Incidental Mutation 'IGL02183:Kdm5b'
ID284323
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Kdm5b
Ensembl Gene ENSMUSG00000042207
Gene Namelysine (K)-specific demethylase 5B
SynonymsJarid1b, Plu1, Rb-Bp2, 2210016I17Rik, 2010009J12Rik, PLU-1, D1Ertd202e
Accession Numbers
Is this an essential gene? Possibly essential (E-score: 0.569) question?
Stock #IGL02183
Quality Score
Status
Chromosome1
Chromosomal Location134560171-134635285 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 134624931 bp
ZygosityHeterozygous
Amino Acid Change Isoleucine to Threonine at position 1215 (I1215T)
Ref Sequence ENSEMBL: ENSMUSP00000107817 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047714] [ENSMUST00000112198]
PDB Structure
Solution structure of the ARID domain of Jarid1b protein [SOLUTION NMR]
Predicted Effect probably benign
Transcript: ENSMUST00000047714
AA Change: I1215T

PolyPhen 2 Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207
AA Change: I1215T

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: I1215T

PolyPhen 2 Score 0.090 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000107817
Gene: ENSMUSG00000042207
AA Change: I1215T

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: ENSMUST00000133725
Predicted Effect noncoding transcript
Transcript: ENSMUST00000191572
Coding Region Coverage
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: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2010300C02Rik G A 1: 37,625,378 P480S possibly damaging Het
Ace2 T A X: 164,177,469 probably benign Het
Acsm4 A T 7: 119,693,852 probably null Het
Apcdd1 T C 18: 62,951,854 M374T probably damaging Het
Arid4b A G 13: 14,169,990 E551G possibly damaging Het
Bag4 A T 8: 25,768,030 L423Q probably damaging Het
Celf1 C T 2: 91,001,486 P96S probably damaging Het
Cry2 G A 2: 92,413,039 R486W probably damaging Het
Csn1s1 G A 5: 87,677,618 S228N possibly damaging Het
Ctnnd2 A G 15: 31,020,740 Y1124C probably damaging Het
Cyp2j7 T C 4: 96,230,147 probably benign Het
Dock7 A T 4: 98,958,991 C1695S possibly damaging Het
Elmo3 T C 8: 105,308,323 L415P probably benign Het
Entpd5 A G 12: 84,380,380 probably benign Het
Gm7534 A G 4: 134,201,980 L338S probably benign Het
Gpatch11 T C 17: 78,842,231 probably null Het
Gprin3 C A 6: 59,353,162 R720I possibly damaging Het
Gria4 T G 9: 4,502,460 T358P probably damaging Het
Hcn2 T C 10: 79,724,813 probably null Het
Hivep3 A G 4: 120,132,024 T1891A probably benign Het
Hmgcr A G 13: 96,663,127 V153A probably damaging Het
Ifnar1 T C 16: 91,505,146 V503A possibly damaging Het
Igf2r G A 17: 12,698,516 probably benign Het
Ighg2b A G 12: 113,307,829 S35P unknown Het
Jmy T C 13: 93,499,242 D22G possibly damaging Het
Krt84 T C 15: 101,532,356 I134V unknown Het
Magi3 T A 3: 104,085,347 M270L probably benign Het
Maneal G A 4: 124,860,416 T198I probably benign Het
Map7d3 A G X: 56,822,231 probably benign Het
Myh7 T A 14: 54,974,731 T1519S probably benign Het
Myo5a T C 9: 75,167,236 probably benign Het
Naip5 T C 13: 100,221,642 S1029G probably benign Het
Olfr1162 T C 2: 88,049,989 T212A possibly damaging Het
Olfr1205 A T 2: 88,832,028 I304F probably benign Het
Olfr125 G T 17: 37,835,413 C138F probably damaging Het
Olfr1279 T A 2: 111,306,418 V71E probably damaging Het
Olfr178 T A 16: 58,889,821 Q133L probably benign Het
Pald1 A T 10: 61,347,141 probably benign Het
Pan2 T A 10: 128,309,075 H230Q possibly damaging Het
Pcdh9 T C 14: 93,886,284 I817V probably benign Het
Piezo2 A G 18: 63,020,634 S2547P probably benign Het
Ppargc1b T A 18: 61,309,096 probably null Het
Prdm6 T C 18: 53,464,677 probably benign Het
Prr5l A T 2: 101,772,120 probably benign Het
Rab3gap2 T A 1: 185,271,468 L1020* probably null Het
Rhbdf1 T C 11: 32,210,543 H669R probably damaging Het
Rnf150 A T 8: 83,003,605 I255F probably damaging Het
Rnf17 T A 14: 56,507,868 D1360E probably null Het
Sag T C 1: 87,828,475 probably null Het
Scn2a C T 2: 65,671,603 T90I probably benign Het
Scn9a T A 2: 66,484,611 probably benign Het
Serpinb13 T C 1: 106,998,910 M212T probably damaging Het
Slc39a14 C T 14: 70,306,685 G484E possibly damaging Het
Slco1a1 A T 6: 141,921,943 probably benign Het
Slitrk3 A T 3: 73,049,979 Y487N probably damaging Het
Stkld1 T C 2: 26,946,659 M279T probably benign Het
Tmem161b T C 13: 84,272,254 Y125H probably damaging Het
Tmem71 A G 15: 66,555,025 probably benign Het
Ubxn7 T C 16: 32,369,383 F142L probably damaging Het
Vmn2r22 A G 6: 123,638,004 L209P probably damaging Het
Wdr73 A T 7: 80,893,760 W136R probably damaging Het
Wif1 C T 10: 121,075,276 R107C probably damaging Het
Ythdf2 G T 4: 132,205,574 L92M probably benign Het
Zfp53 T A 17: 21,500,250 I34N possibly damaging Het
Other mutations in Kdm5b
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00230:Kdm5b APN 1 134620955 missense probably damaging 1.00
IGL01458:Kdm5b APN 1 134621986 missense possibly damaging 0.53
IGL01567:Kdm5b APN 1 134602540 missense probably damaging 1.00
IGL01625:Kdm5b APN 1 134617968 missense possibly damaging 0.74
IGL01970:Kdm5b APN 1 134600727 missense probably damaging 1.00
IGL02592:Kdm5b APN 1 134624853 missense probably damaging 0.99
IGL02695:Kdm5b APN 1 134604485 missense possibly damaging 0.94
IGL02697:Kdm5b APN 1 134588773 splice site probably benign
IGL03036:Kdm5b APN 1 134608937 missense probably damaging 1.00
IGL03056:Kdm5b APN 1 134587979 missense probably damaging 0.99
IGL03206:Kdm5b APN 1 134627317 missense probably benign
IGL03342:Kdm5b APN 1 134602576 missense probably benign 0.00
IGL03388:Kdm5b APN 1 134627322 missense probably benign
amaryllis UTSW 1 134609061 critical splice donor site probably null
R0233:Kdm5b UTSW 1 134604634 splice site probably benign
R0334:Kdm5b UTSW 1 134604522 missense probably damaging 0.99
R0504:Kdm5b UTSW 1 134621023 critical splice donor site probably null
R0505:Kdm5b UTSW 1 134602571 missense probably damaging 0.96
R0521:Kdm5b UTSW 1 134618033 missense possibly damaging 0.65
R1004:Kdm5b UTSW 1 134588904 missense possibly damaging 0.71
R1087:Kdm5b UTSW 1 134600637 missense probably damaging 1.00
R1126:Kdm5b UTSW 1 134613991 missense possibly damaging 0.90
R1221:Kdm5b UTSW 1 134599091 missense probably damaging 0.98
R1230:Kdm5b UTSW 1 134613254 missense probably damaging 1.00
R1345:Kdm5b UTSW 1 134630550 missense possibly damaging 0.94
R1482:Kdm5b UTSW 1 134624897 missense probably damaging 1.00
R1582:Kdm5b UTSW 1 134624853 missense probably damaging 0.99
R1653:Kdm5b UTSW 1 134602481 missense probably damaging 1.00
R1693:Kdm5b UTSW 1 134597576 splice site probably benign
R1721:Kdm5b UTSW 1 134613181 splice site probably benign
R1741:Kdm5b UTSW 1 134618017 missense possibly damaging 0.82
R1762:Kdm5b UTSW 1 134604467 nonsense probably null
R1820:Kdm5b UTSW 1 134597670 missense possibly damaging 0.87
R1872:Kdm5b UTSW 1 134624994 missense probably damaging 1.00
R1966:Kdm5b UTSW 1 134613873 splice site probably null
R2056:Kdm5b UTSW 1 134613214 missense probably benign 0.05
R2059:Kdm5b UTSW 1 134613214 missense probably benign 0.05
R2405:Kdm5b UTSW 1 134609016 missense probably damaging 0.97
R3417:Kdm5b UTSW 1 134587977 missense probably damaging 1.00
R3771:Kdm5b UTSW 1 134613345 missense probably damaging 1.00
R3783:Kdm5b UTSW 1 134630542 missense probably benign
R3803:Kdm5b UTSW 1 134615941 missense probably benign 0.07
R3980:Kdm5b UTSW 1 134619670 missense probably benign 0.11
R3983:Kdm5b UTSW 1 134631304 missense possibly damaging 0.91
R4013:Kdm5b UTSW 1 134627329 missense possibly damaging 0.86
R4162:Kdm5b UTSW 1 134625161 missense probably benign 0.01
R4701:Kdm5b UTSW 1 134606012 intron probably benign
R4791:Kdm5b UTSW 1 134630800 missense possibly damaging 0.82
R4836:Kdm5b UTSW 1 134593315 splice site probably null
R4924:Kdm5b UTSW 1 134631351 missense probably benign 0.00
R5135:Kdm5b UTSW 1 134588746 intron probably benign
R5248:Kdm5b UTSW 1 134620997 missense probably benign 0.11
R5290:Kdm5b UTSW 1 134622099 splice site probably null
R5358:Kdm5b UTSW 1 134607694 nonsense probably null
R5388:Kdm5b UTSW 1 134608897 nonsense probably null
R5396:Kdm5b UTSW 1 134622098 splice site probably null
R5397:Kdm5b UTSW 1 134622098 splice site probably null
R5398:Kdm5b UTSW 1 134622098 splice site probably null
R5399:Kdm5b UTSW 1 134622098 splice site probably null
R5529:Kdm5b UTSW 1 134588003 missense probably damaging 1.00
R5540:Kdm5b UTSW 1 134631241 missense probably damaging 0.98
R5661:Kdm5b UTSW 1 134599073 missense probably benign 0.01
R5663:Kdm5b UTSW 1 134630635 missense probably benign
R5822:Kdm5b UTSW 1 134588773 splice site probably benign
R6226:Kdm5b UTSW 1 134608878 missense probably damaging 0.99
R6368:Kdm5b UTSW 1 134599207 missense probably damaging 1.00
R6681:Kdm5b UTSW 1 134613269 missense possibly damaging 0.90
R6715:Kdm5b UTSW 1 134609061 critical splice donor site probably null
X0063:Kdm5b UTSW 1 134588876 missense probably benign 0.07
Posted On2015-04-16