Incidental Mutation 'R4791:Kdm5b'
ID 368532
Institutional Source Beutler Lab
Gene Symbol Kdm5b
Ensembl Gene ENSMUSG00000042207
Gene Name lysine demethylase 5B
Synonyms 2010009J12Rik, PLU-1, Rb-Bp2, Jarid1b, D1Ertd202e, Plu1, 2210016I17Rik
MMRRC Submission 041976-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.451) question?
Stock # R4791 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 134487916-134560621 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 134558538 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 1515 (E1515G)
Ref Sequence ENSEMBL: ENSMUSP00000107817 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047714] [ENSMUST00000112198]
AlphaFold Q80Y84
PDB Structure Solution structure of the ARID domain of Jarid1b protein [SOLUTION NMR]
Predicted Effect probably benign
Transcript: ENSMUST00000047714
SMART Domains Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207

DomainStartEndE-ValueType
low complexity region 7 30 N/A INTRINSIC
JmjN 31 72 2.87e-20 SMART
ARID 94 183 7.39e-32 SMART
BRIGHT 98 188 1.51e-35 SMART
low complexity region 228 239 N/A INTRINSIC
PHD 311 357 6.15e-14 SMART
JmjC 453 619 2.33e-67 SMART
Pfam:zf-C5HC2 692 744 2.2e-17 PFAM
Pfam:PLU-1 757 1088 5.6e-92 PFAM
low complexity region 1097 1109 N/A INTRINSIC
PHD 1178 1222 6.2e-10 SMART
low complexity region 1225 1236 N/A INTRINSIC
low complexity region 1406 1417 N/A INTRINSIC
low complexity region 1470 1484 N/A INTRINSIC
PHD 1486 1536 1.18e-6 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000112198
AA Change: E1515G

PolyPhen 2 Score 0.816 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000107817
Gene: ENSMUSG00000042207
AA Change: E1515G

DomainStartEndE-ValueType
low complexity region 7 30 N/A INTRINSIC
JmjN 31 72 2.87e-20 SMART
ARID 94 183 7.39e-32 SMART
BRIGHT 98 188 1.51e-35 SMART
low complexity region 228 239 N/A INTRINSIC
PHD 311 357 6.15e-14 SMART
JmjC 453 619 2.33e-67 SMART
Pfam:zf-C5HC2 692 745 6.7e-21 PFAM
Pfam:PLU-1 756 1088 6e-94 PFAM
low complexity region 1097 1109 N/A INTRINSIC
PHD 1178 1222 6.2e-10 SMART
low complexity region 1225 1236 N/A INTRINSIC
low complexity region 1406 1417 N/A INTRINSIC
low complexity region 1470 1484 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000191572
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 94.3%
Validation Efficiency
MGI Phenotype FUNCTION: This gene encodes a lysine-specific histone demethylase that belongs to the jumonji/ARID domain-containing family of histone demethylases. The encoded protein is capable of demethylating tri-, di- and monomethylated lysine 4 of histone H3. This protein plays a role in the transcriptional repression or certain tumor suppressor genes and is upregulated in certain cancer cells. This protein may also play a role in genome stability and DNA repair. Homozygous mutant mice display decreased body weight, decreased female fertility, lower uterine weight, and a delay in mammary development. Knockout of this gene has also been associated with embryonic lethality. [provided by RefSeq, Dec 2016]
PHENOTYPE: Mice homozygous for a gene trapped allele exhibit decreased body weight, background-sensitive premature mortality, decreased female fertility, delayed mammary gland development, decreased serum estradiol levels, and reduced mammary epithelial cell proliferation in early puberty. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 97 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc6 C T 7: 45,631,584 (GRCm39) V1231M probably benign Het
Agl A G 3: 116,580,177 (GRCm39) probably null Het
Ak7 T C 12: 105,676,404 (GRCm39) F35L probably benign Het
Aldh1a1 A G 19: 20,597,349 (GRCm39) N110S probably damaging Het
Arhgef5 C T 6: 43,260,117 (GRCm39) L1368F probably damaging Het
Atp5mf T C 5: 145,121,365 (GRCm39) Y72C possibly damaging Het
Atp6v0a2 T G 5: 124,784,667 (GRCm39) F317V probably benign Het
Bank1 A T 3: 135,960,690 (GRCm39) S56T probably benign Het
Cachd1 T A 4: 100,775,282 (GRCm39) C166S probably damaging Het
Cand1 A G 10: 119,046,607 (GRCm39) I961T probably benign Het
Ccdc73 G A 2: 104,811,450 (GRCm39) probably null Het
Cct6b A T 11: 82,632,830 (GRCm39) probably null Het
Chd2 A C 7: 73,118,325 (GRCm39) S1098A probably benign Het
Col6a4 A T 9: 105,957,401 (GRCm39) V141E possibly damaging Het
Col6a5 T C 9: 105,807,983 (GRCm39) T1022A unknown Het
Cr2 A T 1: 194,838,243 (GRCm39) C698S probably damaging Het
Dnaaf5 C A 5: 139,170,405 (GRCm39) Q786K possibly damaging Het
Dnah6 T C 6: 73,072,057 (GRCm39) D2423G probably benign Het
Dnhd1 T C 7: 105,370,324 (GRCm39) F4583S probably damaging Het
Duoxa2 A T 2: 122,131,679 (GRCm39) T123S probably damaging Het
Edem1 T G 6: 108,818,595 (GRCm39) V201G probably damaging Het
Eef1d C T 15: 75,775,531 (GRCm39) A43T possibly damaging Het
Elavl3 T C 9: 21,935,974 (GRCm39) K249E probably damaging Het
Epg5 G T 18: 77,992,211 (GRCm39) E303* probably null Het
Fam83h T C 15: 75,874,217 (GRCm39) D1040G probably damaging Het
Fndc7 A T 3: 108,783,975 (GRCm39) F211L probably benign Het
Fsip2 A G 2: 82,812,452 (GRCm39) T2924A possibly damaging Het
Gm5616 T C 9: 48,361,983 (GRCm39) noncoding transcript Het
Gpr135 T A 12: 72,116,642 (GRCm39) D375V probably benign Het
Hgd A G 16: 37,452,187 (GRCm39) *446W probably null Het
Hivep2 C A 10: 14,004,713 (GRCm39) T437K probably benign Het
Htra2 A G 6: 83,028,798 (GRCm39) L379P probably damaging Het
Hypk G T 2: 121,288,136 (GRCm39) probably null Het
Ica1l A G 1: 60,049,360 (GRCm39) F198L probably damaging Het
Igsf11 G A 16: 38,845,226 (GRCm39) S319N probably damaging Het
Il12rb1 T C 8: 71,266,012 (GRCm39) S213P possibly damaging Het
Katnal1 C T 5: 148,841,460 (GRCm39) V135M probably damaging Het
Kcnc4 G A 3: 107,354,859 (GRCm39) P530S probably benign Het
Kcnu1 T C 8: 26,403,780 (GRCm39) Y24H probably damaging Het
Kif18a A T 2: 109,118,220 (GRCm39) M12L probably benign Het
Klre1 T C 6: 129,561,118 (GRCm39) S160P probably damaging Het
Lama2 A T 10: 27,343,267 (GRCm39) H68Q probably damaging Het
Lgals8 T C 13: 12,468,203 (GRCm39) K49R possibly damaging Het
Lmf1 G A 17: 25,873,445 (GRCm39) V317M probably damaging Het
Lsr T C 7: 30,657,977 (GRCm39) T328A probably damaging Het
Mark4 C T 7: 19,185,582 (GRCm39) E51K probably benign Het
Mindy2 T C 9: 70,541,283 (GRCm39) probably null Het
Mkks G A 2: 136,718,082 (GRCm39) T400I probably benign Het
Mon2 T A 10: 122,841,962 (GRCm39) M1544L probably benign Het
Mrc2 G A 11: 105,239,257 (GRCm39) probably null Het
Myo5c T G 9: 75,198,198 (GRCm39) L1341R probably damaging Het
Nin T C 12: 70,090,581 (GRCm39) R945G possibly damaging Het
Nox4 T C 7: 86,954,055 (GRCm39) V120A probably benign Het
Or1s2 T A 19: 13,758,706 (GRCm39) C243* probably null Het
Or2aj4 G T 16: 19,385,413 (GRCm39) H73Q possibly damaging Het
Or2z2 A T 11: 58,346,370 (GRCm39) V135E possibly damaging Het
Or4a66 C T 2: 88,531,242 (GRCm39) V144I probably benign Het
Or7g29 T C 9: 19,287,105 (GRCm39) E24G probably benign Het
Plekha2 T A 8: 25,532,778 (GRCm39) R398W probably damaging Het
Pradc1 A G 6: 85,424,173 (GRCm39) W58R probably damaging Het
Pramel20 A G 4: 143,297,559 (GRCm39) probably benign Het
Prrc2b A G 2: 32,107,351 (GRCm39) probably null Het
Psg19 T A 7: 18,528,071 (GRCm39) N224I probably damaging Het
Ranbp17 A C 11: 33,437,746 (GRCm39) V164G probably benign Het
Rasgrp3 A G 17: 75,807,168 (GRCm39) S211G probably benign Het
Rcc1l G A 5: 134,192,615 (GRCm39) P270S possibly damaging Het
Rfx6 T A 10: 51,596,040 (GRCm39) probably null Het
Rnf222 A T 11: 68,783,845 (GRCm39) E137D probably damaging Het
Selenof T G 3: 144,302,584 (GRCm39) Y120D probably damaging Het
Sema3b G T 9: 107,481,012 (GRCm39) D108E probably damaging Het
Shank3 T A 15: 89,384,557 (GRCm39) L143Q probably damaging Het
Shtn1 G C 19: 59,039,305 (GRCm39) R45G probably damaging Het
Sirt4 T C 5: 115,618,373 (GRCm39) T234A possibly damaging Het
Slc25a30 C A 14: 76,000,806 (GRCm39) W266L probably benign Het
Spata20 A T 11: 94,375,412 (GRCm39) N127K probably damaging Het
Spmip4 G T 6: 50,572,817 (GRCm39) P32Q probably damaging Het
St14 C T 9: 31,006,918 (GRCm39) G636D probably benign Het
Stat5a G A 11: 100,756,289 (GRCm39) E170K probably damaging Het
Sugp2 C T 8: 70,695,440 (GRCm39) R138C probably damaging Het
Sult1e1 C A 5: 87,734,589 (GRCm39) W119L possibly damaging Het
Sv2a T C 3: 96,099,874 (GRCm39) V608A possibly damaging Het
Syne2 T C 12: 75,956,018 (GRCm39) Y575H possibly damaging Het
Taok2 G A 7: 126,467,304 (GRCm39) S167L possibly damaging Het
Thoc6 T C 17: 23,889,041 (GRCm39) H151R possibly damaging Het
Tm9sf2 T C 14: 122,377,062 (GRCm39) S197P probably benign Het
Tmem260 CAGGGACCGGCATAG CAG 14: 48,749,451 (GRCm39) probably benign Het
Tmx2 G A 2: 84,508,340 (GRCm39) P15L probably damaging Het
Top1mt C T 15: 75,540,474 (GRCm39) probably null Het
Trpm6 T A 19: 18,845,345 (GRCm39) S1682T probably benign Het
Trrap C T 5: 144,740,087 (GRCm39) R1171W probably damaging Het
Ugt3a1 A G 15: 9,361,665 (GRCm39) D147G probably damaging Het
Utp25 G A 1: 192,810,575 (GRCm39) H143Y probably benign Het
Vnn3 A G 10: 23,740,519 (GRCm39) H274R probably benign Het
Vwf C A 6: 125,620,326 (GRCm39) T1668K Het
Zfp568 T C 7: 29,714,608 (GRCm39) S162P probably damaging Het
Zfp658 T A 7: 43,223,890 (GRCm39) C722S possibly damaging Het
Zfp808 T A 13: 62,319,045 (GRCm39) H91Q probably damaging Het
Other mutations in Kdm5b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00230:Kdm5b APN 1 134,548,693 (GRCm39) missense probably damaging 1.00
IGL01458:Kdm5b APN 1 134,549,724 (GRCm39) missense possibly damaging 0.53
IGL01567:Kdm5b APN 1 134,530,278 (GRCm39) missense probably damaging 1.00
IGL01625:Kdm5b APN 1 134,545,706 (GRCm39) missense possibly damaging 0.74
IGL01970:Kdm5b APN 1 134,528,465 (GRCm39) missense probably damaging 1.00
IGL02183:Kdm5b APN 1 134,552,669 (GRCm39) missense probably benign 0.09
IGL02592:Kdm5b APN 1 134,552,591 (GRCm39) missense probably damaging 0.99
IGL02695:Kdm5b APN 1 134,532,223 (GRCm39) missense possibly damaging 0.94
IGL02697:Kdm5b APN 1 134,516,511 (GRCm39) splice site probably benign
IGL03036:Kdm5b APN 1 134,536,675 (GRCm39) missense probably damaging 1.00
IGL03056:Kdm5b APN 1 134,515,717 (GRCm39) missense probably damaging 0.99
IGL03206:Kdm5b APN 1 134,555,055 (GRCm39) missense probably benign
IGL03342:Kdm5b APN 1 134,530,314 (GRCm39) missense probably benign 0.00
IGL03388:Kdm5b APN 1 134,555,060 (GRCm39) missense probably benign
amaryllis UTSW 1 134,536,799 (GRCm39) critical splice donor site probably null
PIT4486001:Kdm5b UTSW 1 134,556,423 (GRCm39) missense probably damaging 1.00
R0233:Kdm5b UTSW 1 134,532,372 (GRCm39) splice site probably benign
R0334:Kdm5b UTSW 1 134,532,260 (GRCm39) missense probably damaging 0.99
R0504:Kdm5b UTSW 1 134,548,761 (GRCm39) critical splice donor site probably null
R0505:Kdm5b UTSW 1 134,530,309 (GRCm39) missense probably damaging 0.96
R0521:Kdm5b UTSW 1 134,545,771 (GRCm39) missense possibly damaging 0.65
R1004:Kdm5b UTSW 1 134,516,642 (GRCm39) missense possibly damaging 0.71
R1087:Kdm5b UTSW 1 134,528,375 (GRCm39) missense probably damaging 1.00
R1126:Kdm5b UTSW 1 134,541,729 (GRCm39) missense possibly damaging 0.90
R1221:Kdm5b UTSW 1 134,526,829 (GRCm39) missense probably damaging 0.98
R1230:Kdm5b UTSW 1 134,540,992 (GRCm39) missense probably damaging 1.00
R1345:Kdm5b UTSW 1 134,558,288 (GRCm39) missense possibly damaging 0.94
R1482:Kdm5b UTSW 1 134,552,635 (GRCm39) missense probably damaging 1.00
R1582:Kdm5b UTSW 1 134,552,591 (GRCm39) missense probably damaging 0.99
R1653:Kdm5b UTSW 1 134,530,219 (GRCm39) missense probably damaging 1.00
R1693:Kdm5b UTSW 1 134,525,314 (GRCm39) splice site probably benign
R1721:Kdm5b UTSW 1 134,540,919 (GRCm39) splice site probably benign
R1741:Kdm5b UTSW 1 134,545,755 (GRCm39) missense possibly damaging 0.82
R1762:Kdm5b UTSW 1 134,532,205 (GRCm39) nonsense probably null
R1820:Kdm5b UTSW 1 134,525,408 (GRCm39) missense possibly damaging 0.87
R1872:Kdm5b UTSW 1 134,552,732 (GRCm39) missense probably damaging 1.00
R1966:Kdm5b UTSW 1 134,541,611 (GRCm39) splice site probably null
R2056:Kdm5b UTSW 1 134,540,952 (GRCm39) missense probably benign 0.05
R2059:Kdm5b UTSW 1 134,540,952 (GRCm39) missense probably benign 0.05
R2405:Kdm5b UTSW 1 134,536,754 (GRCm39) missense probably damaging 0.97
R3417:Kdm5b UTSW 1 134,515,715 (GRCm39) missense probably damaging 1.00
R3771:Kdm5b UTSW 1 134,541,083 (GRCm39) missense probably damaging 1.00
R3783:Kdm5b UTSW 1 134,558,280 (GRCm39) missense probably benign
R3803:Kdm5b UTSW 1 134,543,679 (GRCm39) missense probably benign 0.07
R3980:Kdm5b UTSW 1 134,547,408 (GRCm39) missense probably benign 0.11
R3983:Kdm5b UTSW 1 134,559,042 (GRCm39) missense possibly damaging 0.91
R4013:Kdm5b UTSW 1 134,555,067 (GRCm39) missense possibly damaging 0.86
R4162:Kdm5b UTSW 1 134,552,899 (GRCm39) missense probably benign 0.01
R4701:Kdm5b UTSW 1 134,533,750 (GRCm39) intron probably benign
R4836:Kdm5b UTSW 1 134,521,053 (GRCm39) splice site probably null
R4924:Kdm5b UTSW 1 134,559,089 (GRCm39) missense probably benign 0.00
R5135:Kdm5b UTSW 1 134,516,484 (GRCm39) intron probably benign
R5248:Kdm5b UTSW 1 134,548,735 (GRCm39) missense probably benign 0.11
R5290:Kdm5b UTSW 1 134,549,837 (GRCm39) splice site probably null
R5358:Kdm5b UTSW 1 134,535,432 (GRCm39) nonsense probably null
R5388:Kdm5b UTSW 1 134,536,635 (GRCm39) nonsense probably null
R5396:Kdm5b UTSW 1 134,549,836 (GRCm39) splice site probably null
R5397:Kdm5b UTSW 1 134,549,836 (GRCm39) splice site probably null
R5398:Kdm5b UTSW 1 134,549,836 (GRCm39) splice site probably null
R5399:Kdm5b UTSW 1 134,549,836 (GRCm39) splice site probably null
R5529:Kdm5b UTSW 1 134,515,741 (GRCm39) missense probably damaging 1.00
R5540:Kdm5b UTSW 1 134,558,979 (GRCm39) missense probably damaging 0.98
R5661:Kdm5b UTSW 1 134,526,811 (GRCm39) missense probably benign 0.01
R5663:Kdm5b UTSW 1 134,558,373 (GRCm39) missense probably benign
R5822:Kdm5b UTSW 1 134,516,511 (GRCm39) splice site probably benign
R6226:Kdm5b UTSW 1 134,536,616 (GRCm39) missense probably damaging 0.99
R6368:Kdm5b UTSW 1 134,526,945 (GRCm39) missense probably damaging 1.00
R6681:Kdm5b UTSW 1 134,541,007 (GRCm39) missense possibly damaging 0.90
R6715:Kdm5b UTSW 1 134,536,799 (GRCm39) critical splice donor site probably null
R7132:Kdm5b UTSW 1 134,526,844 (GRCm39) missense probably damaging 1.00
R7202:Kdm5b UTSW 1 134,552,497 (GRCm39) missense probably benign
R7258:Kdm5b UTSW 1 134,548,759 (GRCm39) missense probably damaging 1.00
R7335:Kdm5b UTSW 1 134,488,177 (GRCm39) missense probably damaging 1.00
R7420:Kdm5b UTSW 1 134,532,235 (GRCm39) missense probably benign 0.14
R7426:Kdm5b UTSW 1 134,523,571 (GRCm39) missense probably benign 0.02
R7452:Kdm5b UTSW 1 134,552,686 (GRCm39) missense probably damaging 1.00
R7595:Kdm5b UTSW 1 134,536,704 (GRCm39) missense probably benign 0.00
R7612:Kdm5b UTSW 1 134,552,656 (GRCm39) nonsense probably null
R7704:Kdm5b UTSW 1 134,515,669 (GRCm39) missense probably damaging 1.00
R7846:Kdm5b UTSW 1 134,545,578 (GRCm39) missense probably damaging 1.00
R8115:Kdm5b UTSW 1 134,547,411 (GRCm39) missense possibly damaging 0.83
R8146:Kdm5b UTSW 1 134,552,864 (GRCm39) missense probably benign 0.05
R8160:Kdm5b UTSW 1 134,541,657 (GRCm39) missense probably damaging 1.00
R8527:Kdm5b UTSW 1 134,533,512 (GRCm39) missense possibly damaging 0.78
R8542:Kdm5b UTSW 1 134,533,512 (GRCm39) missense possibly damaging 0.78
R8930:Kdm5b UTSW 1 134,544,010 (GRCm39) missense probably damaging 1.00
R8932:Kdm5b UTSW 1 134,544,010 (GRCm39) missense probably damaging 1.00
R8950:Kdm5b UTSW 1 134,541,664 (GRCm39) missense possibly damaging 0.84
R9089:Kdm5b UTSW 1 134,535,506 (GRCm39) missense probably damaging 0.98
R9109:Kdm5b UTSW 1 134,528,493 (GRCm39) critical splice donor site probably null
R9133:Kdm5b UTSW 1 134,530,323 (GRCm39) missense probably benign
R9298:Kdm5b UTSW 1 134,528,493 (GRCm39) critical splice donor site probably null
R9423:Kdm5b UTSW 1 134,515,705 (GRCm39) missense possibly damaging 0.85
R9630:Kdm5b UTSW 1 134,512,971 (GRCm39) critical splice donor site probably null
R9670:Kdm5b UTSW 1 134,558,240 (GRCm39) nonsense probably null
X0063:Kdm5b UTSW 1 134,516,614 (GRCm39) missense probably benign 0.07
Z1176:Kdm5b UTSW 1 134,552,773 (GRCm39) missense probably damaging 1.00
Z1177:Kdm5b UTSW 1 134,523,536 (GRCm39) frame shift probably null
Predicted Primers PCR Primer
(F):5'- CTATGACTTAGTGCGTAATGCTG -3'
(R):5'- AAGGGCACTCACTCCATCAG -3'

Sequencing Primer
(F):5'- GTGCGTAATGCTGAAACTCATTCC -3'
(R):5'- CCACCTTCTGAGCGCCG -3'
Posted On 2016-02-04