Incidental Mutation 'IGL02165:Kdm5a'
ID282678
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Kdm5a
Ensembl Gene ENSMUSG00000030180
Gene Namelysine (K)-specific demethylase 5A
SynonymsJarid1a, Rbbp2, RBP2
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #IGL02165
Quality Score
Status
Chromosome6
Chromosomal Location120364124-120444574 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to A at 120415290 bp
ZygosityHeterozygous
Amino Acid Change Valine to Glutamic Acid at position 991 (V991E)
Ref Sequence ENSEMBL: ENSMUSP00000005108 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005108] [ENSMUST00000132009] [ENSMUST00000135802]
Predicted Effect probably damaging
Transcript: ENSMUST00000005108
AA Change: V991E

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: V991E

DomainStartEndE-ValueType
JmjN 18 59 4.06e-20 SMART
ARID 81 170 4.76e-35 SMART
BRIGHT 85 175 2.48e-31 SMART
PHD 295 341 1.16e-14 SMART
Blast:JmjC 384 436 2e-22 BLAST
JmjC 437 603 5.88e-73 SMART
low complexity region 638 651 N/A INTRINSIC
Pfam:zf-C5HC2 676 729 1.3e-21 PFAM
Pfam:PLU-1 740 1072 1.2e-104 PFAM
low complexity region 1091 1119 N/A INTRINSIC
PHD 1163 1216 1.37e-11 SMART
low complexity region 1269 1280 N/A INTRINSIC
low complexity region 1337 1351 N/A INTRINSIC
low complexity region 1403 1414 N/A INTRINSIC
low complexity region 1494 1512 N/A INTRINSIC
coiled coil region 1534 1579 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124847
Predicted Effect probably benign
Transcript: ENSMUST00000132009
SMART Domains Protein: ENSMUSP00000145375
Gene: ENSMUSG00000030180

DomainStartEndE-ValueType
JmjN 18 59 4.06e-20 SMART
ARID 81 170 4.76e-35 SMART
BRIGHT 85 175 2.48e-31 SMART
PHD 295 341 1.16e-14 SMART
JmjC 437 603 1.47e-64 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000135802
SMART Domains Protein: ENSMUSP00000145021
Gene: ENSMUSG00000030180

DomainStartEndE-ValueType
JmjN 18 59 1.7e-22 SMART
ARID 81 170 3.6e-39 SMART
BRIGHT 85 175 1.2e-33 SMART
PHD 295 341 7.3e-17 SMART
Blast:JmjC 384 436 2e-22 BLAST
JmjC 437 603 2.2e-75 SMART
low complexity region 638 651 N/A INTRINSIC
Pfam:zf-C5HC2 676 728 6.3e-15 PFAM
Pfam:PLU-1 741 811 9.8e-16 PFAM
Coding Region Coverage
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the Jumonji, AT-rich interactive domain 1 (JARID1) histone demethylase protein family. The encoded protein plays a role in gene regulation through the histone code by specifically demethylating lysine 4 of histone H3. The encoded protein interacts with many other proteins, including retinoblastoma protein, and is implicated in the transcriptional regulation of Hox genes and cytokines. This gene may play a role in tumor progression. [provided by RefSeq, Aug 2013]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit reduced body size, abnormal involuntary movement and quantitative changes in the hematopoietic stem cell and myeloid progenitor compartments, consistent with enhanced survival and increased cycling. Neonatalsurvival is sensitive to genetic background. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A1cf T A 19: 31,927,186 M199K possibly damaging Het
Abo C A 2: 26,843,429 V255L probably damaging Het
Alas1 A T 9: 106,238,783 M344K probably damaging Het
Ap1m1 A G 8: 72,249,809 I118V probably benign Het
Ap5m1 A T 14: 49,078,728 I252F possibly damaging Het
Arhgef2 G A 3: 88,646,220 R886H probably damaging Het
Atp13a4 T C 16: 29,434,010 E706G probably damaging Het
Baz2a C A 10: 128,119,349 A775E probably benign Het
C3 A T 17: 57,225,092 F210I probably benign Het
Casq1 A G 1: 172,213,381 L280P probably damaging Het
Cebpz A G 17: 78,922,169 F919L probably damaging Het
Dclre1c T A 2: 3,450,381 probably benign Het
Dsc3 T G 18: 19,983,652 M276L probably benign Het
Eftud2 A G 11: 102,851,747 probably benign Het
Elfn2 T A 15: 78,673,418 T310S probably benign Het
Ep300 A G 15: 81,641,391 K1472R probably benign Het
Fbxl2 T C 9: 114,018,031 D8G probably benign Het
Galnt5 T A 2: 57,998,865 M159K probably benign Het
Gm10260 T G 13: 97,760,140 K150T probably benign Het
Gm28048 A T 11: 22,982,072 probably benign Het
Hars2 T A 18: 36,783,394 M1K probably null Het
Hk1 T C 10: 62,281,888 T619A probably damaging Het
Ifi44 C T 3: 151,749,430 V53M probably damaging Het
Ippk T A 13: 49,446,535 V339D possibly damaging Het
Kcnma1 G T 14: 23,336,967 N875K possibly damaging Het
Larp6 A G 9: 60,713,312 E36G probably benign Het
Lonp2 A T 8: 86,709,026 D210V probably damaging Het
Lrrc4c G A 2: 97,629,033 M1I probably null Het
Mmp2 A G 8: 92,833,219 K270R probably null Het
Nexmif C T X: 104,084,754 V1186I probably benign Het
Olfr54 A T 11: 51,027,643 I214F probably benign Het
Olfr744 A G 14: 50,619,011 Y263C probably damaging Het
Pld2 T C 11: 70,555,677 L763P probably damaging Het
Pold1 A T 7: 44,538,060 F644L probably damaging Het
Prrc2b T C 2: 32,214,640 S1377P probably damaging Het
Rttn A G 18: 89,043,041 D1111G probably benign Het
Slc27a5 A G 7: 12,994,948 V130A probably damaging Het
Slfn8 T C 11: 83,017,196 R174G probably benign Het
Slitrk6 G A 14: 110,751,817 P153S probably benign Het
Sorcs3 T C 19: 48,654,072 I388T probably benign Het
Star A T 8: 25,812,815 T262S possibly damaging Het
Strn A T 17: 78,687,620 W2R probably damaging Het
Tnmd T C X: 133,862,952 S172P probably damaging Het
Togaram2 A G 17: 71,697,866 K305R probably benign Het
Trhde C A 10: 114,592,161 W410L probably damaging Het
Trim5 C T 7: 104,279,359 R125Q probably damaging Het
Unc45b C T 11: 82,940,181 probably benign Het
Vmn1r80 T A 7: 12,193,452 M163K probably benign Het
Wdr34 T C 2: 30,032,160 T430A probably benign Het
Wnk4 C A 11: 101,275,291 probably benign Het
Zfp277 T A 12: 40,315,803 I430F possibly damaging Het
Zfp566 A T 7: 30,077,830 C309S probably damaging Het
Zfp740 T G 15: 102,212,674 F141V possibly damaging Het
Zfp87 T A 13: 67,517,870 I158F probably damaging Het
Zswim3 C A 2: 164,821,115 A505D possibly damaging Het
Other mutations in Kdm5a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00540:Kdm5a APN 6 120385719 critical splice donor site probably null 0.00
IGL00706:Kdm5a APN 6 120406636 missense possibly damaging 0.44
IGL01361:Kdm5a APN 6 120399016 missense probably damaging 1.00
IGL01402:Kdm5a APN 6 120390679 nonsense probably null 0.00
IGL01924:Kdm5a APN 6 120394255 critical splice donor site probably null 0.00
IGL01935:Kdm5a APN 6 120408323 missense probably benign 0.02
IGL02472:Kdm5a APN 6 120406730 splice site probably benign
IGL02506:Kdm5a APN 6 120432149 missense probably damaging 0.99
IGL02604:Kdm5a APN 6 120431980 missense probably benign
IGL02633:Kdm5a APN 6 120364719 missense probably damaging 1.00
IGL02876:Kdm5a APN 6 120390644 unclassified probably benign
IGL03009:Kdm5a APN 6 120430086 missense probably damaging 0.98
IGL03027:Kdm5a APN 6 120374990 splice site probably null
IGL03164:Kdm5a APN 6 120439019 missense probably damaging 1.00
IGL03236:Kdm5a APN 6 120438988 missense probably damaging 0.98
IGL03276:Kdm5a APN 6 120402708 splice site probably benign
Augmented UTSW 6 120430016 intron probably benign
calla_lily UTSW 6 120405022 missense probably damaging 1.00
crocus UTSW 6 120399038 missense probably null 0.98
Magnolia UTSW 6 120398978 missense probably damaging 0.99
Selbst UTSW 6 120388105 nonsense probably null
R0320:Kdm5a UTSW 6 120389620 missense probably benign 0.19
R0462:Kdm5a UTSW 6 120402600 missense probably damaging 1.00
R0601:Kdm5a UTSW 6 120402671 missense possibly damaging 0.76
R0628:Kdm5a UTSW 6 120415239 missense probably damaging 1.00
R1024:Kdm5a UTSW 6 120399038 missense probably null 0.98
R2013:Kdm5a UTSW 6 120431990 missense probably benign 0.09
R2015:Kdm5a UTSW 6 120431990 missense probably benign 0.09
R2061:Kdm5a UTSW 6 120381617 missense probably benign
R2188:Kdm5a UTSW 6 120406640 missense possibly damaging 0.59
R3923:Kdm5a UTSW 6 120381664 missense probably benign 0.01
R4013:Kdm5a UTSW 6 120394106 missense probably damaging 1.00
R4016:Kdm5a UTSW 6 120394106 missense probably damaging 1.00
R4017:Kdm5a UTSW 6 120394106 missense probably damaging 1.00
R4030:Kdm5a UTSW 6 120405113 nonsense probably null
R4646:Kdm5a UTSW 6 120374977 missense possibly damaging 0.55
R4737:Kdm5a UTSW 6 120406015 intron probably benign
R4779:Kdm5a UTSW 6 120369099 unclassified probably benign
R4836:Kdm5a UTSW 6 120412402 missense probably damaging 1.00
R5129:Kdm5a UTSW 6 120405022 missense probably damaging 1.00
R5182:Kdm5a UTSW 6 120388105 nonsense probably null
R5183:Kdm5a UTSW 6 120430016 intron probably benign
R5572:Kdm5a UTSW 6 120412375 missense possibly damaging 0.69
R6110:Kdm5a UTSW 6 120412306 missense probably damaging 1.00
R6132:Kdm5a UTSW 6 120374931 missense probably damaging 1.00
R6198:Kdm5a UTSW 6 120438997 missense probably benign 0.37
R6246:Kdm5a UTSW 6 120431910 missense probably damaging 0.97
R6336:Kdm5a UTSW 6 120398978 missense probably damaging 0.99
R6343:Kdm5a UTSW 6 120382933 missense probably benign 0.01
R6612:Kdm5a UTSW 6 120430228 missense probably damaging 0.99
R6647:Kdm5a UTSW 6 120412461 missense probably benign 0.25
R7068:Kdm5a UTSW 6 120430215 missense probably benign 0.40
R7369:Kdm5a UTSW 6 120432004 missense possibly damaging 0.67
R7380:Kdm5a UTSW 6 120405918 missense probably benign 0.35
R7411:Kdm5a UTSW 6 120426815 missense probably damaging 1.00
Posted On2015-04-16