Incidental Mutation 'R8997:Kdm2b'
ID 684769
Institutional Source Beutler Lab
Gene Symbol Kdm2b
Ensembl Gene ENSMUSG00000029475
Gene Name lysine (K)-specific demethylase 2B
Synonyms Cxxc2, Fbxl10, Jhdm1b
MMRRC Submission 068828-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R8997 (G1)
Quality Score 225.009
Status Validated
Chromosome 5
Chromosomal Location 123008727-123127333 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 123018236 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tryptophan to Leucine at position 1068 (W1068L)
Ref Sequence ENSEMBL: ENSMUSP00000038229 (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: W535L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000031435
Gene: ENSMUSG00000029475
AA Change: W535L

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 probably null
Transcript: ENSMUST00000046073
AA Change: W1068L

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000038229
Gene: ENSMUSG00000029475
AA Change: W1068L

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: W1062L

PolyPhen 2 Score 0.960 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000083376
Gene: ENSMUSG00000029475
AA Change: W1062L

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: W1030L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000114052
Gene: ENSMUSG00000029475
AA Change: W1030L

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: W1013L

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000114049
Gene: ENSMUSG00000029475
AA Change: W1013L

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 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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.3%
  • 20x: 98.1%
Validation Efficiency 98% (52/53)
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: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A830018L16Rik G T 1: 11,615,491 (GRCm39) E155* probably null Het
Abhd17a T C 10: 80,422,470 (GRCm39) T71A probably benign Het
Adgrv1 GTT GT 13: 81,553,457 (GRCm39) probably null Het
Adra2a T C 19: 54,035,729 (GRCm39) S362P probably benign Het
Arid1a T A 4: 133,421,343 (GRCm39) N436Y unknown Het
Cma2 T A 14: 56,210,201 (GRCm39) C85S probably benign Het
Cntn1 G A 15: 92,132,347 (GRCm39) V148M probably damaging Het
Cntn3 A G 6: 102,181,023 (GRCm39) V724A probably damaging Het
Dennd1a C T 2: 37,690,497 (GRCm39) G868R probably benign Het
Disp2 C T 2: 118,617,467 (GRCm39) P154S probably damaging Het
Dlgap1 A G 17: 70,823,528 (GRCm39) D171G possibly damaging Het
Dpp4 A C 2: 62,164,958 (GRCm39) I697S probably damaging Het
Dync2h1 A T 9: 7,129,003 (GRCm39) D1837E probably benign Het
Fbxo39 T A 11: 72,208,466 (GRCm39) S273T probably damaging Het
Fgf5 A T 5: 98,423,411 (GRCm39) *265C probably null Het
Fscb A G 12: 64,520,758 (GRCm39) V236A possibly damaging Het
Greb1l A T 18: 10,510,747 (GRCm39) T614S probably damaging Het
Gtdc1 A T 2: 44,715,386 (GRCm39) N52K probably benign Het
Il6ra T C 3: 89,794,418 (GRCm39) D181G probably damaging Het
Inhba T G 13: 16,201,107 (GRCm39) V223G possibly damaging Het
Kcnma1 T C 14: 23,513,037 (GRCm39) probably benign Het
Mdn1 T C 4: 32,773,275 (GRCm39) L5485P probably damaging Het
Muc16 T C 9: 18,518,763 (GRCm39) probably benign Het
Ncapd3 T C 9: 26,959,577 (GRCm39) F338L probably damaging Het
Negr1 T A 3: 156,721,918 (GRCm39) I164N probably damaging Het
Nek9 A T 12: 85,367,565 (GRCm39) C369S probably benign Het
Ninl C T 2: 150,801,816 (GRCm39) E151K probably damaging Het
Nphp1 A T 2: 127,595,982 (GRCm39) S494R possibly damaging Het
Nphp4 G A 4: 152,623,345 (GRCm39) R673H probably damaging Het
Obscn C T 11: 58,934,629 (GRCm39) probably benign Het
Osbpl8 T C 10: 111,091,575 (GRCm39) S82P probably benign Het
Pcdhgb1 C A 18: 37,814,133 (GRCm39) P208Q probably damaging Het
Pik3c2b A G 1: 133,018,517 (GRCm39) E988G possibly damaging Het
Rfc1 A T 5: 65,433,064 (GRCm39) M722K probably damaging Het
Rnf111 A T 9: 70,383,545 (GRCm39) N129K probably damaging Het
Sdccag8 C A 1: 176,783,374 (GRCm39) L628I probably damaging Het
Sgcz G T 8: 39,127,894 (GRCm39) D8E probably benign Het
Sgip1 T A 4: 102,790,781 (GRCm39) F254L Het
Shf A G 2: 122,187,728 (GRCm39) L26P probably damaging Het
Slc39a5 G A 10: 128,232,348 (GRCm39) A484V probably damaging Het
Slco4c1 T A 1: 96,795,672 (GRCm39) I129F probably damaging Het
Tbck A T 3: 132,440,106 (GRCm39) probably null Het
Tcstv7b A T 13: 120,702,515 (GRCm39) M104L probably benign Het
Teddm3 A T 16: 20,971,687 (GRCm39) V294E probably damaging Het
Tent4b T A 8: 88,979,023 (GRCm39) V508D probably benign Het
Treml1 A T 17: 48,667,466 (GRCm39) H117L probably damaging Het
Trip12 G T 1: 84,771,596 (GRCm39) T184N probably benign Het
Tuba3b G T 6: 145,566,954 (GRCm39) M398I possibly damaging Het
Vcam1 T C 3: 115,910,977 (GRCm39) I474V probably benign Het
Wdsub1 A C 2: 59,688,977 (GRCm39) M415R probably damaging Het
Zfp14 A T 7: 29,737,600 (GRCm39) F462I probably damaging Het
Zfp846 G A 9: 20,505,726 (GRCm39) V529I probably benign Het
Zfp873 A G 10: 81,896,990 (GRCm39) T574A 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
R6029:Kdm2b UTSW 5 123,017,650 (GRCm39) missense probably damaging 1.00
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
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'- CTCAGCTTAAACTAGAATGCTGG -3'
(R):5'- ACCCAAGTGCATCCAGATGG -3'

Sequencing Primer
(F):5'- CCGGCTGTAATTAGTCAATATGGGC -3'
(R):5'- ATGGAGCGTCACGTGATC -3'
Posted On 2021-10-11