Incidental Mutation 'IGL01402:Kdm5a'
ID 79672
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Kdm5a
Ensembl Gene ENSMUSG00000030180
Gene Name lysine demethylase 5A
Synonyms Rbbp2, Jarid1a, RBP2
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # IGL01402
Quality Score
Status
Chromosome 6
Chromosomal Location 120341085-120421535 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) T to A at 120367640 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Stop codon at position 445 (L445*)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005108] [ENSMUST00000132009] [ENSMUST00000135802] [ENSMUST00000203373]
AlphaFold Q3UXZ9
Predicted Effect probably null
Transcript: ENSMUST00000005108
AA Change: L445*
SMART Domains Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: L445*

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 probably null
Transcript: ENSMUST00000100996
AA Change: L445*
SMART Domains Protein: ENSMUSP00000098558
Gene: ENSMUSG00000030180
AA Change: L445*

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 676 728 3.6e-17 PFAM
Pfam:PLU-1 741 1072 5e-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
PHD 1614 1659 1.27e-6 SMART
low complexity region 1662 1674 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000132009
AA Change: L445*
SMART Domains Protein: ENSMUSP00000145375
Gene: ENSMUSG00000030180
AA Change: L445*

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 null
Transcript: ENSMUST00000135802
AA Change: L445*
SMART Domains Protein: ENSMUSP00000145021
Gene: ENSMUSG00000030180
AA Change: L445*

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
Predicted Effect probably benign
Transcript: ENSMUST00000203373
SMART Domains Protein: ENSMUSP00000144720
Gene: ENSMUSG00000030180

DomainStartEndE-ValueType
BRIGHT 1 53 8.4e-4 SMART
Blast:JmjC 58 153 3e-56 BLAST
PDB:2E6R|A 121 152 4e-9 PDB
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: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921524L21Rik T C 18: 6,638,653 (GRCm39) S351P possibly damaging Het
Abca2 T C 2: 25,332,015 (GRCm39) S1376P probably damaging Het
Ablim3 A G 18: 62,004,754 (GRCm39) Y12H probably damaging Het
Akr1b7 A G 6: 34,398,052 (GRCm39) R294G possibly damaging Het
Aldh3b1 A C 19: 3,971,205 (GRCm39) V153G probably benign Het
Alk A T 17: 72,181,173 (GRCm39) H1372Q probably damaging Het
Ano9 A C 7: 140,681,955 (GRCm39) Y731* probably null Het
Apol11b G A 15: 77,522,219 (GRCm39) T26M probably damaging Het
Asl T C 5: 130,048,645 (GRCm39) E43G probably damaging Het
Cd4 G A 6: 124,856,341 (GRCm39) T50I probably benign Het
Cfap43 T C 19: 47,784,105 (GRCm39) D476G probably benign Het
Cpa1 A G 6: 30,645,275 (GRCm39) H417R possibly damaging Het
Cpeb3 T C 19: 37,065,948 (GRCm39) D407G probably benign Het
Dcaf15 A T 8: 84,825,026 (GRCm39) C469S probably damaging Het
Dpy19l4 C A 4: 11,273,006 (GRCm39) probably null Het
E4f1 A T 17: 24,663,208 (GRCm39) L699Q probably damaging Het
Eif4g2 A G 7: 110,676,234 (GRCm39) F349S possibly damaging Het
Ermap T C 4: 119,044,355 (GRCm39) Y147C probably damaging Het
Frk A C 10: 34,423,381 (GRCm39) E153A probably damaging Het
Fubp3 G A 2: 31,494,733 (GRCm39) probably null Het
Gdi2 A G 13: 3,614,611 (GRCm39) T319A probably benign Het
Gjc3 A G 5: 137,956,120 (GRCm39) F55S probably damaging Het
Gm10762 C T 2: 128,809,005 (GRCm39) probably benign Het
Got1 A G 19: 43,493,048 (GRCm39) I291T possibly damaging Het
Gpr179 C A 11: 97,229,012 (GRCm39) G1048* probably null Het
Hectd3 G T 4: 116,853,262 (GRCm39) R163L probably damaging Het
Hectd4 T C 5: 121,477,480 (GRCm39) probably benign Het
Ifnb1 T C 4: 88,440,480 (GRCm39) R178G probably benign Het
Ino80 T A 2: 119,287,199 (GRCm39) D56V possibly damaging Het
Kctd1 T A 18: 15,102,610 (GRCm39) Q857L probably damaging Het
Lins1 G A 7: 66,363,676 (GRCm39) V524I probably damaging Het
Lrp1 A T 10: 127,430,901 (GRCm39) Y383N probably damaging Het
Malrd1 G A 2: 16,106,768 (GRCm39) probably null Het
Mgam A C 6: 40,621,879 (GRCm39) K84Q probably benign Het
Mlh3 A T 12: 85,314,703 (GRCm39) F494L probably benign Het
Mpped1 T C 15: 83,676,414 (GRCm39) F60S possibly damaging Het
Myo1e A G 9: 70,245,048 (GRCm39) Y382C probably benign Het
Ncor1 C A 11: 62,231,300 (GRCm39) V836F probably damaging Het
Nktr G A 9: 121,570,218 (GRCm39) probably null Het
Or10al4 A G 17: 38,037,193 (GRCm39) T93A probably benign Het
Or4d5 A G 9: 40,012,558 (GRCm39) I76T probably benign Het
Or5k8 G A 16: 58,644,958 (GRCm39) T38I probably damaging Het
Rnf144a T A 12: 26,377,300 (GRCm39) Y93F probably benign Het
Rubcn G A 16: 32,647,666 (GRCm39) T636M probably damaging Het
Scn5a A C 9: 119,315,536 (GRCm39) L1724R probably damaging Het
Sel1l A G 12: 91,808,607 (GRCm39) S45P possibly damaging Het
Serpina3k A G 12: 104,306,882 (GRCm39) D38G probably benign Het
Sh3bgr A C 16: 96,007,690 (GRCm39) K18N probably damaging Het
Slc28a2 T G 2: 122,282,538 (GRCm39) I287M probably damaging Het
St8sia6 T C 2: 13,670,318 (GRCm39) N214S probably damaging Het
Syt11 A G 3: 88,669,523 (GRCm39) I123T probably benign Het
Tcerg1l A T 7: 137,861,568 (GRCm39) I387N probably damaging Het
Tfg C A 16: 56,514,856 (GRCm39) probably benign Het
Tgm4 A G 9: 122,880,519 (GRCm39) K307E possibly damaging Het
Tmem177 T C 1: 119,837,791 (GRCm39) D296G probably damaging Het
Tmem270 C T 5: 134,930,763 (GRCm39) probably benign Het
Tnrc6b G T 15: 80,764,745 (GRCm39) G749V possibly damaging Het
Trp63 C A 16: 25,639,135 (GRCm39) probably benign Het
Ugt1a8 T C 1: 88,015,617 (GRCm39) L10P probably benign Het
Vmn2r107 A T 17: 20,596,009 (GRCm39) K854M probably damaging Het
Vmn2r45 T C 7: 8,484,467 (GRCm39) N446S probably damaging Het
Vps13c A T 9: 67,820,486 (GRCm39) probably null Het
Wdr91 G A 6: 34,865,998 (GRCm39) P518L probably benign Het
Yap1 G A 9: 7,934,742 (GRCm39) probably benign Het
Zfp282 A C 6: 47,874,770 (GRCm39) D325A probably damaging Het
Other mutations in Kdm5a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00540:Kdm5a APN 6 120,362,680 (GRCm39) critical splice donor site probably null 0.00
IGL00706:Kdm5a APN 6 120,383,597 (GRCm39) missense possibly damaging 0.44
IGL01361:Kdm5a APN 6 120,375,977 (GRCm39) missense probably damaging 1.00
IGL01924:Kdm5a APN 6 120,371,216 (GRCm39) critical splice donor site probably null 0.00
IGL01935:Kdm5a APN 6 120,385,284 (GRCm39) missense probably benign 0.02
IGL02165:Kdm5a APN 6 120,392,251 (GRCm39) missense probably damaging 1.00
IGL02472:Kdm5a APN 6 120,383,691 (GRCm39) splice site probably benign
IGL02506:Kdm5a APN 6 120,409,110 (GRCm39) missense probably damaging 0.99
IGL02604:Kdm5a APN 6 120,408,941 (GRCm39) missense probably benign
IGL02633:Kdm5a APN 6 120,341,680 (GRCm39) missense probably damaging 1.00
IGL02876:Kdm5a APN 6 120,367,605 (GRCm39) unclassified probably benign
IGL03009:Kdm5a APN 6 120,407,047 (GRCm39) missense probably damaging 0.98
IGL03027:Kdm5a APN 6 120,351,951 (GRCm39) splice site probably null
IGL03164:Kdm5a APN 6 120,415,980 (GRCm39) missense probably damaging 1.00
IGL03236:Kdm5a APN 6 120,415,949 (GRCm39) missense probably damaging 0.98
IGL03276:Kdm5a APN 6 120,379,669 (GRCm39) splice site probably benign
Anastasia UTSW 6 120,407,192 (GRCm39) nonsense probably null
Augmented UTSW 6 120,406,977 (GRCm39) intron probably benign
Calla_lily UTSW 6 120,381,983 (GRCm39) missense probably damaging 1.00
crocus UTSW 6 120,375,999 (GRCm39) missense probably null 0.98
Magnolia UTSW 6 120,375,939 (GRCm39) missense probably damaging 0.99
Saffron UTSW 6 120,366,581 (GRCm39) missense probably benign 0.19
Selbst UTSW 6 120,365,066 (GRCm39) nonsense probably null
R0320:Kdm5a UTSW 6 120,366,581 (GRCm39) missense probably benign 0.19
R0462:Kdm5a UTSW 6 120,379,561 (GRCm39) missense probably damaging 1.00
R0601:Kdm5a UTSW 6 120,379,632 (GRCm39) missense possibly damaging 0.76
R0628:Kdm5a UTSW 6 120,392,200 (GRCm39) missense probably damaging 1.00
R1024:Kdm5a UTSW 6 120,375,999 (GRCm39) missense probably null 0.98
R2013:Kdm5a UTSW 6 120,408,951 (GRCm39) missense probably benign 0.09
R2015:Kdm5a UTSW 6 120,408,951 (GRCm39) missense probably benign 0.09
R2061:Kdm5a UTSW 6 120,358,578 (GRCm39) missense probably benign
R2188:Kdm5a UTSW 6 120,383,601 (GRCm39) missense possibly damaging 0.59
R3923:Kdm5a UTSW 6 120,358,625 (GRCm39) missense probably benign 0.01
R4013:Kdm5a UTSW 6 120,371,067 (GRCm39) missense probably damaging 1.00
R4016:Kdm5a UTSW 6 120,371,067 (GRCm39) missense probably damaging 1.00
R4017:Kdm5a UTSW 6 120,371,067 (GRCm39) missense probably damaging 1.00
R4030:Kdm5a UTSW 6 120,382,074 (GRCm39) nonsense probably null
R4646:Kdm5a UTSW 6 120,351,938 (GRCm39) missense possibly damaging 0.55
R4737:Kdm5a UTSW 6 120,382,976 (GRCm39) intron probably benign
R4779:Kdm5a UTSW 6 120,346,060 (GRCm39) unclassified probably benign
R4836:Kdm5a UTSW 6 120,389,363 (GRCm39) missense probably damaging 1.00
R5129:Kdm5a UTSW 6 120,381,983 (GRCm39) missense probably damaging 1.00
R5182:Kdm5a UTSW 6 120,365,066 (GRCm39) nonsense probably null
R5183:Kdm5a UTSW 6 120,406,977 (GRCm39) intron probably benign
R5572:Kdm5a UTSW 6 120,389,336 (GRCm39) missense possibly damaging 0.69
R6110:Kdm5a UTSW 6 120,389,267 (GRCm39) missense probably damaging 1.00
R6132:Kdm5a UTSW 6 120,351,892 (GRCm39) missense probably damaging 1.00
R6198:Kdm5a UTSW 6 120,415,958 (GRCm39) missense probably benign 0.37
R6246:Kdm5a UTSW 6 120,408,871 (GRCm39) missense probably damaging 0.97
R6336:Kdm5a UTSW 6 120,375,939 (GRCm39) missense probably damaging 0.99
R6343:Kdm5a UTSW 6 120,359,894 (GRCm39) missense probably benign 0.01
R6612:Kdm5a UTSW 6 120,407,189 (GRCm39) missense probably damaging 0.99
R6647:Kdm5a UTSW 6 120,389,422 (GRCm39) missense probably benign 0.25
R7068:Kdm5a UTSW 6 120,407,176 (GRCm39) missense probably benign 0.40
R7369:Kdm5a UTSW 6 120,408,965 (GRCm39) missense possibly damaging 0.67
R7380:Kdm5a UTSW 6 120,382,879 (GRCm39) missense probably benign 0.35
R7411:Kdm5a UTSW 6 120,403,776 (GRCm39) missense probably damaging 1.00
R7521:Kdm5a UTSW 6 120,409,148 (GRCm39) nonsense probably null
R7570:Kdm5a UTSW 6 120,404,803 (GRCm39) missense probably damaging 0.99
R7647:Kdm5a UTSW 6 120,404,747 (GRCm39) missense probably benign 0.01
R7704:Kdm5a UTSW 6 120,404,025 (GRCm39) missense probably damaging 1.00
R7796:Kdm5a UTSW 6 120,367,724 (GRCm39) missense probably damaging 1.00
R7875:Kdm5a UTSW 6 120,375,979 (GRCm39) nonsense probably null
R8265:Kdm5a UTSW 6 120,383,557 (GRCm39) missense possibly damaging 0.72
R8297:Kdm5a UTSW 6 120,358,516 (GRCm39) missense probably benign 0.00
R8336:Kdm5a UTSW 6 120,396,407 (GRCm39) missense probably benign 0.00
R8471:Kdm5a UTSW 6 120,407,192 (GRCm39) nonsense probably null
R8872:Kdm5a UTSW 6 120,365,101 (GRCm39) missense probably damaging 1.00
R8890:Kdm5a UTSW 6 120,366,624 (GRCm39) missense probably damaging 1.00
R9028:Kdm5a UTSW 6 120,416,092 (GRCm39) missense probably benign
R9064:Kdm5a UTSW 6 120,403,869 (GRCm39) small deletion probably benign
R9114:Kdm5a UTSW 6 120,382,887 (GRCm39) nonsense probably null
R9316:Kdm5a UTSW 6 120,381,973 (GRCm39) missense probably damaging 1.00
R9353:Kdm5a UTSW 6 120,404,730 (GRCm39) missense probably benign 0.01
R9412:Kdm5a UTSW 6 120,365,991 (GRCm39) missense probably damaging 1.00
R9416:Kdm5a UTSW 6 120,365,056 (GRCm39) missense probably damaging 1.00
R9431:Kdm5a UTSW 6 120,392,253 (GRCm39) missense probably damaging 1.00
R9711:Kdm5a UTSW 6 120,367,658 (GRCm39) missense probably damaging 1.00
Posted On 2013-11-05