Incidental Mutation 'R6029:Kdm2b'
ID 480251
Institutional Source Beutler Lab
Gene Symbol Kdm2b
Ensembl Gene ENSMUSG00000029475
Gene Name lysine (K)-specific demethylase 2B
Synonyms Cxxc2, Fbxl10, Jhdm1b
MMRRC Submission 044201-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6029 (G1)
Quality Score 225.009
Status Validated
Chromosome 5
Chromosomal Location 123008727-123127333 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 123017650 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Lysine at position 1052 (M1052K)
Ref Sequence ENSEMBL: ENSMUSP00000114052 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031435] [ENSMUST00000046073] [ENSMUST00000086200] [ENSMUST00000118027] [ENSMUST00000121739] [ENSMUST00000127403] [ENSMUST00000152872]
AlphaFold Q6P1G2
Predicted Effect probably damaging
Transcript: ENSMUST00000031435
AA Change: M557K

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000031435
Gene: ENSMUSG00000029475
AA Change: M557K

DomainStartEndE-ValueType
Pfam:zf-CXXC 45 91 1.6e-17 PFAM
PHD 101 163 8.58e-4 SMART
low complexity region 259 290 N/A INTRINSIC
low complexity region 370 380 N/A INTRINSIC
low complexity region 457 473 N/A INTRINSIC
low complexity region 485 499 N/A INTRINSIC
FBOX 505 545 1.69e-2 SMART
LRR 588 610 1.31e2 SMART
LRR 612 637 2.9e2 SMART
LRR 652 676 2.04e2 SMART
LRR 677 702 1.1e1 SMART
LRR 732 757 3.91e1 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000046073
AA Change: M1090K

PolyPhen 2 Score 0.771 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000038229
Gene: ENSMUSG00000029475
AA Change: M1090K

DomainStartEndE-ValueType
Blast:JmjC 23 101 4e-41 BLAST
JmjC 147 315 3.61e-41 SMART
low complexity region 380 401 N/A INTRINSIC
low complexity region 406 424 N/A INTRINSIC
PDB:2YU2|A 472 546 1e-17 PDB
Pfam:zf-CXXC 578 624 3e-17 PFAM
PHD 634 696 8.58e-4 SMART
low complexity region 792 823 N/A INTRINSIC
low complexity region 903 913 N/A INTRINSIC
low complexity region 990 1006 N/A INTRINSIC
low complexity region 1018 1032 N/A INTRINSIC
FBOX 1038 1078 1.69e-2 SMART
LRR 1121 1143 1.31e2 SMART
LRR 1145 1170 2.9e2 SMART
LRR 1185 1209 2.04e2 SMART
LRR 1210 1235 1.1e1 SMART
LRR 1265 1290 3.91e1 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000086200
AA Change: M1084K

PolyPhen 2 Score 0.971 (Sensitivity: 0.77; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000083376
Gene: ENSMUSG00000029475
AA Change: M1084K

DomainStartEndE-ValueType
Blast:JmjC 17 95 4e-41 BLAST
JmjC 141 309 3.61e-41 SMART
low complexity region 374 395 N/A INTRINSIC
low complexity region 400 418 N/A INTRINSIC
PDB:2YU2|A 466 540 1e-17 PDB
Pfam:zf-CXXC 572 618 2.1e-17 PFAM
PHD 628 690 8.58e-4 SMART
low complexity region 786 817 N/A INTRINSIC
low complexity region 897 907 N/A INTRINSIC
low complexity region 984 1000 N/A INTRINSIC
low complexity region 1012 1026 N/A INTRINSIC
FBOX 1032 1072 1.69e-2 SMART
LRR 1115 1137 1.31e2 SMART
LRR 1139 1164 2.9e2 SMART
LRR 1179 1203 2.04e2 SMART
LRR 1204 1229 1.1e1 SMART
LRR 1259 1284 3.91e1 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000118027
AA Change: M1052K

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000114052
Gene: ENSMUSG00000029475
AA Change: M1052K

DomainStartEndE-ValueType
Blast:JmjC 23 101 4e-41 BLAST
JmjC 147 315 3.61e-41 SMART
low complexity region 380 401 N/A INTRINSIC
low complexity region 406 424 N/A INTRINSIC
PDB:2YU2|A 472 546 9e-18 PDB
Pfam:zf-CXXC 578 624 2.1e-17 PFAM
PHD 634 696 8.58e-4 SMART
low complexity region 865 875 N/A INTRINSIC
low complexity region 952 968 N/A INTRINSIC
low complexity region 980 994 N/A INTRINSIC
FBOX 1000 1040 1.69e-2 SMART
LRR 1083 1105 1.31e2 SMART
LRR 1107 1132 2.9e2 SMART
LRR 1147 1171 2.04e2 SMART
LRR 1172 1197 1.1e1 SMART
LRR 1227 1252 3.91e1 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000121739
AA Change: M1035K

PolyPhen 2 Score 0.968 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000114049
Gene: ENSMUSG00000029475
AA Change: M1035K

DomainStartEndE-ValueType
Blast:JmjC 1 46 2e-19 BLAST
JmjC 92 260 3.61e-41 SMART
low complexity region 325 346 N/A INTRINSIC
low complexity region 351 369 N/A INTRINSIC
PDB:2YU2|A 417 491 1e-17 PDB
Pfam:zf-CXXC 523 569 5.4e-17 PFAM
PHD 579 641 8.58e-4 SMART
low complexity region 737 768 N/A INTRINSIC
low complexity region 848 858 N/A INTRINSIC
low complexity region 935 951 N/A INTRINSIC
low complexity region 963 977 N/A INTRINSIC
FBOX 983 1023 1.69e-2 SMART
LRR 1066 1088 1.31e2 SMART
LRR 1090 1115 2.9e2 SMART
LRR 1130 1154 2.04e2 SMART
LRR 1155 1180 1.1e1 SMART
LRR 1210 1235 3.91e1 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000127403
Predicted Effect noncoding transcript
Transcript: ENSMUST00000173355
Predicted Effect noncoding transcript
Transcript: ENSMUST00000174357
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129998
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139674
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132419
Predicted Effect probably benign
Transcript: ENSMUST00000152872
SMART Domains Protein: ENSMUSP00000119746
Gene: ENSMUSG00000029475

DomainStartEndE-ValueType
PHD 25 87 8.58e-4 SMART
low complexity region 243 253 N/A INTRINSIC
Meta Mutation Damage Score 0.7349 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.7%
  • 20x: 92.7%
Validation Efficiency 97% (87/90)
MGI Phenotype FUNCTION: The protein encoded by this gene is a H3K36-specific histone demethylase, which contains an N-terminal jumonji C domain, a CxxC zinc finger domain, a plant homeodomain finger, an F-box, and eight leucine-rich repeats. Amongst its demonstrated functions, this protein plays roles in the suppression of premature cellular senescence, leukemia maintenance and development, maintenance of mouse embryonic stem cell pluripotency, and induced pluripotent stem cell generation. Mice homozygous for a targeted deletion of the zinc finger domain display embryonic lethality with development ceasing at approximately 7 to 8 days post coitum, demonstrating an essential role in early development. A pseudogene of this gene is found on chromosome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
PHENOTYPE: Mice homozygous for a targeted allele that does not express the long form protein exhibit exencephaly, fetal and postnatal lethality, coloboma, curly tail, oligozoospermia, increased apoptosis, and increased neuronal precursor proliferation. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 90 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4932414N04Rik G A 2: 68,524,370 (GRCm39) probably null Het
Adi1 G A 12: 28,729,318 (GRCm39) probably benign Het
Afg3l2 G T 18: 67,554,329 (GRCm39) L458M probably damaging Het
Apob A G 12: 8,066,243 (GRCm39) E4371G probably damaging Het
Ash1l T C 3: 88,892,326 (GRCm39) Y1402H probably damaging Het
Aspm T G 1: 139,408,728 (GRCm39) C2538W possibly damaging Het
Brd10 A G 19: 29,732,367 (GRCm39) probably benign Het
Btbd16 T C 7: 130,420,802 (GRCm39) V353A probably benign Het
Cad C T 5: 31,212,327 (GRCm39) S10L possibly damaging Het
Cdc42bpa T C 1: 179,939,352 (GRCm39) S877P probably damaging Het
Cep152 A T 2: 125,405,552 (GRCm39) V1660D probably benign Het
Clrn2 G T 5: 45,617,528 (GRCm39) G133V probably damaging Het
Clstn2 T C 9: 97,338,634 (GRCm39) I842V probably benign Het
Cpt1c C T 7: 44,614,548 (GRCm39) A434T probably benign Het
D130052B06Rik G T 11: 33,573,477 (GRCm39) V70L possibly damaging Het
Dlg1 T A 16: 31,612,388 (GRCm39) V317E probably damaging Het
Dock10 T C 1: 80,514,663 (GRCm39) E1084G possibly damaging Het
Dync2h1 A G 9: 7,157,646 (GRCm39) V827A probably benign Het
E030030I06Rik A G 10: 22,024,832 (GRCm39) L27P unknown Het
Ero1b T A 13: 12,589,714 (GRCm39) L39Q probably damaging Het
Erp27 T C 6: 136,888,609 (GRCm39) D123G probably damaging Het
Fasn G T 11: 120,711,735 (GRCm39) F148L probably damaging Het
Fbxl5 T C 5: 43,922,746 (GRCm39) E218G probably damaging Het
Fbxw28 A T 9: 109,158,493 (GRCm39) D210E probably damaging Het
Gm10653 T A 9: 62,748,796 (GRCm39) probably benign Het
Gm17067 A G 7: 42,357,554 (GRCm39) L316S probably benign Het
Gm29106 T C 1: 118,127,990 (GRCm39) S561P probably damaging Het
Hmcn1 C A 1: 150,508,188 (GRCm39) K3699N probably benign Het
Itch T A 2: 155,021,009 (GRCm39) probably null Het
Itpr3 C T 17: 27,317,145 (GRCm39) A800V probably damaging Het
Kdm4b T C 17: 56,703,576 (GRCm39) M712T probably damaging Het
Kmt5b A G 19: 3,852,104 (GRCm39) E137G probably damaging Het
Krt33a G A 11: 99,903,289 (GRCm39) T251I probably benign Het
Lrrc4b G T 7: 44,111,754 (GRCm39) R542L probably benign Het
Macf1 C A 4: 123,401,126 (GRCm39) S653I probably damaging Het
Macrod2 G A 2: 142,160,367 (GRCm39) V408M probably damaging Het
Macroh2a2 T C 10: 61,583,541 (GRCm39) T200A possibly damaging Het
Mapkapk3 G T 9: 107,166,425 (GRCm39) A40E possibly damaging Het
Mmp20 G A 9: 7,639,302 (GRCm39) V157I probably benign Het
Mrps28 T C 3: 8,988,805 (GRCm39) R18G possibly damaging Het
Msrb2 T A 2: 19,399,122 (GRCm39) C162S probably damaging Het
Naa80 A G 9: 107,460,753 (GRCm39) Y216C probably damaging Het
Nckap5 T G 1: 125,953,523 (GRCm39) T1078P possibly damaging Het
Nectin3 T C 16: 46,256,763 (GRCm39) Y91C probably benign Het
Nf2 G T 11: 4,734,566 (GRCm39) probably null Het
Or10d1b G A 9: 39,613,696 (GRCm39) A123V probably damaging Het
Or13a23-ps1 A T 7: 140,118,789 (GRCm39) M120L unknown Het
Or1e16 AGCGGTCGTAGGC AGC 11: 73,286,480 (GRCm39) probably null Het
Or2y10 A T 11: 49,455,428 (GRCm39) I227F possibly damaging Het
Or4c29 T C 2: 88,740,380 (GRCm39) D119G probably damaging Het
Or4g7 T A 2: 111,309,310 (GRCm39) Y60* probably null Het
Or8b36 ATTGCTGTTT ATTGCTGTTTGCTGTTT 9: 37,937,836 (GRCm39) probably null Het
Oxr1 T G 15: 41,689,297 (GRCm39) L507W probably damaging Het
Plxna2 A T 1: 194,481,883 (GRCm39) K1451M probably damaging Het
Plxna2 A G 1: 194,476,735 (GRCm39) M1184V probably benign Het
Pofut1 G A 2: 153,101,713 (GRCm39) probably null Het
Ppp1r16b T C 2: 158,597,137 (GRCm39) V257A possibly damaging Het
Prss56 G A 1: 87,115,279 (GRCm39) W498* probably null Het
Ptpru A G 4: 131,498,604 (GRCm39) F1329S probably damaging Het
Pusl1 A G 4: 155,973,920 (GRCm39) F278S probably damaging Het
Qars1 A T 9: 108,390,889 (GRCm39) L470F probably damaging Het
Rbm8a2 T C 1: 175,806,312 (GRCm39) D55G probably benign Het
Rora T A 9: 69,271,734 (GRCm39) N181K probably benign Het
Rufy3 A G 5: 88,775,114 (GRCm39) D262G probably damaging Het
Sh3gl2 G A 4: 85,299,651 (GRCm39) V212M probably damaging Het
Sis G A 3: 72,835,641 (GRCm39) T907I probably benign Het
Slc38a3 A T 9: 107,529,374 (GRCm39) I456N probably damaging Het
Slc4a8 T A 15: 100,705,220 (GRCm39) C809S probably benign Het
Snap91 A T 9: 86,707,133 (GRCm39) probably null Het
Spaca6 A G 17: 18,051,458 (GRCm39) T45A probably benign Het
Speer1m A T 5: 11,970,680 (GRCm39) L84F probably damaging Het
Spry1 T C 3: 37,696,997 (GRCm39) I80T possibly damaging Het
St8sia2 A G 7: 73,610,458 (GRCm39) L275P possibly damaging Het
Supt7l C A 5: 31,684,331 (GRCm39) probably null Het
Tdo2 T A 3: 81,868,747 (GRCm39) K304N probably damaging Het
Tdrd12 A T 7: 35,184,655 (GRCm39) Y753N probably damaging Het
Topbp1 A T 9: 103,222,152 (GRCm39) Q1341L probably benign Het
Trim14 G T 4: 46,506,998 (GRCm39) A406E probably benign Het
Trp63 C T 16: 25,686,964 (GRCm39) R393W probably damaging Het
Trrap T C 5: 144,754,489 (GRCm39) V1932A possibly damaging Het
Trrap T C 5: 144,762,724 (GRCm39) M2399T possibly damaging Het
Unc45b A G 11: 82,804,153 (GRCm39) N110S probably damaging Het
Usp32 G T 11: 84,916,408 (GRCm39) H845Q probably damaging Het
Usp44 G A 10: 93,682,494 (GRCm39) D268N probably damaging Het
Vmn1r18 T G 6: 57,367,451 (GRCm39) R34S possibly damaging Het
Vmn2r103 T A 17: 20,014,478 (GRCm39) Y423* probably null Het
Wapl A T 14: 34,461,204 (GRCm39) E1054V possibly damaging Het
Zbtb8b A G 4: 129,322,286 (GRCm39) Y392H probably damaging Het
Zdhhc2 A T 8: 40,925,968 (GRCm39) Q321L probably null Het
Zfp983 A G 17: 21,881,401 (GRCm39) D443G probably benign Het
Other mutations in Kdm2b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00578:Kdm2b APN 5 123,099,630 (GRCm39) missense probably damaging 1.00
IGL02061:Kdm2b APN 5 123,021,404 (GRCm39) missense probably damaging 1.00
IGL02142:Kdm2b APN 5 123,085,898 (GRCm39) missense probably damaging 0.99
IGL02143:Kdm2b APN 5 123,085,898 (GRCm39) missense probably damaging 0.99
IGL02147:Kdm2b APN 5 123,085,898 (GRCm39) missense probably damaging 0.99
IGL02294:Kdm2b APN 5 123,099,537 (GRCm39) missense probably damaging 1.00
IGL02309:Kdm2b APN 5 123,085,883 (GRCm39) missense probably damaging 0.99
IGL03039:Kdm2b APN 5 123,019,734 (GRCm39) missense probably benign 0.06
IGL03134:Kdm2b UTSW 5 123,070,737 (GRCm39) missense probably damaging 1.00
PIT4520001:Kdm2b UTSW 5 123,079,110 (GRCm39) missense probably damaging 1.00
R0008:Kdm2b UTSW 5 123,019,806 (GRCm39) missense probably benign 0.08
R0592:Kdm2b UTSW 5 123,099,197 (GRCm39) splice site probably benign
R0894:Kdm2b UTSW 5 123,122,523 (GRCm39) critical splice donor site probably null
R1078:Kdm2b UTSW 5 123,099,604 (GRCm39) missense possibly damaging 0.83
R1387:Kdm2b UTSW 5 123,018,331 (GRCm39) missense probably damaging 1.00
R1441:Kdm2b UTSW 5 123,070,943 (GRCm39) missense probably benign 0.25
R1550:Kdm2b UTSW 5 123,019,120 (GRCm39) missense probably damaging 1.00
R1795:Kdm2b UTSW 5 123,122,523 (GRCm39) critical splice donor site probably null
R2060:Kdm2b UTSW 5 123,021,428 (GRCm39) missense probably damaging 1.00
R2161:Kdm2b UTSW 5 123,018,762 (GRCm39) missense probably damaging 1.00
R2259:Kdm2b UTSW 5 123,020,479 (GRCm39) missense probably damaging 1.00
R3843:Kdm2b UTSW 5 123,072,856 (GRCm39) missense probably damaging 0.98
R3844:Kdm2b UTSW 5 123,072,856 (GRCm39) missense probably damaging 0.98
R3859:Kdm2b UTSW 5 123,018,290 (GRCm39) missense probably damaging 1.00
R4506:Kdm2b UTSW 5 123,026,688 (GRCm39) missense possibly damaging 0.58
R4680:Kdm2b UTSW 5 123,072,849 (GRCm39) missense probably damaging 0.99
R4786:Kdm2b UTSW 5 123,018,917 (GRCm39) critical splice acceptor site probably null
R4894:Kdm2b UTSW 5 123,079,030 (GRCm39) nonsense probably null
R5265:Kdm2b UTSW 5 123,016,651 (GRCm39) missense probably damaging 1.00
R5522:Kdm2b UTSW 5 123,087,225 (GRCm39) missense probably damaging 1.00
R5746:Kdm2b UTSW 5 123,017,427 (GRCm39) missense probably damaging 1.00
R5813:Kdm2b UTSW 5 123,009,931 (GRCm39) missense probably benign 0.37
R5920:Kdm2b UTSW 5 123,018,359 (GRCm39) missense probably damaging 1.00
R5961:Kdm2b UTSW 5 123,070,724 (GRCm39) missense probably benign 0.37
R6280:Kdm2b UTSW 5 123,016,687 (GRCm39) missense probably damaging 1.00
R6303:Kdm2b UTSW 5 123,019,807 (GRCm39) missense probably benign 0.34
R6304:Kdm2b UTSW 5 123,019,807 (GRCm39) missense probably benign 0.34
R6383:Kdm2b UTSW 5 123,072,841 (GRCm39) missense probably damaging 1.00
R6432:Kdm2b UTSW 5 123,018,254 (GRCm39) missense probably damaging 1.00
R6513:Kdm2b UTSW 5 123,018,302 (GRCm39) missense probably damaging 0.99
R6526:Kdm2b UTSW 5 123,099,532 (GRCm39) missense probably damaging 1.00
R7213:Kdm2b UTSW 5 123,059,532 (GRCm39) missense probably damaging 0.99
R7226:Kdm2b UTSW 5 123,059,512 (GRCm39) missense possibly damaging 0.60
R7292:Kdm2b UTSW 5 123,018,854 (GRCm39) missense probably damaging 0.98
R7893:Kdm2b UTSW 5 123,085,802 (GRCm39) missense probably benign 0.12
R8021:Kdm2b UTSW 5 123,070,982 (GRCm39) missense probably damaging 0.99
R8038:Kdm2b UTSW 5 123,098,958 (GRCm39) intron probably benign
R8162:Kdm2b UTSW 5 123,072,856 (GRCm39) missense probably damaging 0.98
R8397:Kdm2b UTSW 5 123,018,579 (GRCm39) missense probably benign 0.03
R8411:Kdm2b UTSW 5 123,018,239 (GRCm39) missense probably damaging 1.00
R8899:Kdm2b UTSW 5 123,125,851 (GRCm39) nonsense probably null
R8997:Kdm2b UTSW 5 123,018,236 (GRCm39) missense probably null 0.99
R9142:Kdm2b UTSW 5 123,127,112 (GRCm39) unclassified probably benign
R9192:Kdm2b UTSW 5 123,070,679 (GRCm39) missense probably benign 0.05
R9238:Kdm2b UTSW 5 123,009,889 (GRCm39) missense probably damaging 0.98
R9455:Kdm2b UTSW 5 123,099,537 (GRCm39) missense probably damaging 1.00
R9644:Kdm2b UTSW 5 123,120,842 (GRCm39) missense probably damaging 0.98
R9731:Kdm2b UTSW 5 123,125,823 (GRCm39) missense probably benign 0.03
Z1177:Kdm2b UTSW 5 123,018,860 (GRCm39) missense probably damaging 0.98
Predicted Primers PCR Primer
(F):5'- ATCCATGAGCAGCCTGACAG -3'
(R):5'- AATGTCGGCAGGGTAGATGC -3'

Sequencing Primer
(F):5'- TGACAGCACCAAGTCTCGGAG -3'
(R):5'- CTAAGTAAGTTACAGAGGGCTGAATC -3'
Posted On 2017-06-26