Incidental Mutation 'IGL02633:Kdm5a'
ID 301402
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 # IGL02633
Quality Score
Status
Chromosome 6
Chromosomal Location 120341085-120421535 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 120341680 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 36 (I36V)
Ref Sequence ENSEMBL: ENSMUSP00000145021 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000005108] [ENSMUST00000127146] [ENSMUST00000132009] [ENSMUST00000135802] [ENSMUST00000146667]
AlphaFold Q3UXZ9
Predicted Effect probably damaging
Transcript: ENSMUST00000005108
AA Change: I36V

PolyPhen 2 Score 0.968 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: I36V

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 benign
Transcript: ENSMUST00000127146
SMART Domains Protein: ENSMUSP00000120896
Gene: ENSMUSG00000030177

DomainStartEndE-ValueType
coiled coil region 39 102 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000132009
AA Change: I36V

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000145375
Gene: ENSMUSG00000030180
AA Change: I36V

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 damaging
Transcript: ENSMUST00000135802
AA Change: I36V

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000145021
Gene: ENSMUSG00000030180
AA Change: I36V

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: ENSMUST00000146667
SMART Domains Protein: ENSMUSP00000114664
Gene: ENSMUSG00000030177

DomainStartEndE-ValueType
coiled coil region 57 91 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000152293
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: 37 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abitram T C 4: 56,806,131 (GRCm39) V181A possibly damaging Het
Aff4 T C 11: 53,300,198 (GRCm39) probably benign Het
Ap1g2 T C 14: 55,338,104 (GRCm39) probably null Het
Aspn A T 13: 49,705,363 (GRCm39) Y75F possibly damaging Het
Atm G A 9: 53,359,453 (GRCm39) T2783I probably damaging Het
Cacnb1 A T 11: 97,913,199 (GRCm39) I18N probably damaging Het
Casr T C 16: 36,336,017 (GRCm39) I97M probably damaging Het
Cnga2 T A X: 71,048,655 (GRCm39) probably benign Het
Coasy T A 11: 100,976,147 (GRCm39) L425Q probably damaging Het
Cps1 A G 1: 67,162,396 (GRCm39) T25A probably benign Het
Dnah1 T C 14: 31,006,772 (GRCm39) Y2181C probably benign Het
Efna3 A C 3: 89,222,749 (GRCm39) S230A probably damaging Het
Eng A G 2: 32,563,286 (GRCm39) I281V probably damaging Het
Erlec1 T A 11: 30,898,430 (GRCm39) R14* probably null Het
Gbp9 C T 5: 105,231,431 (GRCm39) probably benign Het
Gzmg T C 14: 56,394,160 (GRCm39) M245V probably damaging Het
Krt87 A G 15: 101,389,095 (GRCm39) V79A probably damaging Het
Limd1 A T 9: 123,308,987 (GRCm39) probably benign Het
Lmo4 T C 3: 143,899,683 (GRCm39) S155G probably benign Het
Mrpl44 G A 1: 79,753,862 (GRCm39) V5I probably benign Het
Mrpl49 T C 19: 6,104,931 (GRCm39) T146A possibly damaging Het
Mrpl58 T C 11: 115,301,457 (GRCm39) probably benign Het
Nab1 C T 1: 52,529,292 (GRCm39) V202M probably damaging Het
Nav3 T A 10: 109,527,997 (GRCm39) M2229L probably benign Het
Notch2 C T 3: 98,024,013 (GRCm39) probably benign Het
Nub1 A G 5: 24,897,931 (GRCm39) I106V probably benign Het
Prom1 A T 5: 44,172,117 (GRCm39) S595T probably benign Het
Rbfox1 T A 16: 7,110,078 (GRCm39) S165R probably damaging Het
Sipa1l2 G A 8: 126,174,507 (GRCm39) T1257I probably damaging Het
Smarcc2 T C 10: 128,305,556 (GRCm39) S327P probably damaging Het
Tdpoz1 T C 3: 93,578,056 (GRCm39) M243V probably benign Het
Ttn G T 2: 76,549,289 (GRCm39) T23469K probably damaging Het
Ube2u T C 4: 100,339,971 (GRCm39) probably benign Het
Umodl1 T C 17: 31,208,462 (GRCm39) Y836H probably damaging Het
Vmn2r45 A G 7: 8,488,728 (GRCm39) Y101H probably benign Het
Vps13a T A 19: 16,697,772 (GRCm39) Q781L possibly damaging Het
Vwce G A 19: 10,625,858 (GRCm39) V457M 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
IGL01402:Kdm5a APN 6 120,367,640 (GRCm39) nonsense probably null 0.00
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
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 2015-04-16