Incidental Mutation 'R9203:Kdm5d'
ID 698355
Institutional Source Beutler Lab
Gene Symbol Kdm5d
Ensembl Gene ENSMUSG00000056673
Gene Name lysine demethylase 5D
Synonyms Smcy, HY, Jarid1d
MMRRC Submission
Accession Numbers
Essential gene? Probably non essential (E-score: 0.071) question?
Stock # R9203 (G1)
Quality Score 221.999
Status Not validated
Chromosome Y
Chromosomal Location 897566-943813 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 940981 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 1122 (Y1122C)
Ref Sequence ENSEMBL: ENSMUSP00000061095 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000055032] [ENSMUST00000186696] [ENSMUST00000186726]
AlphaFold Q62240
Predicted Effect probably damaging
Transcript: ENSMUST00000055032
AA Change: Y1122C

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: Y1122C

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.3%
Validation Efficiency
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: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Anapc1 T C 2: 128,465,422 (GRCm39) H1686R possibly damaging Het
Ankrd33b A G 15: 31,298,028 (GRCm39) M243T probably benign Het
Appl1 G T 14: 26,682,970 (GRCm39) S104* probably null Het
Appl2 A T 10: 83,476,879 (GRCm39) Y48* probably null Het
Cacna1d T C 14: 29,773,669 (GRCm39) N1694S probably benign Het
Cc2d2a G T 5: 43,891,179 (GRCm39) D1372Y probably benign Het
Cdh4 C T 2: 179,422,196 (GRCm39) R107C probably damaging Het
Celsr1 G T 15: 85,917,286 (GRCm39) S229* probably null Het
Cfap54 T G 10: 92,880,990 (GRCm39) M358L probably benign Het
Csnka2ip T A 16: 64,298,630 (GRCm39) D578V unknown Het
Ctns T C 11: 73,082,563 (GRCm39) I56V probably benign Het
Dnah9 A G 11: 65,746,113 (GRCm39) I4000T possibly damaging Het
Dock2 A G 11: 34,622,366 (GRCm39) V91A possibly damaging Het
Dpep2 T C 8: 106,712,885 (GRCm39) H335R probably damaging Het
Eno1 C T 4: 150,332,539 (GRCm39) R400* probably null Het
Fam114a1 C A 5: 65,137,300 (GRCm39) P81H probably damaging Het
Gemin6 A G 17: 80,535,237 (GRCm39) T66A probably benign Het
Grm4 T C 17: 27,653,980 (GRCm39) I657V probably benign Het
H2ac22 T C 13: 21,971,057 (GRCm39) N111S probably benign Het
Has3 T C 8: 107,600,852 (GRCm39) C105R probably damaging Het
Hecw1 T C 13: 14,491,243 (GRCm39) E170G probably benign Het
Hoxd3 T C 2: 74,576,744 (GRCm39) V208A probably damaging Het
Hypk C T 2: 121,288,163 (GRCm39) Q75* probably null Het
Itpkb T A 1: 180,161,004 (GRCm39) W377R probably benign Het
Kbtbd2 A T 6: 56,755,987 (GRCm39) V583E probably damaging Het
Kif7 A C 7: 79,354,472 (GRCm39) L771R probably damaging Het
Krt9 C G 11: 100,079,734 (GRCm39) G553R unknown Het
Lama3 G A 18: 12,595,869 (GRCm39) A933T probably benign Het
Muc16 A G 9: 18,462,984 (GRCm39) I7406T unknown Het
Ndst4 C T 3: 125,518,385 (GRCm39) S354L probably benign Het
Ntng2 G T 2: 29,084,998 (GRCm39) C535* probably null Het
Omg A G 11: 79,393,051 (GRCm39) M269T probably benign Het
Or1x6 A T 11: 50,939,161 (GRCm39) T76S possibly damaging Het
Or52e3 A T 7: 102,869,862 (GRCm39) *312C probably null Het
Parp2 T C 14: 51,056,850 (GRCm39) S325P probably benign Het
Pclo C T 5: 14,728,528 (GRCm39) T2462M unknown Het
Pi4ka G T 16: 17,100,165 (GRCm39) H1912N Het
Piezo2 T C 18: 63,290,302 (GRCm39) I152M probably benign Het
Pigv A T 4: 133,392,990 (GRCm39) L60Q probably damaging Het
Plcz1 T A 6: 139,953,481 (GRCm39) K379* probably null Het
Poll T C 19: 45,542,091 (GRCm39) N405S probably benign Het
Pou6f2 T A 13: 18,303,615 (GRCm39) I467F Het
Pramel11 T A 4: 143,623,646 (GRCm39) N176I probably benign Het
Psg26 T C 7: 18,212,382 (GRCm39) I324M probably damaging Het
Ptprh T A 7: 4,574,970 (GRCm39) I350F probably damaging Het
Slpi C T 2: 164,196,817 (GRCm39) V126I probably benign Het
Smarca5 C T 8: 81,431,258 (GRCm39) W986* probably null Het
Sorcs1 A G 19: 50,250,733 (GRCm39) I366T probably damaging Het
Sv2c G T 13: 96,224,745 (GRCm39) S188* probably null Het
Sycp2 T C 2: 177,996,906 (GRCm39) K1099R probably damaging Het
Tdp2 C A 13: 25,020,916 (GRCm39) Y178* probably null Het
Trabd2b A G 4: 114,460,122 (GRCm39) E420G probably damaging Het
Uggt2 A T 14: 119,294,975 (GRCm39) H550Q probably benign Het
Vmn2r66 T C 7: 84,654,950 (GRCm39) K453R probably benign Het
Vsig10l A G 7: 43,112,657 (GRCm39) M1V probably null Het
Wdr70 G A 15: 7,902,684 (GRCm39) S646L probably benign Het
Zfp219 A T 14: 52,246,405 (GRCm39) S241T probably damaging Het
Zfp24 G A 18: 24,147,326 (GRCm39) H329Y 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
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
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'- TTTCTGTGCCTGACCCTGAG -3'
(R):5'- TGATCTATTGAACCCAGGACAGAG -3'

Sequencing Primer
(F):5'- TGCCTGACCCTGAGCACATAAG -3'
(R):5'- CCCCTATAGGCTTGGTATATAAATGG -3'
Posted On 2022-02-07