Incidental Mutation 'R0013:Kdm5d'
ID 32675
Institutional Source Beutler Lab
Gene Symbol Kdm5d
Ensembl Gene ENSMUSG00000056673
Gene Name lysine demethylase 5D
Synonyms Smcy, HY, Jarid1d
MMRRC Submission 038308-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.071) question?
Stock # R0013 (G1)
Quality Score 225
Status Validated
Chromosome Y
Chromosomal Location 897566-943813 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 941715 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Asparagine at position 1305 (K1305N)
Ref Sequence ENSEMBL: ENSMUSP00000061095 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000055032] [ENSMUST00000186696] [ENSMUST00000186726]
AlphaFold Q62240
Predicted Effect probably benign
Transcript: ENSMUST00000055032
AA Change: K1305N

PolyPhen 2 Score 0.366 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: K1305N

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 benign
Transcript: ENSMUST00000186696
SMART Domains Protein: ENSMUSP00000140663
Gene: ENSMUSG00000056673

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000189955
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 94.8%
Validation Efficiency 94% (79/84)
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: 79 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610028H24Rik A G 10: 76,293,346 (GRCm39) M156V probably benign Het
Adnp2 A T 18: 80,172,960 (GRCm39) V483D probably damaging Het
Aff1 G T 5: 103,976,350 (GRCm39) E491* probably null Het
Agl A T 3: 116,570,257 (GRCm39) C911* probably null Het
Akt2 A G 7: 27,335,483 (GRCm39) D284G probably damaging Het
Alox15 A G 11: 70,240,461 (GRCm39) M240T possibly damaging Het
Antxr2 A G 5: 98,127,844 (GRCm39) V229A probably damaging Het
Arap2 G A 5: 62,840,827 (GRCm39) L680F probably damaging Het
Btaf1 A G 19: 36,935,773 (GRCm39) T188A probably benign Het
Btnl6 G A 17: 34,734,505 (GRCm39) Q86* probably null Het
C2cd3 T A 7: 100,065,269 (GRCm39) L685H probably damaging Het
Cdh23 T C 10: 60,248,952 (GRCm39) T878A possibly damaging Het
Clec4b2 T C 6: 123,179,108 (GRCm39) Y137H probably damaging Het
Dchs1 T A 7: 105,405,043 (GRCm39) T2500S possibly damaging Het
Def6 A G 17: 28,436,066 (GRCm39) Y75C probably damaging Het
Dhx33 A T 11: 70,884,461 (GRCm39) F448L probably damaging Het
Dner C T 1: 84,472,614 (GRCm39) probably benign Het
Dnmbp G A 19: 43,890,670 (GRCm39) P366S probably benign Het
Eif4g3 T C 4: 137,903,159 (GRCm39) C1160R possibly damaging Het
Elmod1 G A 9: 53,820,185 (GRCm39) probably benign Het
Faah C A 4: 115,861,588 (GRCm39) L305F probably damaging Het
Flt1 A G 5: 147,507,824 (GRCm39) probably benign Het
Fyco1 A T 9: 123,651,471 (GRCm39) N1196K probably benign Het
Galnt18 T C 7: 111,153,664 (GRCm39) N320S probably damaging Het
Garin3 A G 11: 46,297,631 (GRCm39) T312A unknown Het
Glp2r C A 11: 67,600,538 (GRCm39) G437V possibly damaging Het
Gm4884 T C 7: 40,693,716 (GRCm39) S562P probably damaging Het
Gm9936 A G 5: 114,995,408 (GRCm39) probably benign Het
Gpn2 C A 4: 133,312,103 (GRCm39) P112T probably damaging Het
Grm4 A G 17: 27,650,549 (GRCm39) Y816H probably benign Het
Helz2 A T 2: 180,882,752 (GRCm39) S14T probably benign Het
Htt T C 5: 34,977,448 (GRCm39) L778P probably benign Het
Il11ra1 T C 4: 41,765,060 (GRCm39) S129P probably damaging Het
Ints11 T C 4: 155,971,625 (GRCm39) F315S probably damaging Het
Itga11 A T 9: 62,683,895 (GRCm39) N1059Y possibly damaging Het
Jak3 A G 8: 72,136,971 (GRCm39) S716G probably damaging Het
Kcns1 G T 2: 164,010,563 (GRCm39) D65E probably benign Het
Kif26a G T 12: 112,144,314 (GRCm39) V1523L probably benign Het
Mboat7 A G 7: 3,686,821 (GRCm39) S340P probably damaging Het
Mctp2 T C 7: 71,879,156 (GRCm39) I234V probably benign Het
Mex3c G A 18: 73,723,622 (GRCm39) A572T probably benign Het
Mpp3 C A 11: 101,896,251 (GRCm39) R424L probably benign Het
Mroh4 T A 15: 74,480,086 (GRCm39) probably benign Het
Myo9a A T 9: 59,767,489 (GRCm39) probably benign Het
Myog T A 1: 134,217,973 (GRCm39) H60Q probably damaging Het
Nlrp9a T A 7: 26,270,650 (GRCm39) probably null Het
Notch1 A G 2: 26,363,830 (GRCm39) V868A possibly damaging Het
Or10g9b A T 9: 39,917,651 (GRCm39) I198N probably damaging Het
Or1j20 A G 2: 36,760,172 (GRCm39) N198S probably damaging Het
Or1p1 T A 11: 74,179,877 (GRCm39) I135N possibly damaging Het
Or5d18 T C 2: 87,864,610 (GRCm39) Y291C possibly damaging Het
Pink1 T C 4: 138,044,712 (GRCm39) T342A probably benign Het
Plb1 T A 5: 32,506,959 (GRCm39) probably benign Het
Plec T C 15: 76,062,446 (GRCm39) D2524G probably damaging Het
Plekhg4 G T 8: 106,102,028 (GRCm39) E6* probably null Het
Polq T C 16: 36,882,201 (GRCm39) F1455S possibly damaging Het
Ppm1e A G 11: 87,139,884 (GRCm39) probably benign Het
Prkaca G A 8: 84,714,932 (GRCm39) M119I possibly damaging Het
Prss46 G T 9: 110,679,123 (GRCm39) S108I probably damaging Het
Ptma C T 1: 86,457,498 (GRCm39) probably benign Het
Rab11fip4 C T 11: 79,580,479 (GRCm39) T437M probably benign Het
Rngtt T A 4: 33,379,409 (GRCm39) M437K probably benign Het
Rrn3 T A 16: 13,630,977 (GRCm39) D604E possibly damaging Het
Scn4a A G 11: 106,239,231 (GRCm39) probably benign Het
Sis A G 3: 72,817,809 (GRCm39) L1468P possibly damaging Het
Slit3 A G 11: 35,598,745 (GRCm39) M1450V probably benign Het
Smg5 T C 3: 88,256,540 (GRCm39) S269P probably benign Het
Sntg1 T C 1: 8,533,686 (GRCm39) T323A probably damaging Het
Son C T 16: 91,448,550 (GRCm39) T37I probably damaging Het
Stk17b T C 1: 53,803,291 (GRCm39) I41M probably benign Het
Tgm5 T A 2: 120,907,363 (GRCm39) Y120F probably damaging Het
Tppp A G 13: 74,169,479 (GRCm39) K73R possibly damaging Het
Ttn C A 2: 76,569,502 (GRCm39) K27130N probably damaging Het
Ttn C T 2: 76,738,096 (GRCm39) V4148I probably benign Het
Tut4 T A 4: 108,388,152 (GRCm39) probably benign Het
Uba7 A T 9: 107,855,448 (GRCm39) Y375F probably damaging Het
Ugcg T C 4: 59,213,931 (GRCm39) L171P possibly damaging Het
Vsig2 T C 9: 37,453,872 (GRCm39) probably benign Het
Zfp839 T A 12: 110,834,820 (GRCm39) S692T possibly damaging Het
Other mutations in Kdm5d
AlleleSourceChrCoordTypePredicted EffectPPH Score
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
R6450:Kdm5d UTSW Y 927,056 (GRCm39) missense probably damaging 1.00
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'- CCTGGAGACCATCTTGTCATTGCTG -3'
(R):5'- TTGCTTACTCCCCACAGAGAGCAC -3'

Sequencing Primer
(F):5'- TGCTGGTAGGACTACAGAGACTG -3'
(R):5'- caaccttcctaatgctgtaacc -3'
Posted On 2013-05-09