Incidental Mutation 'R1441:Kdm2b'
ID 161002
Institutional Source Beutler Lab
Gene Symbol Kdm2b
Ensembl Gene ENSMUSG00000029475
Gene Name lysine (K)-specific demethylase 2B
Synonyms Cxxc2, Fbxl10, Jhdm1b
MMRRC Submission 039496-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1441 (G1)
Quality Score 225
Status Not validated
Chromosome 5
Chromosomal Location 123008727-123127333 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 123070943 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Lysine at position 379 (E379K)
Ref Sequence ENSEMBL: ENSMUSP00000118488 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000046073] [ENSMUST00000086200] [ENSMUST00000118027] [ENSMUST00000121739] [ENSMUST00000127403] [ENSMUST00000145082] [ENSMUST00000156474]
AlphaFold Q6P1G2
Predicted Effect probably benign
Transcript: ENSMUST00000046073
AA Change: E385K

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000038229
Gene: ENSMUSG00000029475
AA Change: E385K

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 benign
Transcript: ENSMUST00000086200
AA Change: E379K

PolyPhen 2 Score 0.035 (Sensitivity: 0.94; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000083376
Gene: ENSMUSG00000029475
AA Change: E379K

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 benign
Transcript: ENSMUST00000118027
AA Change: E385K

PolyPhen 2 Score 0.143 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000114052
Gene: ENSMUSG00000029475
AA Change: E385K

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 benign
Transcript: ENSMUST00000121739
AA Change: E330K

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000114049
Gene: ENSMUSG00000029475
AA Change: E330K

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 noncoding transcript
Transcript: ENSMUST00000123479
Predicted Effect probably benign
Transcript: ENSMUST00000127403
Predicted Effect noncoding transcript
Transcript: ENSMUST00000138929
Predicted Effect probably benign
Transcript: ENSMUST00000145082
AA Change: E185K

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000114731
Gene: ENSMUSG00000029475
AA Change: E185K

DomainStartEndE-ValueType
JmjC 1 115 4.87e-15 SMART
Blast:JmjC 118 286 7e-65 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000156474
AA Change: E379K

PolyPhen 2 Score 0.250 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000118488
Gene: ENSMUSG00000029475
AA Change: E379K

DomainStartEndE-ValueType
Blast:JmjC 17 95 3e-42 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 466 512 1e-8 PDB
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147544
Predicted Effect noncoding transcript
Transcript: ENSMUST00000143273
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.1%
  • 10x: 95.6%
  • 20x: 90.4%
Validation Efficiency
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: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts18 A T 8: 114,481,194 (GRCm39) probably null Het
Ankrd16 T C 2: 11,783,557 (GRCm39) L53P probably damaging Het
Arsk A T 13: 76,223,083 (GRCm39) N171K probably benign Het
Brwd1 A C 16: 95,867,351 (GRCm39) C161W probably damaging Het
Card9 T C 2: 26,249,402 (GRCm39) N53S probably benign Het
Ccdc13 A T 9: 121,642,515 (GRCm39) V403E probably benign Het
Ccdc83 T A 7: 89,893,351 (GRCm39) E135D probably damaging Het
Ccser1 C T 6: 62,357,016 (GRCm39) T818I probably benign Het
Cd44 T A 2: 102,676,763 (GRCm39) T301S probably damaging Het
Eepd1 G A 9: 25,394,499 (GRCm39) M254I probably benign Het
Ephb4 C T 5: 137,359,509 (GRCm39) R360C probably damaging Het
Fam149a G T 8: 45,808,684 (GRCm39) Q150K probably damaging Het
G6pc2 G A 2: 69,051,198 (GRCm39) C97Y probably damaging Het
Gcsam T A 16: 45,433,401 (GRCm39) M15K probably benign Het
Impdh2 C A 9: 108,441,975 (GRCm39) T201K probably benign Het
Mcm3ap T C 10: 76,307,000 (GRCm39) V371A probably benign Het
Mink1 T A 11: 70,497,940 (GRCm39) N514K possibly damaging Het
Mmp12 C T 9: 7,354,787 (GRCm39) P330L probably damaging Het
Mroh2a A G 1: 88,169,353 (GRCm39) D676G possibly damaging Het
Myo1a C T 10: 127,555,148 (GRCm39) P838L probably benign Het
Naip5 T C 13: 100,356,225 (GRCm39) H1130R possibly damaging Het
Ninl C A 2: 150,813,044 (GRCm39) G204V probably benign Het
Or12k5 C A 2: 36,895,131 (GRCm39) R165L possibly damaging Het
Or2a54 T C 6: 43,092,880 (GRCm39) V68A probably benign Het
Or4k51 T C 2: 111,585,347 (GRCm39) F251S probably damaging Het
Or5ac20 G A 16: 59,104,228 (GRCm39) L211F probably benign Het
Or5an11 T A 19: 12,245,750 (GRCm39) L52* probably null Het
Or8c15 T C 9: 38,120,777 (GRCm39) C141R probably damaging Het
Phactr4 G A 4: 132,104,559 (GRCm39) T256I probably benign Het
Pip4p2 A T 4: 14,892,477 (GRCm39) I114L possibly damaging Het
Ptpn22 G T 3: 103,781,563 (GRCm39) W114L probably damaging Het
Rasa1 C T 13: 85,400,540 (GRCm39) probably null Het
Rbks C T 5: 31,817,341 (GRCm39) V143I probably benign Het
Rbm19 T C 5: 120,269,241 (GRCm39) F515L probably damaging Het
Ror1 A G 4: 100,298,180 (GRCm39) T518A probably benign Het
Rpusd4 C A 9: 35,184,065 (GRCm39) A240E probably damaging Het
Rufy3 T C 5: 88,780,374 (GRCm39) L374P probably damaging Het
Sf3a3 T C 4: 124,618,935 (GRCm39) S299P probably damaging Het
Slc7a12 T G 3: 14,562,414 (GRCm39) S264A possibly damaging Het
Tasor T A 14: 27,186,217 (GRCm39) C805* probably null Het
Tm9sf1 T C 14: 55,873,782 (GRCm39) Y572C probably damaging Het
Tpcn2 G A 7: 144,813,871 (GRCm39) S475L probably benign Het
Trim17 A G 11: 58,856,018 (GRCm39) D25G probably damaging Het
Ttn T A 2: 76,572,121 (GRCm39) K26257N probably damaging Het
Txndc11 C A 16: 10,952,414 (GRCm39) probably benign Het
Utrn A G 10: 12,559,039 (GRCm39) S1405P probably damaging Het
Vmn2r58 G A 7: 41,486,864 (GRCm39) T677I probably damaging 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
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
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'- TGGACAACGTCCTCTTGAGGAACC -3'
(R):5'- AGGCATACTGCACGGCTAAGCAAC -3'

Sequencing Primer
(F):5'- CGTATGGCAGGGGCTTTAG -3'
(R):5'- ACGGCTAAGCAACCTGTG -3'
Posted On 2014-03-14