Incidental Mutation 'IGL03342:Kdm5b'
ID417255
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 non essential (E-score: 0.434) question?
Stock #IGL03342
Quality Score
Status
Chromosome1
Chromosomal Location134560171-134635285 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) G to A at 134602576 bp
ZygosityHeterozygous
Amino Acid Change Aspartic acid to Asparagine at position 442 (D442N)
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: D442N

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207
AA Change: D442N

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 noncoding transcript
Transcript: ENSMUST00000112197
SMART Domains Protein: ENSMUSP00000107816
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 225 236 N/A INTRINSIC
PHD 308 354 6.15e-14 SMART
JmjC 450 595 2.6e-24 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112198
AA Change: D442N

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000107817
Gene: ENSMUSG00000042207
AA Change: D442N

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
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: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca5 G A 11: 110,287,691 T1152M possibly damaging Het
Abcg2 G T 6: 58,665,135 R136I probably damaging Het
Acap2 A G 16: 31,105,492 V641A probably damaging Het
Afg3l2 A T 18: 67,407,320 D706E probably benign Het
Bbs1 A T 19: 4,897,593 L311Q probably damaging Het
Cacna1e A G 1: 154,466,944 probably null Het
Car2 A T 3: 14,895,569 D129V probably benign Het
Catsper2 T C 2: 121,406,736 I228V probably damaging Het
Cdhr3 C A 12: 33,051,055 R452M probably benign Het
Chrm1 A T 19: 8,679,308 Q459L probably benign Het
Cnbd1 C T 4: 19,098,264 probably benign Het
Coa7 A G 4: 108,332,229 D42G probably damaging Het
Ctsz T C 2: 174,429,140 Y187C possibly damaging Het
Cxcr6 C T 9: 123,810,407 Q165* probably null Het
Cyp3a11 G A 5: 145,855,117 P489S probably damaging Het
Cyp4f15 A T 17: 32,697,936 I276F probably damaging Het
Dsg1b T A 18: 20,409,460 M1008K probably benign Het
Dsg4 T A 18: 20,451,823 I198N probably damaging Het
Dtymk C A 1: 93,794,819 E87D probably benign Het
Dysf T A 6: 84,190,872 D1749E probably benign Het
Dzip3 G T 16: 48,929,623 Q1050K probably damaging Het
Echs1 C T 7: 140,110,113 probably benign Het
Enc1 T A 13: 97,246,470 I496N possibly damaging Het
Epc2 A T 2: 49,536,646 Y139F probably benign Het
Exo1 A T 1: 175,892,127 N246I probably benign Het
Flg2 A G 3: 93,201,235 K190R probably damaging Het
Gm5424 A T 10: 62,072,192 noncoding transcript Het
Gpbp1l1 A C 4: 116,574,543 T133P probably benign Het
Gpr155 A G 2: 73,349,678 F146S probably damaging Het
Grm1 T A 10: 11,079,971 I190L probably benign Het
Hif3a C T 7: 17,041,122 R515H possibly damaging Het
Manba A T 3: 135,517,987 I212F possibly damaging Het
Map3k13 A G 16: 21,892,231 E88G possibly damaging Het
Mapk7 A G 11: 61,491,390 L163P probably damaging Het
Med1 A T 11: 98,189,180 probably null Het
Mtrf1 C T 14: 79,415,871 probably benign Het
Mtrf1 T A 14: 79,415,872 probably null Het
Mtrf1 A G 14: 79,415,980 D365G possibly damaging Het
Myadm C T 7: 3,296,887 T55I possibly damaging Het
Nlgn1 A T 3: 26,133,262 I158N probably damaging Het
Nlrc4 A G 17: 74,445,318 L690P probably damaging Het
Nlrp1a A T 11: 71,122,791 D544E probably benign Het
Nlrp2 A T 7: 5,317,483 L20Q probably damaging Het
Olfr1053 A T 2: 86,315,235 I17N possibly damaging Het
Olfr1504 A G 19: 13,887,437 Y258H probably damaging Het
Olfr390 T A 11: 73,787,483 S182T probably benign Het
Padi3 G A 4: 140,810,598 Q4* probably null Het
Pfkl A T 10: 78,005,475 I13K possibly damaging Het
Pinx1 A G 14: 63,919,569 D315G probably benign Het
Prickle3 A G X: 7,663,496 D47G probably benign Het
Psmd10 A T X: 140,956,654 V5E probably damaging Het
Rasgrf2 C A 13: 91,987,979 V605F probably damaging Het
Smarca1 G T X: 47,892,269 A84D probably damaging Het
Sp2 A G 11: 96,961,762 V112A probably damaging Het
Srgap3 G A 6: 112,775,687 R279C probably damaging Het
Ssfa2 G A 2: 79,660,452 M971I probably damaging Het
Trav21-dv12 T C 14: 53,876,044 L10P unknown Het
Vmn1r236 A T 17: 21,286,974 H118L probably benign Het
Vmn2r120 A G 17: 57,509,372 M661T probably benign Het
Vmn2r17 A T 5: 109,427,916 I218F probably damaging Het
Vmn2r41 G T 7: 8,138,683 A594D probably damaging Het
Zc2hc1a A G 3: 7,524,223 E103G possibly damaging Het
Zfp62 G T 11: 49,215,471 G130* probably null 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
IGL02183:Kdm5b APN 1 134624931 missense probably benign 0.09
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
IGL03388:Kdm5b APN 1 134627322 missense probably benign
amaryllis UTSW 1 134609061 critical splice donor site probably null
PIT4486001:Kdm5b UTSW 1 134628685 missense probably damaging 1.00
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
R7132:Kdm5b UTSW 1 134599106 missense probably damaging 1.00
R7202:Kdm5b UTSW 1 134624759 missense probably benign
R7258:Kdm5b UTSW 1 134621021 missense probably damaging 1.00
R7335:Kdm5b UTSW 1 134560439 missense probably damaging 1.00
R7420:Kdm5b UTSW 1 134604497 missense probably benign 0.14
R7426:Kdm5b UTSW 1 134595833 missense probably benign 0.02
R7452:Kdm5b UTSW 1 134624948 missense probably damaging 1.00
X0063:Kdm5b UTSW 1 134588876 missense probably benign 0.07
Posted On2016-08-02