Incidental Mutation 'R4924:Kdm5b'
ID 378837
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 042526-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.268) question?
Stock # R4924 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 134560171-134635285 bp(+) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) A to G at 134631351 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Lysine to Glutamic Acid at position 1538 (K1538E)
Ref Sequence ENSEMBL: ENSMUSP00000038138 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047714] [ENSMUST00000112198]
AlphaFold Q80Y84
Predicted Effect probably benign
Transcript: ENSMUST00000047714
AA Change: K1538E

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207
AA Change: K1538E

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
SMART Domains Protein: ENSMUSP00000107817
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 692 745 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: 99.0%
  • 3x: 98.2%
  • 10x: 96.0%
  • 20x: 91.6%
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: 76 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aatk G A 11: 120,011,525 (GRCm38) H625Y probably damaging Het
Adamts4 C T 1: 171,259,074 (GRCm38) R812W probably damaging Het
Ajuba A C 14: 54,571,599 (GRCm38) probably null Het
Aox2 T A 1: 58,305,344 (GRCm38) V532D probably damaging Het
Arpc1b G A 5: 145,126,815 (GRCm38) S295N probably benign Het
Baiap2 A G 11: 119,997,024 (GRCm38) S335G probably damaging Het
BC051142 C T 17: 34,459,977 (GRCm38) P221L probably damaging Het
Brap T G 5: 121,665,255 (GRCm38) N155K probably damaging Het
Btn1a1 A G 13: 23,464,226 (GRCm38) probably benign Het
Ccl12 G A 11: 82,102,649 (GRCm38) V38I probably benign Het
Cemip T C 7: 83,952,938 (GRCm38) Y881C probably damaging Het
Cep128 T C 12: 91,022,400 (GRCm38) silent Het
Chd5 A C 4: 152,366,429 (GRCm38) D670A possibly damaging Het
Cmip T C 8: 117,257,255 (GRCm38) Y52H probably benign Het
Dmtn A G 14: 70,617,959 (GRCm38) I30T probably benign Het
Dscaml1 T A 9: 45,745,189 (GRCm38) M1609K probably damaging Het
Edar C A 10: 58,629,375 (GRCm38) E55D probably damaging Het
Ehmt1 A T 2: 24,839,722 (GRCm38) I601N probably damaging Het
Fam120a A T 13: 48,902,096 (GRCm38) N705K probably benign Het
Gm21718 G T 14: 51,312,835 (GRCm38) noncoding transcript Het
Gnaz A G 10: 74,991,713 (GRCm38) D99G probably benign Het
Helz G A 11: 107,602,339 (GRCm38) G196D probably damaging Het
Hif1a T C 12: 73,939,557 (GRCm38) S341P probably damaging Het
Hivep1 G T 13: 42,158,316 (GRCm38) S1344I probably benign Het
Hspa1l T A 17: 34,977,856 (GRCm38) Y290* probably null Het
Ift81 A G 5: 122,594,616 (GRCm38) L285S possibly damaging Het
Inpp4b T A 8: 82,122,624 (GRCm38) N891K probably damaging Het
Irx6 C T 8: 92,678,353 (GRCm38) T283M probably benign Het
Kif13a A G 13: 46,929,599 (GRCm38) V8A probably damaging Het
Krtap15 T A 16: 88,829,148 (GRCm38) N34K probably damaging Het
Lama2 T G 10: 27,369,141 (GRCm38) I215L probably damaging Het
Ldlrad3 C T 2: 102,069,983 (GRCm38) R58H possibly damaging Het
Lvrn C T 18: 46,894,725 (GRCm38) P869L probably damaging Het
Myo1d A G 11: 80,674,678 (GRCm38) F411S probably damaging Het
Myo5b T A 18: 74,695,384 (GRCm38) H702Q probably benign Het
Nat8f4 G T 6: 85,901,419 (GRCm38) Q41K probably benign Het
Nckap5 C A 1: 126,027,028 (GRCm38) E596* probably null Het
Nek10 T A 14: 14,846,594 (GRCm38) probably null Het
Notch3 T C 17: 32,144,731 (GRCm38) Y1145C probably damaging Het
Nr4a2 A T 2: 57,112,023 (GRCm38) H76Q probably benign Het
Nup98 T C 7: 102,134,978 (GRCm38) Q1049R probably damaging Het
Olfr1080 A T 2: 86,553,509 (GRCm38) F205Y probably damaging Het
Olfr1298 A T 2: 111,645,776 (GRCm38) S74T possibly damaging Het
Olfr172 T A 16: 58,760,619 (GRCm38) R186* probably null Het
Pepd T C 7: 35,020,984 (GRCm38) Y231H probably benign Het
Plagl1 G T 10: 13,127,557 (GRCm38) A190S possibly damaging Het
Plat T A 8: 22,778,253 (GRCm38) I345N probably damaging Het
Pnmt A G 11: 98,387,460 (GRCm38) E120G probably damaging Het
Prkrip1 C A 5: 136,198,943 (GRCm38) probably null Het
Pygm G A 19: 6,393,724 (GRCm38) A572T probably damaging Het
Rbm4b T C 19: 4,757,372 (GRCm38) F39L probably damaging Het
Rpe65 A G 3: 159,622,631 (GRCm38) H388R probably benign Het
Scn4a G T 11: 106,320,088 (GRCm38) A1701E possibly damaging Het
Sdk2 C A 11: 113,857,758 (GRCm38) W616L probably damaging Het
Serpina3m T A 12: 104,391,470 (GRCm38) S218T probably benign Het
Siglece C T 7: 43,659,873 (GRCm38) R87H probably damaging Het
Sim1 C A 10: 50,909,902 (GRCm38) L284M probably damaging Het
Smok3c G T 5: 138,065,582 (GRCm38) E444* probably null Het
Snx4 T C 16: 33,294,730 (GRCm38) V427A probably benign Het
Srp68 A T 11: 116,260,858 (GRCm38) V304E probably damaging Het
Stag1 A T 9: 100,796,755 (GRCm38) H243L possibly damaging Het
Stx6 T C 1: 155,173,991 (GRCm38) V14A probably damaging Het
Sv2b T A 7: 75,136,421 (GRCm38) Y417F probably benign Het
Tas2r103 A G 6: 133,036,198 (GRCm38) Y302H probably benign Het
Thop1 T C 10: 81,080,194 (GRCm38) S404P probably benign Het
Trp53bp1 G T 2: 121,221,220 (GRCm38) C988* probably null Het
Ube3c A G 5: 29,631,271 (GRCm38) E630G possibly damaging Het
Usf3 T C 16: 44,217,355 (GRCm38) S733P probably benign Het
Vmn1r195 A G 13: 22,279,019 (GRCm38) T220A probably benign Het
Vmn1r201 A T 13: 22,474,712 (GRCm38) H32L probably benign Het
Wnt2 A G 6: 18,023,240 (GRCm38) C137R probably damaging Het
Ythdc2 T C 18: 44,847,804 (GRCm38) S489P probably damaging Het
Zfp248 A G 6: 118,429,072 (GRCm38) C418R probably damaging Het
Zfp946 T G 17: 22,455,521 (GRCm38) F419V probably damaging Het
Zfp994 C T 17: 22,200,757 (GRCm38) E404K probably damaging Het
Zfpm1 T C 8: 122,334,608 (GRCm38) V304A 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
R2059: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
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'- CCCGATTTTGAATGGCATTGTTTC -3'
(R):5'- TCGTAATCAGTAGAGACCCCTG -3'

Sequencing Primer
(F):5'- GAATGGCATTGTTTCCTCTGAAC -3'
(R):5'- GTCAGCATTTTAAACTTCAACAACC -3'
Posted On 2016-04-15