General Structure Information
| PDB ID | 3v83 |
| HGNC Gene Label(s) | TF |
| Structure Name | the 2.1 angstrom crystal structure of diferric human transferrin |
| Resolution | 2.1Å |
| Reference | AUTH N.NOINAJ,N.C.EASLEY,M.OKE,N.MIZUNO,J.GUMBART,E.BOURA,AUTH 2 A.N.STEERE,O.ZAK,P.AISEN,E.TAJKHORSHID,R.W.EVANS,AUTH 3 A.R.GORRINGE,A.B.MASON,A.C.STEVEN,S.K.BUCHANANTITL STRUCTURAL BASIS FOR IRON PIRACY BY PATHOGENIC NEISSERIA.REF NATURE V. 483 53 2012REFN ISSN 0028-0836PMID 22327295DOI 10.1038/NATURE10823 |
Variant Set Distributions
ExAC Variants
| Number Of Residues | 675 |
| Number Of SNVs | 157 |
| Number Of Permutations | 37365 |
| Optimal Distance Threshold | 16.0 |
| K Statistic | 0.093 |
| p-value | 0.4 |
ClinVar
| Number Of Residues | 675 |
| Number Of SNVs | 8 |
| Number Of Permutations | 1959 |
| Optimal Distance Threshold | 7.0 |
| K Statistic | 0.036 |
| p-value | 0.69 |
COSMIC
| Number Of Residues | 675 |
| Number Of SNVs | 14 |
| Number Of Permutations | 5527 |
| Optimal Distance Threshold | 29.0 |
| K Statistic | 0.462 |
| p-value | 0.582 |
Ripley’s K Analysis Plots
ExACClinVarCOSMIC
Variant Set Comparisons
ClinVar vs. ExAC
| Number Of ExAC SNVs | 157 |
| Number Of ClinVar SNVs | 7 |
| Optimal Distance Threshold | 15.0 |
| K Statistic | -0.079 |
| p-value | 0.799 |
Cosmic vs. ExAC
| Number Of ExAC SNVs | 157 |
| Number Of COSMIC SNVs | 14 |
| Optimal Distance Threshold | 29.0 |
| K Statistic | 0.142 |
| p-value | 0.244 |
Pathogenic Proximity Analysis
ClinVar PathProx Analysis
COSMIC PathProx Analysis
Mapped Variants
[+] ExAC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 3:133467289 | COSM1536380 | R>K | D:7 | (-43.53, -23.87, 7.93) |
| 3:133467297 | A>S | D:10 | (-53.83, -26.88, 10.46) | |
| 3:133467304 | S>L | D:12 | (-57.86, -30.73, 12.28) | |
| 3:133467322 | COSM1536379 | K>M | D:18 | (-59.04, -25.41, 2.86) |
| 3:133467331 | rs146477698 | S>N | D:21 | (-56.35, -27.64, -1.85) |
| 3:133467336 | rs377691845 COSM4113693 |
R>C | D:23 | (-48.96, -27.47, -1.49) |
| 3:133467346 | rs538522488 | M>T | D:26 | (-50.94, -21.61, -5.24) |
| 3:133467354 | rs144636315 | V>I | D:29 | (-51.24, -20.63, -10.50) |
| 3:133467369 | G>S | D:34 | (-42.78, -18.63, -5.92) | |
| 3:133467377 | rs8177318 | S>R | D:36 | (-45.29, -22.03, -1.64) |
| 3:133467424 | I>T | D:52 | (-45.29, -20.58, 14.74) | |
| 3:133467427 | rs142819812 | A>V | D:53 | (-42.41, -20.39, 18.18) |
| 3:133472445 | E>K | D:56 | (-42.81, -26.96, 14.31) | |
| 3:133472449 | rs41298977 | A>V | D:57 | (-44.38, -23.13, 11.63) |
| 3:133472454 | A>T | D:59 | (-48.62, -19.38, 9.82) | |
| 3:133472503 | rs200551981 | N>S | D:75 | (-45.09, -17.55, 22.17) |
| 3:133472504 | N>K | D:75 | (-45.09, -17.55, 22.17) | |
| 3:133472524 | A>E | D:82 | (-55.52, -8.75, 7.84) | |
| 3:133472533 | COSM1616948 | Y>C | D:85 | (-64.13, -8.75, 7.52) |
| 3:133472544 | rs143440081 | E>Q | D:89 | (-65.83, -1.37, -2.77) |
| 3:133473342 | rs41298985 | P>L | D:91 | (-62.39, -2.05, 3.46) |
| 3:133473347 | rs199624323 | T>A | D:93 | (-60.53, -3.68, 9.90) |
| 3:133473365 | rs534968613 | A>T | D:99 | (-76.10, -11.95, 21.30) |
| 3:133473390 | rs147540361 | F>S | D:107 | (-82.83, -14.04, 28.12) |
| 3:133473396 | rs377049120 | M>T | D:109 | (-76.90, -9.04, 28.43) |
| 3:133473400 | COSM1484638 | N>K | D:110 | (-79.43, -7.76, 32.83) |
| 3:133473407 | COSM1038561 | R>G | D:113 | (-77.59, -16.26, 37.68) |
| 3:133473408 | COSM277660 | R>Q | D:113 | (-77.59, -16.26, 37.68) |
| 3:133473429 | T>M | D:120 | (-66.65, -19.40, 19.57) | |
| 3:133473432 | G>D | D:121 | (-64.13, -19.79, 22.29) | |
| 3:133473435 | L>R | D:122 | (-61.42, -20.04, 25.85) | |
| 3:133473437 | rs1799830 | G>S | D:123 | (-60.56, -16.17, 24.05) |
| 3:133473446 | A>T | D:126 | (-67.37, -12.72, 20.42) | |
| 3:133473479 | C>G | D:137 | (-67.06, -7.64, 37.63) | |
| 3:133473495 | P>L | D:142 | (-65.93, -16.85, 43.90) | |
| 3:133473497 | R>C | D:143 | (-64.80, -12.08, 40.89) | |
| 3:133473498 | rs371174384 | R>H | D:143 | (-64.80, -12.08, 40.89) |
| 3:133474215 | N>H | D:152 | (-71.09, -21.91, 38.71) | |
| 3:133474225 | rs150679929 | S>L | D:155 | (-76.82, -23.93, 33.26) |
| 3:133474254 | rs139768770 | T>A | D:165 | (-61.07, -32.14, 33.42) |
| 3:133474255 | T>M | D:165 | (-61.07, -32.14, 33.42) | |
| 3:133474263 | P>A | D:168 | (-67.29, -29.91, 33.95) | |
| 3:133474288 | rs144665384 | G>E | D:176 | (-64.50, -31.78, 25.56) |
| 3:133474305 | L>F | D:182 | (-63.85, -32.35, 14.22) | |
| 3:133474320 | rs144129858 | G>S | D:187 | (-67.39, -21.58, 16.58) |
| 3:133474332 | A>P | D:191 | (-72.37, -21.57, 18.39) | |
| 3:133474339 | K>R | D:193 | (-75.80, -26.36, 15.42) | |
| 3:133475149 | D>A | D:201 | (-80.55, -20.45, 25.94) | |
| 3:133475152 | rs377693204 | V>G | D:202 | (-76.89, -17.69, 24.32) |
| 3:133475155 | A>G | D:203 | (-75.00, -17.20, 20.91) | |
| 3:133475176 | I>T | D:210 | (-77.98, -15.89, 11.63) | |
| 3:133475681 | L>S | D:214 | (-80.56, -20.08, 9.00) | |
| 3:133475684 | A>V | D:215 | (-82.24, -20.56, 5.21) | |
| 3:133475689 | K>E | D:217 | (-87.07, -16.17, 7.06) | |
| 3:133475701 | D>N | D:221 | (-88.22, -14.09, 12.20) | |
| 3:133475705 | Q>R | D:222 | (-88.31, -17.92, 15.70) | |
| 3:133475732 | T>S | D:231 | (-83.27, -4.18, 24.65) | |
| 3:133475734 | rs373955170 | R>W | D:232 | (-84.61, -9.47, 23.06) |
| 3:133475740 | rs201799754 | P>S | D:234 | (-84.21, -7.45, 15.09) |
| 3:133475741 | COSM3784330 | P>L | D:234 | (-84.21, -7.45, 15.09) |
| 3:133475768 | L>W | D:243 | (-72.08, -6.68, 22.89) | |
| 3:133475773 | Q>E | D:245 | (-66.92, -2.28, 17.23) | |
| 3:133475780 | P>L | D:247 | (-60.32, -6.44, 16.08) | |
| 3:133475789 | COSM3587658 | T>I | D:250 | (-54.64, -11.68, 12.01) |
| 3:133475791 | rs371174706 | V>I | D:251 | (-52.01, -13.86, 9.87) |
| 3:133475792 | rs200512772 | V>D | D:251 | (-52.01, -13.86, 9.87) |
| 3:133475794 | rs200493748 COSM1267664 |
V>M | D:252 | (-49.73, -14.70, 13.31) |
| 3:133475795 | rs374766049 | V>A | D:252 | (-49.73, -14.70, 13.31) |
| 3:133475797 | rs150329556 | A>S | D:253 | (-45.69, -14.38, 12.85) |
| 3:133475801 | COSM1038563 | R>Q | D:254 | (-41.58, -16.68, 13.55) |
| 3:133475812 | rs1799899 | G>S | D:258 | (-41.43, -14.67, 9.97) |
| 3:133475829 | rs141969756 | I>M | D:263 | (-46.77, -14.54, 4.81) |
| 3:133475830 | W>R | D:264 | (-49.18, -9.29, 1.42) | |
| 3:133475836 | rs368538762 | L>F | D:266 | (-48.89, -16.72, -0.29) |
| 3:133475843 | N>S | D:268 | (-51.70, -10.58, -2.53) | |
| 3:133475847 | Q>H | D:269 | (-49.93, -14.15, -5.57) | |
| 3:133476629 | rs8177238 | D>G | D:277 | (-66.57, -14.37, -7.06) |
| 3:133476630 | D>E | D:277 | (-66.57, -14.37, -7.06) | |
| 3:133476641 | E>V | D:281 | (-60.69, -24.18, -9.76) | |
| 3:133476645 | F>L | D:282 | (-59.17, -22.91, -3.53) | |
| 3:133476659 | S>C | D:287 | (-65.21, -25.21, 1.97) | |
| 3:133476662 | rs138539550 | P>L | D:288 | (-66.57, -28.14, 0.67) |
| 3:133476670 | K>Q | D:291 | (-68.69, -22.77, 7.50) | |
| 3:133476673 | rs375110212 COSM217262 |
D>N | D:292 | (-64.88, -20.27, 9.17) |
| 3:133476687 | K>N | D:296 | (-63.61, -15.35, 9.06) | |
| 3:133476688 | D>N | D:297 | (-66.53, -18.01, 5.07) | |
| 3:133476697 | H>Y | D:300 | (-64.84, -9.99, 1.27) | |
| 3:133476698 | rs41295774 | H>R | D:300 | (-64.84, -9.99, 1.27) |
| 3:133476700 | G>R | D:301 | (-59.52, -10.29, 2.32) | |
| 3:133476719 | rs572642927 | P>R | D:307 | (-44.63, -1.69, 9.88) |
| 3:133476726 | rs369469144 | M>I | D:309 | (-49.52, -2.08, 13.86) |
| 3:133476728 | D>G | D:310 | (-47.48, -3.57, 17.97) | |
| 3:133476730 | A>P | D:311 | (-49.93, -6.37, 18.95) | |
| 3:133476769 | rs150854910 | R>W | D:324 | (-54.29, -6.56, 31.14) |
| 3:133476770 | rs528945191 COSM129674 |
R>Q | D:324 | (-54.29, -6.56, 31.14) |
| 3:133476778 | rs143019827 | R>W | D:327 | (-57.12, -13.68, 29.53) |
| 3:133476779 | R>Q | D:327 | (-57.12, -13.68, 29.53) | |
| 3:133476788 | rs374953101 | T>I | D:330 | (-58.59, -8.24, 37.52) |
| 3:133478021 | P>S | D:332 | (-60.94, -2.44, 37.13) | |
| 3:133478034 | T>K | D:336 | (-60.90, 8.86, 38.56) | |
| 3:133478037 | D>G | D:337 | (-61.76, 6.20, 41.46) | |
| 3:133478043 | C>S | D:339 | (-55.49, 9.69, 40.37) | |
| 3:133478106 | V>A | D:360 | (-37.99, 15.08, 42.75) | |
| 3:133478110 | N>K | D:361 | (-39.48, 19.04, 42.62) | |
| 3:133478111 | S>R | D:362 | (-43.71, 16.34, 42.28) | |
| 3:133478114 | rs146075620 | V>I | D:363 | (-43.67, 14.86, 45.71) |
| 3:133478123 | I>L | D:366 | (-44.83, 13.71, 37.74) | |
| 3:133478128 | rs564672147 | E>D | D:367 | (-43.93, 8.84, 37.35) |
| 3:133478150 | rs121918680 | E>K | D:375 | (-43.72, 9.00, 15.86) |
| 3:133478162 | COSM728345 COSM1229026 |
A>T | D:379 | (-46.91, 4.82, 21.19) |
| 3:133478173 | rs201518705 | M>I | D:382 | (-51.28, 4.70, 21.89) |
| 3:133483027 | N>S | D:383 | (-49.15, 1.33, 24.97) | |
| 3:133483036 | rs149754236 | A>V | D:386 | (-47.22, 6.55, 28.87) |
| 3:133483098 | V>I | D:407 | (-55.64, 18.21, 28.13) | |
| 3:133483099 | V>A | D:407 | (-55.64, 18.21, 28.13) | |
| 3:133483119 | K>E | D:414 | (-49.16, 37.14, 28.42) | |
| 3:133483743 | rs559219054 COSM3714363 |
P>R | D:422 | (-58.14, 31.14, 24.60) |
| 3:133485124 | Y>H | D:426 | (-47.33, 29.33, 16.85) | |
| 3:133485133 | rs2692696 | I>V | D:429 | (-41.90, 32.50, 9.98) |
| 3:133485142 | V>M | D:432 | (-33.81, 35.32, 5.48) | |
| 3:133485143 | rs142116896 | V>A | D:432 | (-33.81, 35.32, 5.48) |
| 3:133485155 | A>V | D:436 | (-29.06, 37.50, 1.53) | |
| 3:133485162 | D>E | D:438 | (-32.33, 37.56, -4.27) | |
| 3:133485182 | K>I | D:445 | (-34.65, 25.07, -6.85) | |
| 3:133485192 | rs145761244 | K>N | D:448 | (-28.34, 25.72, 1.71) |
| 3:133485203 | rs147780972 | T>M | D:452 | (-37.82, 22.37, 13.50) |
| 3:133485215 | COSM581645 | R>K | D:456 | (-42.04, 20.65, 14.63) |
| 3:133485220 | rs121918679 CM003057 |
A>T | D:458 | (-43.23, 25.76, 11.25) |
| 3:133485234 | I>M | D:462 | (-47.09, 25.63, 7.08) | |
| 3:133485247 | L>V | D:467 | (-43.21, 23.82, -1.61) | |
| 3:133485275 | F>C | D:476 | (-40.21, 18.41, -0.35) | |
| 3:133486878 | COSM4113699 | F>V | D:479 | (-36.99, 22.93, -4.13) |
| 3:133486891 | G>V | D:483 | (-30.35, 20.25, 4.74) | |
| 3:133486914 | rs201418252 | D>H | D:491 | (-29.79, 9.00, 2.58) |
| 3:133486916 | rs376830242 | D>E | D:491 | (-29.79, 9.00, 2.58) |
| 3:133486920 | S>G | D:493 | (-30.45, 16.30, 1.36) | |
| 3:133486944 | rs202087286 | S>A | D:501 | (-22.33, 13.43, 16.15) |
| 3:133486953 | rs371276115 | N>Y | D:504 | (-26.66, 11.66, 17.07) |
| 3:133486969 | rs201739807 | N>S | D:509 | (-33.25, 14.31, 19.39) |
| 3:133486984 | Y>C | D:514 | (-28.46, 22.65, 13.45) | |
| 3:133486989 | G>S | D:516 | (-35.63, 23.08, 16.54) | |
| 3:133486995 | T>A | D:518 | (-32.90, 27.51, 18.60) | |
| 3:133487001 | rs369813809 COSM1038571 |
A>T | D:520 | (-33.02, 26.14, 12.97) |
| 3:133489354 | C>Y | D:523 | (-28.83, 26.23, 10.54) | |
| 3:133489360 | V>A | D:525 | (-26.44, 31.60, 11.57) | |
| 3:133489362 | E>Q | D:526 | (-23.78, 27.95, 11.69) | |
| 3:133489395 | rs546634950 | T>S | D:537 | (-37.00, 32.37, 17.08) |
| 3:133489396 | rs373607093 | T>I | D:537 | (-37.00, 32.37, 17.08) |
| 3:133489405 | Q>L | D:540 | (-36.57, 34.11, 21.71) | |
| 3:133489414 | rs41296590 | G>V | D:543 | (-29.26, 40.45, 22.00) |
| 3:133494307 | L>R | D:554 | (-26.64, 37.39, 16.67) | |
| 3:133494340 | D>G | D:565 | (-45.88, 39.01, -1.36) | |
| 3:133494354 | rs1049296 | P>S | D:570 | (-39.00, 43.47, 9.14) |
| 3:133494363 | rs138315129 | E>K | D:573 | (-43.23, 43.97, 10.40) |
| 3:133494388 | R>K | D:581 | (-52.18, 32.29, 13.53) | |
| 3:133494394 | rs41296598 | P>L | D:583 | (-51.66, 25.61, 16.23) |
| 3:133494450 | R>C | D:602 | (-54.70, 23.72, 36.49) | |
| 3:133494451 | rs367888376 | R>H | D:602 | (-54.70, 23.72, 36.49) |
| 3:133494459 | Q>E | D:605 | (-49.28, 25.55, 35.99) | |
| 3:133495903 | G>V | D:609 | (-44.17, 28.27, 36.86) | |
| 3:133495907 | S>R | D:610 | (-44.65, 31.88, 35.35) | |
| 3:133495911 | rs554041786 | V>I | D:612 | (-40.67, 30.76, 39.65) |
| 3:133495914 | rs574409965 | T>A | D:613 | (-38.15, 33.50, 40.92) |
| 3:133495924 | rs199594823 | S>L | D:616 | (-31.07, 29.32, 39.92) |
| 3:133495932 | rs557957738 | F>I | D:619 | (-38.28, 22.81, 38.40) |
| 3:133495943 | rs140038158 | F>L | D:622 | (-43.12, 26.36, 31.82) |
| 3:133495944 | COSM1616949 | R>W | D:623 | (-38.52, 28.51, 31.62) |
| 3:133495945 | rs373020329 | R>Q | D:623 | (-38.52, 28.51, 31.62) |
| 3:133496007 | rs561678680 | R>G | D:644 | (-60.33, 24.23, 21.84) |
| 3:133496049 | A>P | D:658 | (-53.15, 21.67, 5.77) | |
| 3:133496065 | rs180822278 | R>T | D:663 | (-50.78, 13.09, 3.00) |
| 3:133497447 | T>A | D:675 | (-54.79, 5.38, 9.19) | |
| 3:133497450 | F>I | D:676 | (-54.77, -0.63, 9.03) | |
| 3:133497454 | rs57329669 | R>H | D:677 | (-60.08, 1.02, 9.63) |
[+] ClinVar Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 3:133472451 | rs121918681 | D>N | D:58 | (-44.12, -20.18, 9.35) |
| 3:133475813 | rs121918676 | G>D | D:258 | (-41.43, -14.67, 9.97) |
| 3:133476698 | rs41295774 | H>R | D:300 | (-64.84, -9.99, 1.27) |
| 3:133478150 | rs121918680 | E>K | D:375 | (-43.72, 9.00, 15.86) |
| 3:133485220 | rs121918679 | A>T | D:458 | (-43.23, 25.76, 11.25) |
| 3:133494354 | rs1049296 | P>S | D:570 | (-39.00, 43.47, 9.14) |
| 3:133495956 | rs121918678 | K>E | D:627 | (-32.48, 22.92, 24.30) |
| 3:133496032 | rs121918677 | G>E | D:652 | (-58.74, 23.54, 13.32) |
[+] COSMIC Missense Variants
| Position | Variant | AA Change | PDB Chain Position | Structure Coordinates |
|---|---|---|---|---|
| 3:133467351 | COSM1616947 | S>G | D:28 | (-51.25, -24.90, -10.55) |
| 3:133472533 | COSM1616948 | Y>C | D:85 | (-64.13, -8.75, 7.52) |
| 3:133475801 | COSM1038563 | R>Q | D:254 | (-41.58, -16.68, 13.55) |
| 3:133475812 | COSM3736306 | G>S | D:258 | (-41.43, -14.67, 9.97) |
| 3:133476673 | COSM217262 | D>Y | D:292 | (-64.88, -20.27, 9.17) |
| 3:133476751 | COSM164873 | E>Q | D:318 | (-59.27, 0.53, 24.60) |
| 3:133478078 | COSM1693489 | E>K | D:351 | (-36.85, 16.17, 27.41) |
| 3:133478150 | COSM1038567 | E>K | D:375 | (-43.72, 9.00, 15.86) |
| 3:133478162 | COSM728345 | A>S | D:379 | (-46.91, 4.82, 21.19) |
| 3:133483724 | COSM1316680 | D>N | D:416 | (-54.53, 38.08, 32.93) |
| 3:133483743 | COSM3714363 | P>L | D:422 | (-58.14, 31.14, 24.60) |
| 3:133494370 | COSM204490 | A>V | D:575 | (-48.41, 40.22, 11.29) |
| 3:133494435 | COSM204491 | V>I | D:597 | (-53.53, 14.98, 33.23) |
| 3:133495917 | COSM236595 | D>Y | D:614 | (-34.99, 32.30, 40.32) |
| 3:133495944 | COSM1616949 | R>W | D:623 | (-38.52, 28.51, 31.62) |