M | A:454 | (24.52, -31.62, 5.96) | |
| 7:127528056 | A>G | A:457 | (28.97, -27.92, 5.11) | |
| 7:127544804 | I>V | A:462 | (31.20, -21.20, 9.68) | |
| 7:127544817 | rs144122605 | K>R | A:466 | (30.05, -18.55, 2.50) |
| 7:127544844 | rs145473877 | P>R | A:475 | (22.44, -8.76, 0.60) |
| 7:127544846 | I>L | A:476 | (19.40, -5.23, -0.15) | |
| 7:127544853 | rs192914914 | R>H | A:478 | (16.44, -2.26, -3.71) |
| 7:127544864 | I>V | A:482 | (4.79, -2.85, -13.74) | |
| 7:127544865 | I>T | A:482 | (4.79, -2.85, -13.74) | |
| 7:127569264 | F>L | A:492 | (8.23, 0.82, -18.00) | |
| 7:127569283 | A>T | A:499 | (14.83, -3.49, -26.20) | |
| 7:127569289 | R>C | A:501 | (14.78, -11.00, -28.58) | |
| 7:127569313 | V>I | A:509 | (1.68, -19.57, -15.37) | |
| 7:127569320 | S>N | A:511 | (-2.68, -19.11, -18.52) | |
| 7:127569329 | rs143989011 | R>L | A:514 | (-1.73, -13.69, -17.70) |
| 7:127569364 | I>V | A:526 | (6.20, -7.80, -16.40) | |
| 7:127569372 | F>L | A:528 | (4.04, -11.26, -21.79) | |
| 7:127631029 | rs376321160 | L>F | A:542 | (-18.33, -14.46, -11.81) |
| 7:127631062 | S>G | A:553 | (-7.99, -24.55, -20.66) | |
| 7:127631063 | S>I | A:553 | (-7.99, -24.55, -20.66) | |
| 7:127631093 | L>Q | A:563 | (8.12, -25.42, -21.55) | |
| 7:127631096 | V>A | A:564 | (8.29, -21.49, -19.11) | |
| 7:127631105 | R>Q | A:567 | (12.12, -22.91, -17.36) | |
| 7:127714563 | E>K | A:572 | (9.79, -9.83, -28.91) | |
| 7:127714573 | S>N | A:575 | (1.67, -4.18, -27.11) | |
| 7:127714575 | M>L | A:576 | (-0.41, -2.24, -23.59) | |
| 7:127714580 | D>E | A:577 | (-3.78, -4.83, -22.11) | |
| 7:127714587 | rs371056767 | G>S | A:580 | (-1.20, -4.03, -18.17) |
| 7:127714599 | COSM3877915 | G>S | A:584 | (4.16, -10.82, -27.11) |
| 7:127714614 | rs371656294 | D>N | A:589 | (15.43, -23.03, -25.41) |
| 7:127714615 | D>A | A:589 | (15.43, -23.03, -25.41) | |
| 7:127714617 | rs144956035 | G>S | A:590 | (14.47, -21.37, -29.93) |
| 7:127714632 | rs376616596 | V>I | A:595 | (4.42, -21.47, -32.56) |
| 7:127714642 | V>A | A:598 | (-0.61, -23.53, -32.52) | |
| 7:127714708 | rs141988056 | S>C | A:620 | (2.69, -24.51, -40.36) |
| 7:127714713 | rs148173300 | E>K | A:622 | (-3.26, -23.52, -37.51) |
| 7:127714722 | A>T | A:625 | (-3.15, -29.27, -35.91) | |
| 7:127714733 | COSM1622313 | K>N | A:628 | (-3.35, -33.94, -35.66) |
| 7:127721454 | P>A | A:646 | (-30.69, -37.54, -15.86) | |
| 7:127721457 | V>M | A:647 | (-32.92, -35.29, -12.76) | |
| 7:127721461 | L>P | A:648 | (-32.76, -36.14, -7.94) | |
| 7:127721476 | R>Q | A:653 | (-44.19, -29.75, -10.23) | |
| 7:127721496 | V>M | A:660 | (-39.76, -12.83, -14.75) | |
| 7:127721535 | COSM203448 | V>M | A:673 | (-35.14, -13.69, -17.86) |
| 7:127721544 | V>L | A:676 | (-38.86, -8.01, -11.30) | |
| 7:127721553 | rs148285818 | G>S | A:679 | (-34.53, -3.63, -11.45) |
| 7:127724797 | M>T | A:686 | (-26.95, 1.37, -16.17) | |
| 7:127724808 | R>C | A:690 | (-25.75, 4.70, -18.99) | |
| 7:127724809 | rs375174369 | R>H | A:690 | (-25.75, 4.70, -18.99) |
| 7:127724812 | N>S | A:691 | (-23.62, 9.60, -15.42) | |
| 7:127724817 | I>V | A:693 | (-19.41, 6.70, -19.66) | |
| 7:127724832 | rs192770678 | P>T | A:698 | (-14.75, 6.00, -24.37) |
| 7:127724841 | G>S | A:701 | (-9.87, 2.70, -31.09) | |
| 7:127724845 | COSM3632999 | S>F | A:702 | (-8.21, 2.64, -27.86) |
| 7:127724848 | Y>C | A:703 | (-10.93, -2.20, -26.12) | |
| 7:127724856 | R>C | A:706 | (-8.42, -11.29, -23.97) | |
| 7:127724857 | rs552426263 COSM203449 |
R>H | A:706 | (-8.42, -11.29, -23.97) |
| 7:127724880 | K>E | A:714 | (-22.76, 2.74, -28.24) | |
| 7:127724886 | V>I | A:716 | (-28.88, 0.58, -31.63) | |
| 7:127724893 | G>E | A:718 | (-26.83, 4.91, -27.82) | |
| 7:127725767 | rs369890577 COSM3698152 |
R>C | A:722 | (-23.01, -4.80, -17.47) |
| 7:127725774 | R>Q | A:724 | (-19.43, -11.84, -22.06) | |
| 7:127725788 | E>K | A:729 | (-14.46, -11.77, -37.24) | |
| 7:127725827 | G>S | A:742 | (-29.22, -11.38, -24.08) | |
| 7:127727002 | P>T | A:748 | (-17.38, -1.80, -34.02) | |
| 7:127727009 | rs376458386 | T>I | A:750 | (-15.33, 2.11, -32.37) |
| 7:127727011 | R>C | A:751 | (-20.45, 1.42, -31.06) | |
| 7:127727012 | rs139075193 | R>H | A:751 | (-20.45, 1.42, -31.06) |
| 7:127727029 | rs539780027 | P>T | A:757 | (-14.27, -1.94, -11.45) |
| 7:127727030 | rs145154397 | P>R | A:757 | (-14.27, -1.94, -11.45) |
| 7:127727044 | R>W | A:762 | (-15.94, -6.90, -8.13) | |
| 7:127727045 | R>Q | A:762 | (-15.94, -6.90, -8.13) | |
| 7:127727053 | rs370234965 | P>S | A:765 | (-25.14, -9.46, -10.54) |
| 7:127727066 | T>M | A:769 | (-31.04, -15.91, -16.96) | |
| 7:127727068 | rs201675724 | E>Q | A:770 | (-30.06, -19.34, -21.10) |
| 7:127729548 | A>D | A:784 | (-41.25, -25.07, -37.13) | |
| 7:127729553 | T>A | A:786 | (-39.59, -19.87, -37.10) | |
| 7:127729554 | rs368551208 | T>M | A:786 | (-39.59, -19.87, -37.10) |
| 7:127729562 | rs368225881 | V>M | A:789 | (-39.95, -18.26, -32.09) |
| 7:127729565 | D>Y | A:790 | (-42.65, -16.05, -34.43) | |
| 7:127729571 | rs144250740 | V>I | A:792 | (-42.97, -16.94, -27.83) |
| 7:127729574 | V>I | A:793 | (-41.95, -13.09, -29.63) | |
| 7:127729578 | rs527280375 | R>Q | A:794 | (-47.02, -13.02, -31.30) |
| 7:127729592 | T>A | A:799 | (-43.46, -9.40, -21.05) | |
| 7:127729616 | H>Y | A:807 | (-35.46, -29.71, -15.44) | |
| 7:127729617 | H>R | A:807 | (-35.46, -29.71, -15.44) | |
| 7:127729624 | S>R | A:809 | (-29.74, -29.28, -18.40) | |
| 7:127729628 | rs150524780 | G>S | A:811 | (-27.60, -26.71, -20.02) |
| 7:127729651 | rs369876205 | Q>H | A:818 | (-47.66, -19.01, -15.36) |
| 7:127729665 | rs574714244 | K>R | A:823 | (-52.07, -17.44, -13.63) |
| 7:127729667 | rs542324912 | G>S | A:824 | (-50.94, -19.67, -18.45) |
| 7:127729708 | M>I | A:837 | (-44.33, -31.96, -30.22) | |
| 7:127729718 | R>C | A:841 | (-38.01, -35.68, -18.01) | |
| 7:127729719 | rs200084233 | R>H | A:841 | (-38.01, -35.68, -18.01) |
| 7:127729732 | Q>H | A:845 | (-40.73, -35.28, -9.96) | |
| 7:127731889 | I>V | A:850 | (-45.78, -35.63, -18.65) | |
| 7:127731899 | rs145841136 | Y>C | A:853 | (-47.45, -30.56, -21.25) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 7:127447556 | COSM203430 | R>C | A:366 | (8.31, -8.43, -2.13) |
| 7:127484422 | COSM2768710 | E>K | A:405 | (4.30, -18.13, 8.12) |
| 7:127569322 | COSM3662910 | G>S | A:512 | (-1.34, -20.35, -21.44) |
| 7:127631015 | COSM1755061 | R>K | A:537 | (-10.14, -17.40, -21.30) |
| 7:127721541 | COSM3715605 | D>N | A:675 | (-35.35, -10.56, -10.86) |
| 7:127724820 | COSM599068 | A>S | A:694 | (-20.07, 11.14, -19.66) |
| 7:127727080 | COSM4425905 | A>T | A:774 | (-40.34, -27.61, -20.05) |