Incidental Mutation 'R6450:Kdm5d'
ID 519388
Institutional Source Beutler Lab
Gene Symbol Kdm5d
Ensembl Gene ENSMUSG00000056673
Gene Name lysine demethylase 5D
Synonyms Smcy, HY, Jarid1d
MMRRC Submission 044586-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.071) question?
Stock # R6450 (G1)
Quality Score 221.999
Status Validated
Chromosome Y
Chromosomal Location 897566-943813 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 927056 bp (GRCm39)
Zygosity Homozygous
Amino Acid Change Arginine to Leucine at position 598 (R598L)
Ref Sequence ENSEMBL: ENSMUSP00000140663 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000055032] [ENSMUST00000186696] [ENSMUST00000186726]
AlphaFold Q62240
Predicted Effect probably damaging
Transcript: ENSMUST00000055032
AA Change: R598L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: R598L

DomainStartEndE-ValueType
JmjN 13 54 3.45e-23 SMART
ARID 76 165 4.84e-36 SMART
BRIGHT 80 170 4.48e-38 SMART
PHD 325 371 8.56e-13 SMART
JmjC 467 633 2.52e-63 SMART
Pfam:zf-C5HC2 706 758 5.2e-18 PFAM
Pfam:PLU-1 771 1096 1.4e-89 PFAM
low complexity region 1147 1156 N/A INTRINSIC
low complexity region 1164 1181 N/A INTRINSIC
PHD 1182 1243 2.54e-6 SMART
coiled coil region 1290 1318 N/A INTRINSIC
low complexity region 1340 1351 N/A INTRINSIC
low complexity region 1395 1406 N/A INTRINSIC
low complexity region 1453 1459 N/A INTRINSIC
low complexity region 1525 1541 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000186696
AA Change: R598L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000140663
Gene: ENSMUSG00000056673
AA Change: R598L

DomainStartEndE-ValueType
JmjN 13 54 3.45e-23 SMART
ARID 76 165 4.84e-36 SMART
BRIGHT 80 170 4.48e-38 SMART
PHD 325 371 8.56e-13 SMART
JmjC 467 633 2.52e-63 SMART
low complexity region 675 689 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000186726
SMART Domains Protein: ENSMUSP00000140462
Gene: ENSMUSG00000056673

DomainStartEndE-ValueType
JmjN 13 54 1.4e-25 SMART
ARID 76 165 3.8e-40 SMART
BRIGHT 80 170 2.3e-40 SMART
Blast:ARID 175 260 1e-41 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000187296
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.8%
  • 10x: 98.5%
  • 20x: 95.1%
Validation Efficiency 97% (68/70)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein containing zinc finger domains. A short peptide derived from this protein is a minor histocompatibility antigen which can lead to graft rejection of male donor cells in a female recipient. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
Allele List at MGI
Other mutations in this stock
Total: 71 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca14 C G 7: 119,815,449 (GRCm39) N232K probably benign Het
Acaca T A 11: 84,171,294 (GRCm39) V5E probably damaging Het
Adam18 A T 8: 25,119,691 (GRCm39) D529E probably benign Het
Adgrb3 T C 1: 25,459,683 (GRCm39) T798A probably benign Het
Alyref T C 11: 120,486,872 (GRCm39) T130A probably benign Het
Arhgap24 A G 5: 103,044,990 (GRCm39) S591G probably benign Het
Carmil1 C T 13: 24,220,547 (GRCm39) G655E probably damaging Het
Cdc42bpg T A 19: 6,364,518 (GRCm39) probably null Het
Clec12a T A 6: 129,330,366 (GRCm39) L48H probably damaging Het
Coq2 C A 5: 100,809,770 (GRCm39) probably benign Het
Crb2 C A 2: 37,683,838 (GRCm39) F1113L possibly damaging Het
Ctla4 A T 1: 60,951,872 (GRCm39) M134L probably benign Het
Dnase1l1 C T X: 73,320,644 (GRCm39) probably null Homo
Dync2i1 A T 12: 116,210,347 (GRCm39) Y314* probably null Het
Efhb A G 17: 53,759,632 (GRCm39) V290A possibly damaging Het
Epha8 T C 4: 136,659,210 (GRCm39) N843S probably damaging Het
Eva1a A T 6: 82,069,086 (GRCm39) I138F probably damaging Het
Fat2 T A 11: 55,180,136 (GRCm39) I1402F probably damaging Het
Fat3 A T 9: 15,910,466 (GRCm39) H1845Q possibly damaging Het
Gimap8 T A 6: 48,633,385 (GRCm39) F401L probably benign Het
Gpr162 C T 6: 124,838,152 (GRCm39) R166Q possibly damaging Het
H2ac8 A G 13: 23,755,119 (GRCm39) V55A probably damaging Het
Hdac4 G A 1: 91,912,433 (GRCm39) P348S possibly damaging Het
Hmcn2 T C 2: 31,251,812 (GRCm39) V849A probably benign Het
Inpp5b T A 4: 124,686,045 (GRCm39) N696K probably damaging Het
Kidins220 T C 12: 25,107,190 (GRCm39) S1548P probably benign Het
Kif2b C A 11: 91,467,192 (GRCm39) V364L probably damaging Het
Kitl A G 10: 99,923,256 (GRCm39) M1V probably null Het
Klra9 G T 6: 130,155,995 (GRCm39) Y253* probably null Het
Map6 T C 7: 98,917,245 (GRCm39) I6T probably damaging Het
Mastl T C 2: 23,010,941 (GRCm39) T768A probably damaging Het
Mettl16 T C 11: 74,696,164 (GRCm39) V335A probably benign Het
Mpl T C 4: 118,305,897 (GRCm39) probably null Het
Myo5c C T 9: 75,193,860 (GRCm39) T1205I probably benign Het
Nav2 C A 7: 49,244,114 (GRCm39) L2114I probably damaging Het
Neb T A 2: 52,084,481 (GRCm39) K5330* probably null Het
Nfe2l1 C T 11: 96,718,161 (GRCm39) E125K possibly damaging Het
Onecut3 A G 10: 80,331,922 (GRCm39) K361E probably damaging Het
Or4f47 T A 2: 111,972,725 (GRCm39) L145* probably null Het
Osbpl6 A G 2: 76,395,174 (GRCm39) N370S possibly damaging Het
Otud4 T A 8: 80,399,626 (GRCm39) M780K probably benign Het
P2rx4 A G 5: 122,865,304 (GRCm39) T310A possibly damaging Het
Pcdha11 G T 18: 37,146,215 (GRCm39) D769Y probably damaging Het
Pcgf6 C T 19: 47,037,527 (GRCm39) R124H probably benign Het
Pibf1 T A 14: 99,374,646 (GRCm39) Y362N probably damaging Het
Ppm1g T C 5: 31,360,468 (GRCm39) E422G probably benign Het
Prmt8 T C 6: 127,709,606 (GRCm39) I85V possibly damaging Het
Prss27 A T 17: 24,263,988 (GRCm39) K225* probably null Het
Rai1 A T 11: 60,077,429 (GRCm39) T498S probably benign Het
Sbf2 C A 7: 110,062,070 (GRCm39) G23V probably damaging Het
Sdha C T 13: 74,482,412 (GRCm39) probably null Het
Sgo2a C T 1: 58,042,092 (GRCm39) Q140* probably null Het
Sh3rf3 A G 10: 58,819,966 (GRCm39) D259G probably damaging Het
Slc27a3 C A 3: 90,292,777 (GRCm39) D631Y probably damaging Het
Slc7a10 T C 7: 34,886,015 (GRCm39) S37P possibly damaging Het
Slco6d1 A G 1: 98,349,192 (GRCm39) T88A probably benign Het
Smad4 A T 18: 73,810,817 (GRCm39) S56T possibly damaging Het
Smarcd1 A G 15: 99,605,766 (GRCm39) I346V possibly damaging Het
Spast C T 17: 74,675,835 (GRCm39) P260S probably benign Het
Spata31f1e C A 4: 42,792,489 (GRCm39) G548W probably damaging Het
Sprr2i A T 3: 92,316,017 (GRCm39) probably benign Het
Sptbn5 A G 2: 119,877,616 (GRCm39) probably benign Het
Taar9 A T 10: 23,985,138 (GRCm39) Y99N probably damaging Het
Trappc10 A T 10: 78,045,284 (GRCm39) M468K possibly damaging Het
Trim66 T C 7: 109,059,945 (GRCm39) R814G probably benign Het
Tspan31 A G 10: 126,904,227 (GRCm39) C157R probably damaging Het
Vmn2r90 A G 17: 17,953,498 (GRCm39) D554G possibly damaging Het
Vmn2r91 A T 17: 18,305,527 (GRCm39) D70V probably damaging Het
Wdfy4 C T 14: 32,830,649 (GRCm39) G928R probably damaging Het
Zfp346 G T 13: 55,261,517 (GRCm39) K102N probably damaging Het
Zmym4 G A 4: 126,789,099 (GRCm39) P1002S probably damaging Het
Other mutations in Kdm5d
AlleleSourceChrCoordTypePredicted EffectPPH Score
R0013:Kdm5d UTSW Y 941,715 (GRCm39) missense probably benign 0.37
R0013:Kdm5d UTSW Y 941,715 (GRCm39) missense probably benign 0.37
R0426:Kdm5d UTSW Y 942,437 (GRCm39) splice site probably benign
R0486:Kdm5d UTSW Y 927,107 (GRCm39) missense probably damaging 1.00
R0620:Kdm5d UTSW Y 927,330 (GRCm39) missense probably damaging 0.98
R0781:Kdm5d UTSW Y 910,539 (GRCm39) missense probably damaging 1.00
R1015:Kdm5d UTSW Y 941,687 (GRCm39) missense possibly damaging 0.95
R1110:Kdm5d UTSW Y 910,539 (GRCm39) missense probably damaging 1.00
R1163:Kdm5d UTSW Y 898,029 (GRCm39) missense probably benign 0.18
R1203:Kdm5d UTSW Y 941,011 (GRCm39) missense probably damaging 1.00
R1238:Kdm5d UTSW Y 941,282 (GRCm39) missense probably damaging 1.00
R1723:Kdm5d UTSW Y 927,753 (GRCm39) missense probably damaging 1.00
R1842:Kdm5d UTSW Y 927,798 (GRCm39) missense probably damaging 1.00
R1885:Kdm5d UTSW Y 940,781 (GRCm39) splice site probably null
R2131:Kdm5d UTSW Y 941,483 (GRCm39) missense probably benign 0.02
R2571:Kdm5d UTSW Y 940,932 (GRCm39) missense probably benign 0.11
R2931:Kdm5d UTSW Y 942,992 (GRCm39) missense probably benign 0.18
R3123:Kdm5d UTSW Y 900,558 (GRCm39) missense possibly damaging 0.63
R3919:Kdm5d UTSW Y 939,914 (GRCm39) missense probably damaging 1.00
R4018:Kdm5d UTSW Y 910,441 (GRCm39) splice site probably benign
R4031:Kdm5d UTSW Y 916,910 (GRCm39) missense probably damaging 1.00
R4403:Kdm5d UTSW Y 899,830 (GRCm39) missense probably damaging 1.00
R4571:Kdm5d UTSW Y 927,110 (GRCm39) missense probably damaging 1.00
R4583:Kdm5d UTSW Y 914,134 (GRCm39) missense probably damaging 1.00
R4962:Kdm5d UTSW Y 940,624 (GRCm39) missense probably damaging 1.00
R5105:Kdm5d UTSW Y 941,752 (GRCm39) missense probably benign 0.00
R5249:Kdm5d UTSW Y 916,692 (GRCm39) missense probably damaging 1.00
R5367:Kdm5d UTSW Y 941,645 (GRCm39) missense probably benign 0.05
R5373:Kdm5d UTSW Y 927,995 (GRCm39) missense probably benign 0.09
R5374:Kdm5d UTSW Y 927,995 (GRCm39) missense probably benign 0.09
R5876:Kdm5d UTSW Y 900,525 (GRCm39) missense probably damaging 1.00
R5909:Kdm5d UTSW Y 941,306 (GRCm39) missense probably benign 0.01
R6014:Kdm5d UTSW Y 921,528 (GRCm39) missense probably benign 0.45
R6109:Kdm5d UTSW Y 921,501 (GRCm39) missense probably damaging 1.00
R6251:Kdm5d UTSW Y 921,693 (GRCm39) missense probably damaging 1.00
R6349:Kdm5d UTSW Y 916,847 (GRCm39) missense probably damaging 0.99
R6595:Kdm5d UTSW Y 939,829 (GRCm39) missense probably benign
R6628:Kdm5d UTSW Y 900,525 (GRCm39) missense probably damaging 1.00
R6745:Kdm5d UTSW Y 927,112 (GRCm39) missense probably benign 0.28
R6867:Kdm5d UTSW Y 927,425 (GRCm39) missense probably benign
R6963:Kdm5d UTSW Y 937,975 (GRCm39) missense probably benign 0.01
R7163:Kdm5d UTSW Y 899,940 (GRCm39) missense probably damaging 1.00
R7374:Kdm5d UTSW Y 941,491 (GRCm39) missense probably benign 0.41
R7483:Kdm5d UTSW Y 914,044 (GRCm39) missense possibly damaging 0.50
R7501:Kdm5d UTSW Y 941,488 (GRCm39) missense probably damaging 1.00
R7815:Kdm5d UTSW Y 940,702 (GRCm39) missense probably damaging 1.00
R7835:Kdm5d UTSW Y 900,558 (GRCm39) missense possibly damaging 0.63
R8057:Kdm5d UTSW Y 927,355 (GRCm39) missense possibly damaging 0.48
R8080:Kdm5d UTSW Y 910,742 (GRCm39) missense probably benign 0.01
R8130:Kdm5d UTSW Y 940,658 (GRCm39) missense possibly damaging 0.75
R8213:Kdm5d UTSW Y 941,515 (GRCm39) missense probably damaging 1.00
R8261:Kdm5d UTSW Y 936,929 (GRCm39) missense probably damaging 0.99
R8344:Kdm5d UTSW Y 942,477 (GRCm39) missense probably benign 0.05
R8348:Kdm5d UTSW Y 914,056 (GRCm39) missense probably benign 0.00
R8445:Kdm5d UTSW Y 916,874 (GRCm39) missense probably damaging 1.00
R8448:Kdm5d UTSW Y 914,056 (GRCm39) missense probably benign 0.00
R8754:Kdm5d UTSW Y 941,594 (GRCm39) missense probably damaging 1.00
R9203:Kdm5d UTSW Y 940,981 (GRCm39) missense probably damaging 0.99
R9259:Kdm5d UTSW Y 942,640 (GRCm39) missense possibly damaging 0.84
R9541:Kdm5d UTSW Y 910,801 (GRCm39) missense probably damaging 1.00
R9668:Kdm5d UTSW Y 943,075 (GRCm39) missense possibly damaging 0.73
Predicted Primers PCR Primer
(F):5'- TCTCGCAACAATAGTCTTTTACTTCTA -3'
(R):5'- TCGGCGGTAGTGTTCAATAC -3'

Sequencing Primer
(F):5'- GTCCATAAATGAATTTGGTGGTA -3'
(R):5'- TACACTGGCGTCCAACAGGTAG -3'
Posted On 2018-05-24