Incidental Mutation 'R2059:Kdm5b'
ID 228431
Institutional Source Beutler Lab
Gene Symbol Kdm5b
Ensembl Gene ENSMUSG00000042207
Gene Name lysine (K)-specific demethylase 5B
Synonyms Jarid1b, Plu1, Rb-Bp2, 2210016I17Rik, 2010009J12Rik, PLU-1, D1Ertd202e
MMRRC Submission 040064-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.268) question?
Stock # R2059 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 134560171-134635285 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to A at 134613214 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glutamic Acid at position 681 (D681E)
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
AA Change: D681E

PolyPhen 2 Score 0.055 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207
AA Change: D681E

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 probably benign
Transcript: ENSMUST00000112198
AA Change: D681E

PolyPhen 2 Score 0.055 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000107817
Gene: ENSMUSG00000042207
AA Change: D681E

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
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.5%
Validation Efficiency 99% (99/100)
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
2210010C04Rik G A 6: 41,032,381 (GRCm38) T173I probably benign Het
Adgrf3 G A 5: 30,199,491 (GRCm38) H316Y possibly damaging Het
Adgrf5 A G 17: 43,428,586 (GRCm38) Y72C possibly damaging Het
Ak5 T A 3: 152,660,637 (GRCm38) L42F probably damaging Het
Alas1 T C 9: 106,241,290 (GRCm38) E211G probably damaging Het
Alkbh1 C T 12: 87,443,750 (GRCm38) probably benign Het
Als2cl T C 9: 110,885,438 (GRCm38) V118A probably benign Het
Ano1 G C 7: 144,611,390 (GRCm38) L641V probably damaging Het
Arfgef1 C T 1: 10,188,752 (GRCm38) probably null Het
Atf6b A T 17: 34,648,575 (GRCm38) probably null Het
Atf7ip T G 6: 136,609,348 (GRCm38) probably benign Het
Atp2b4 G T 1: 133,726,537 (GRCm38) Q777K probably benign Het
Baz2a T A 10: 128,113,578 (GRCm38) S347R probably damaging Het
C2cd3 T C 7: 100,455,493 (GRCm38) probably benign Het
Cage1 A G 13: 38,023,380 (GRCm38) V163A probably benign Het
Cdh12 T A 15: 21,583,740 (GRCm38) N555K probably benign Het
Cenpj G A 14: 56,563,955 (GRCm38) P187L possibly damaging Het
Cep112 T A 11: 108,519,261 (GRCm38) probably null Het
Cfap54 A T 10: 92,942,979 (GRCm38) probably benign Het
Cgref1 T G 5: 30,933,645 (GRCm38) D275A possibly damaging Het
Clgn A C 8: 83,399,978 (GRCm38) N103H probably benign Het
Corin A G 5: 72,316,051 (GRCm38) V905A possibly damaging Het
Csta1 A C 16: 36,122,322 (GRCm38) D72E probably benign Het
Cul5 A T 9: 53,667,156 (GRCm38) L44Q probably damaging Het
Dmbt1 G A 7: 131,106,170 (GRCm38) A1381T possibly damaging Het
Dync1i2 G A 2: 71,249,853 (GRCm38) probably null Het
Enoph1 A G 5: 100,059,219 (GRCm38) D55G probably damaging Het
Fam160b2 A G 14: 70,585,049 (GRCm38) V744A possibly damaging Het
Fat4 T A 3: 38,891,170 (GRCm38) M1404K possibly damaging Het
Foxi2 G T 7: 135,410,677 (GRCm38) G98V probably damaging Het
Galr2 T C 11: 116,282,939 (GRCm38) S132P probably damaging Het
Gcm2 T C 13: 41,109,954 (GRCm38) M1V probably null Het
Gm15446 C T 5: 109,942,496 (GRCm38) H205Y probably damaging Het
Gm21775 T A Y: 10,553,910 (GRCm38) I153N probably benign Het
Grip1 A G 10: 120,038,698 (GRCm38) K789R possibly damaging Het
Gsk3b T A 16: 38,187,909 (GRCm38) D192E probably benign Het
Herc2 T A 7: 56,163,897 (GRCm38) H2625Q probably damaging Het
Hoxc9 A G 15: 102,984,123 (GRCm38) D256G probably benign Het
Il7 A T 3: 7,573,915 (GRCm38) N130K probably damaging Het
Irf2 A T 8: 46,807,345 (GRCm38) N104I probably damaging Het
Kat6a A G 8: 22,939,305 (GRCm38) N1559D possibly damaging Het
Kcnq4 G T 4: 120,698,002 (GRCm38) F661L probably benign Het
Khdrbs1 T C 4: 129,725,721 (GRCm38) E209G probably damaging Het
Lama3 A T 18: 12,528,333 (GRCm38) R2116S probably damaging Het
Mir124-2hg C A 3: 17,785,713 (GRCm38) E65* probably null Het
Mphosph10 T A 7: 64,376,751 (GRCm38) L650F probably damaging Het
Mrpl48 T C 7: 100,549,333 (GRCm38) E204G probably damaging Het
Msl3l2 T A 10: 56,115,944 (GRCm38) L255Q probably damaging Het
Mx1 T A 16: 97,454,179 (GRCm38) K225* probably null Het
Nf1 T C 11: 79,556,723 (GRCm38) V435A probably damaging Het
Nid1 A C 13: 13,500,473 (GRCm38) H926P probably benign Het
Nlrp9a T A 7: 26,557,362 (GRCm38) I46K possibly damaging Het
Nop2 T A 6: 125,139,860 (GRCm38) M359K probably null Het
Nox1 T C X: 134,095,244 (GRCm38) probably benign Het
Ogdhl G A 14: 32,332,884 (GRCm38) R263K probably damaging Het
Olfr1388 T A 11: 49,444,451 (GRCm38) V200E probably damaging Het
Olfr293 A T 7: 86,664,383 (GRCm38) K240N probably damaging Het
Pbsn T C X: 77,847,976 (GRCm38) K72E probably damaging Het
Pde12 T C 14: 26,668,880 (GRCm38) I225V probably benign Het
Ppt2 A T 17: 34,622,844 (GRCm38) probably benign Het
Prl3a1 A G 13: 27,270,144 (GRCm38) D35G probably benign Het
Ptprk T A 10: 28,566,603 (GRCm38) I893N probably damaging Het
Ptprz1 T C 6: 22,986,323 (GRCm38) probably benign Het
Rab3c A G 13: 110,260,516 (GRCm38) V72A probably damaging Het
Rbms2 A G 10: 128,137,518 (GRCm38) S251P probably benign Het
Rfwd3 A G 8: 111,297,495 (GRCm38) V65A probably benign Het
Rps6kl1 T A 12: 85,139,623 (GRCm38) Y211F probably benign Het
Saal1 T C 7: 46,699,456 (GRCm38) Q317R probably damaging Het
Scg3 T C 9: 75,665,716 (GRCm38) D311G probably damaging Het
Sdk2 C A 11: 113,854,332 (GRCm38) M712I probably damaging Het
Serinc2 T G 4: 130,260,785 (GRCm38) Y158S probably damaging Het
Serpinb9c A T 13: 33,156,871 (GRCm38) C81* probably null Het
Sgpp2 T A 1: 78,416,951 (GRCm38) L197Q probably damaging Het
Shroom3 A T 5: 92,683,784 (GRCm38) T40S probably damaging Het
Sik1 A G 17: 31,848,797 (GRCm38) S435P probably benign Het
Slc7a3 A G X: 101,080,767 (GRCm38) V464A probably benign Het
Snd1 T C 6: 28,745,207 (GRCm38) F517S probably damaging Het
Spata13 A C 14: 60,759,591 (GRCm38) I1165L possibly damaging Het
St8sia5 A T 18: 77,254,763 (GRCm38) I390F probably damaging Het
Stat5b A T 11: 100,787,332 (GRCm38) S652T probably benign Het
Stom A G 2: 35,316,025 (GRCm38) S231P probably damaging Het
Sult1b1 A G 5: 87,535,033 (GRCm38) Y18H probably damaging Het
Tgm4 T C 9: 123,061,770 (GRCm38) I54T probably damaging Het
Tmem176b G A 6: 48,836,333 (GRCm38) T64I probably damaging Het
Tmem87a A T 2: 120,369,292 (GRCm38) I457N probably damaging Het
Trim12c A G 7: 104,348,191 (GRCm38) F53L possibly damaging Het
Ttc6 T A 12: 57,737,693 (GRCm38) D1849E probably benign Het
Ubap2l A T 3: 90,031,376 (GRCm38) probably benign Het
Ush2a T G 1: 188,381,549 (GRCm38) probably null Het
Usp17la A C 7: 104,861,171 (GRCm38) T328P probably damaging Het
Ust A G 10: 8,207,566 (GRCm38) Y349H probably damaging Het
V1rd19 A T 7: 24,003,834 (GRCm38) M242L probably benign Het
Vmn1r33 T A 6: 66,612,202 (GRCm38) M123L probably benign Het
Vps13c A T 9: 67,860,833 (GRCm38) K111N probably damaging Het
Vwa3a A G 7: 120,758,949 (GRCm38) D81G probably damaging Het
Zfp318 G A 17: 46,397,024 (GRCm38) R336Q probably damaging Het
Zfp609 A G 9: 65,704,434 (GRCm38) S416P possibly damaging Het
Other mutations in Kdm5b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00230:Kdm5b APN 1 134,620,955 (GRCm38) missense probably damaging 1.00
IGL01458:Kdm5b APN 1 134,621,986 (GRCm38) missense possibly damaging 0.53
IGL01567:Kdm5b APN 1 134,602,540 (GRCm38) missense probably damaging 1.00
IGL01625:Kdm5b APN 1 134,617,968 (GRCm38) missense possibly damaging 0.74
IGL01970:Kdm5b APN 1 134,600,727 (GRCm38) missense probably damaging 1.00
IGL02183:Kdm5b APN 1 134,624,931 (GRCm38) missense probably benign 0.09
IGL02592:Kdm5b APN 1 134,624,853 (GRCm38) missense probably damaging 0.99
IGL02695:Kdm5b APN 1 134,604,485 (GRCm38) missense possibly damaging 0.94
IGL02697:Kdm5b APN 1 134,588,773 (GRCm38) splice site probably benign
IGL03036:Kdm5b APN 1 134,608,937 (GRCm38) missense probably damaging 1.00
IGL03056:Kdm5b APN 1 134,587,979 (GRCm38) missense probably damaging 0.99
IGL03206:Kdm5b APN 1 134,627,317 (GRCm38) missense probably benign
IGL03342:Kdm5b APN 1 134,602,576 (GRCm38) missense probably benign 0.00
IGL03388:Kdm5b APN 1 134,627,322 (GRCm38) missense probably benign
amaryllis UTSW 1 134,609,061 (GRCm38) critical splice donor site probably null
PIT4486001:Kdm5b UTSW 1 134,628,685 (GRCm38) missense probably damaging 1.00
R0233:Kdm5b UTSW 1 134,604,634 (GRCm38) splice site probably benign
R0334:Kdm5b UTSW 1 134,604,522 (GRCm38) missense probably damaging 0.99
R0504:Kdm5b UTSW 1 134,621,023 (GRCm38) critical splice donor site probably null
R0505:Kdm5b UTSW 1 134,602,571 (GRCm38) missense probably damaging 0.96
R0521:Kdm5b UTSW 1 134,618,033 (GRCm38) missense possibly damaging 0.65
R1004:Kdm5b UTSW 1 134,588,904 (GRCm38) missense possibly damaging 0.71
R1087:Kdm5b UTSW 1 134,600,637 (GRCm38) missense probably damaging 1.00
R1126:Kdm5b UTSW 1 134,613,991 (GRCm38) missense possibly damaging 0.90
R1221:Kdm5b UTSW 1 134,599,091 (GRCm38) missense probably damaging 0.98
R1230:Kdm5b UTSW 1 134,613,254 (GRCm38) missense probably damaging 1.00
R1345:Kdm5b UTSW 1 134,630,550 (GRCm38) missense possibly damaging 0.94
R1482:Kdm5b UTSW 1 134,624,897 (GRCm38) missense probably damaging 1.00
R1582:Kdm5b UTSW 1 134,624,853 (GRCm38) missense probably damaging 0.99
R1653:Kdm5b UTSW 1 134,602,481 (GRCm38) missense probably damaging 1.00
R1693:Kdm5b UTSW 1 134,597,576 (GRCm38) splice site probably benign
R1721:Kdm5b UTSW 1 134,613,181 (GRCm38) splice site probably benign
R1741:Kdm5b UTSW 1 134,618,017 (GRCm38) missense possibly damaging 0.82
R1762:Kdm5b UTSW 1 134,604,467 (GRCm38) nonsense probably null
R1820:Kdm5b UTSW 1 134,597,670 (GRCm38) missense possibly damaging 0.87
R1872:Kdm5b UTSW 1 134,624,994 (GRCm38) missense probably damaging 1.00
R1966:Kdm5b UTSW 1 134,613,873 (GRCm38) splice site probably null
R2056:Kdm5b UTSW 1 134,613,214 (GRCm38) missense probably benign 0.05
R2405:Kdm5b UTSW 1 134,609,016 (GRCm38) missense probably damaging 0.97
R3417:Kdm5b UTSW 1 134,587,977 (GRCm38) missense probably damaging 1.00
R3771:Kdm5b UTSW 1 134,613,345 (GRCm38) missense probably damaging 1.00
R3783:Kdm5b UTSW 1 134,630,542 (GRCm38) missense probably benign
R3803:Kdm5b UTSW 1 134,615,941 (GRCm38) missense probably benign 0.07
R3980:Kdm5b UTSW 1 134,619,670 (GRCm38) missense probably benign 0.11
R3983:Kdm5b UTSW 1 134,631,304 (GRCm38) missense possibly damaging 0.91
R4013:Kdm5b UTSW 1 134,627,329 (GRCm38) missense possibly damaging 0.86
R4162:Kdm5b UTSW 1 134,625,161 (GRCm38) missense probably benign 0.01
R4701:Kdm5b UTSW 1 134,606,012 (GRCm38) intron probably benign
R4791:Kdm5b UTSW 1 134,630,800 (GRCm38) missense possibly damaging 0.82
R4836:Kdm5b UTSW 1 134,593,315 (GRCm38) splice site probably null
R4924:Kdm5b UTSW 1 134,631,351 (GRCm38) missense probably benign 0.00
R5135:Kdm5b UTSW 1 134,588,746 (GRCm38) intron probably benign
R5248:Kdm5b UTSW 1 134,620,997 (GRCm38) missense probably benign 0.11
R5290:Kdm5b UTSW 1 134,622,099 (GRCm38) splice site probably null
R5358:Kdm5b UTSW 1 134,607,694 (GRCm38) nonsense probably null
R5388:Kdm5b UTSW 1 134,608,897 (GRCm38) nonsense probably null
R5396:Kdm5b UTSW 1 134,622,098 (GRCm38) splice site probably null
R5397:Kdm5b UTSW 1 134,622,098 (GRCm38) splice site probably null
R5398:Kdm5b UTSW 1 134,622,098 (GRCm38) splice site probably null
R5399:Kdm5b UTSW 1 134,622,098 (GRCm38) splice site probably null
R5529:Kdm5b UTSW 1 134,588,003 (GRCm38) missense probably damaging 1.00
R5540:Kdm5b UTSW 1 134,631,241 (GRCm38) missense probably damaging 0.98
R5661:Kdm5b UTSW 1 134,599,073 (GRCm38) missense probably benign 0.01
R5663:Kdm5b UTSW 1 134,630,635 (GRCm38) missense probably benign
R5822:Kdm5b UTSW 1 134,588,773 (GRCm38) splice site probably benign
R6226:Kdm5b UTSW 1 134,608,878 (GRCm38) missense probably damaging 0.99
R6368:Kdm5b UTSW 1 134,599,207 (GRCm38) missense probably damaging 1.00
R6681:Kdm5b UTSW 1 134,613,269 (GRCm38) missense possibly damaging 0.90
R6715:Kdm5b UTSW 1 134,609,061 (GRCm38) critical splice donor site probably null
R7132:Kdm5b UTSW 1 134,599,106 (GRCm38) missense probably damaging 1.00
R7202:Kdm5b UTSW 1 134,624,759 (GRCm38) missense probably benign
R7258:Kdm5b UTSW 1 134,621,021 (GRCm38) missense probably damaging 1.00
R7335:Kdm5b UTSW 1 134,560,439 (GRCm38) missense probably damaging 1.00
R7420:Kdm5b UTSW 1 134,604,497 (GRCm38) missense probably benign 0.14
R7426:Kdm5b UTSW 1 134,595,833 (GRCm38) missense probably benign 0.02
R7452:Kdm5b UTSW 1 134,624,948 (GRCm38) missense probably damaging 1.00
R7595:Kdm5b UTSW 1 134,608,966 (GRCm38) missense probably benign 0.00
R7612:Kdm5b UTSW 1 134,624,918 (GRCm38) nonsense probably null
R7704:Kdm5b UTSW 1 134,587,931 (GRCm38) missense probably damaging 1.00
R7846:Kdm5b UTSW 1 134,617,840 (GRCm38) missense probably damaging 1.00
R8115:Kdm5b UTSW 1 134,619,673 (GRCm38) missense possibly damaging 0.83
R8146:Kdm5b UTSW 1 134,625,126 (GRCm38) missense probably benign 0.05
R8160:Kdm5b UTSW 1 134,613,919 (GRCm38) missense probably damaging 1.00
R8527:Kdm5b UTSW 1 134,605,774 (GRCm38) missense possibly damaging 0.78
R8542:Kdm5b UTSW 1 134,605,774 (GRCm38) missense possibly damaging 0.78
R8930:Kdm5b UTSW 1 134,616,272 (GRCm38) missense probably damaging 1.00
R8932:Kdm5b UTSW 1 134,616,272 (GRCm38) missense probably damaging 1.00
R8950:Kdm5b UTSW 1 134,613,926 (GRCm38) missense possibly damaging 0.84
R9089:Kdm5b UTSW 1 134,607,768 (GRCm38) missense probably damaging 0.98
R9109:Kdm5b UTSW 1 134,600,755 (GRCm38) critical splice donor site probably null
R9133:Kdm5b UTSW 1 134,602,585 (GRCm38) missense probably benign
R9298:Kdm5b UTSW 1 134,600,755 (GRCm38) critical splice donor site probably null
R9423:Kdm5b UTSW 1 134,587,967 (GRCm38) missense possibly damaging 0.85
R9630:Kdm5b UTSW 1 134,585,233 (GRCm38) critical splice donor site probably null
R9670:Kdm5b UTSW 1 134,630,502 (GRCm38) nonsense probably null
X0063:Kdm5b UTSW 1 134,588,876 (GRCm38) missense probably benign 0.07
Z1176:Kdm5b UTSW 1 134,625,035 (GRCm38) missense probably damaging 1.00
Z1177:Kdm5b UTSW 1 134,595,798 (GRCm38) frame shift probably null
Predicted Primers PCR Primer
(F):5'- GCCTCATCCAAAGAAGGATTCTC -3'
(R):5'- AACTCATCCTTACTTACCGCAG -3'

Sequencing Primer
(F):5'- TCTGTCTTCAGATACGCTAGAAGAGG -3'
(R):5'- CGCAGGTTATACTTATACGGGG -3'
Posted On 2014-09-17