Incidental Mutation 'R0620:Kdm5d'
ID 58642
Institutional Source Beutler Lab
Gene Symbol Kdm5d
Ensembl Gene ENSMUSG00000056673
Gene Name lysine demethylase 5D
Synonyms Smcy, HY, Jarid1d
MMRRC Submission 038809-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.071) question?
Stock # R0620 (G1)
Quality Score 225
Status Validated
Chromosome Y
Chromosomal Location 897566-943813 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 927330 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Lysine at position 650 (M650K)
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: M650K

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: M650K

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: M650K

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000140663
Gene: ENSMUSG00000056673
AA Change: M650K

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
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 99.0%
  • 10x: 97.8%
  • 20x: 96.1%
Validation Efficiency 100% (74/74)
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: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts9 T C 6: 92,835,094 (GRCm39) T679A possibly damaging Het
Ahr T C 12: 35,558,193 (GRCm39) T276A probably benign Het
Akap9 A T 5: 4,114,136 (GRCm39) Q3138H probably damaging Het
Armt1 T A 10: 4,382,689 (GRCm39) F7I probably benign Het
B3galt2 A G 1: 143,521,878 (GRCm39) R5G probably damaging Het
Bod1l T C 5: 41,958,576 (GRCm39) N2750S probably benign Het
Cadps2 T A 6: 23,583,395 (GRCm39) E365V probably damaging Het
Cd200r3 T A 16: 44,778,080 (GRCm39) probably null Het
Cemip2 T A 19: 21,795,335 (GRCm39) S743T probably benign Het
Cst7 T A 2: 150,417,806 (GRCm39) probably benign Het
Defb30 A T 14: 63,287,212 (GRCm39) probably benign Het
Dido1 C T 2: 180,301,644 (GRCm39) G2087S probably benign Het
Dio2 A G 12: 90,704,845 (GRCm39) Y72H probably benign Het
Dnah11 C T 12: 117,951,204 (GRCm39) E3035K probably damaging Het
Dnajb13 T C 7: 100,152,456 (GRCm39) K287E possibly damaging Het
Dnajc11 G A 4: 152,058,085 (GRCm39) V244I possibly damaging Het
Ect2 C T 3: 27,193,801 (GRCm39) A226T probably damaging Het
Ercc8 G A 13: 108,310,595 (GRCm39) probably null Het
Fam120b T A 17: 15,623,189 (GRCm39) M389K probably benign Het
Fam151a A G 4: 106,605,128 (GRCm39) M497V probably benign Het
Fam186b C A 15: 99,178,009 (GRCm39) G439V probably benign Het
Fank1 A G 7: 133,478,494 (GRCm39) Y185C probably damaging Het
Gart T C 16: 91,427,490 (GRCm39) probably benign Het
Glb1l T C 1: 75,176,364 (GRCm39) Y572C probably damaging Het
Gm11563 C T 11: 99,549,263 (GRCm39) A164T unknown Het
Gnb4 C T 3: 32,645,356 (GRCm39) V112I probably benign Het
Gsdmc3 T A 15: 63,731,542 (GRCm39) D330V probably damaging Het
H2-DMa C T 17: 34,356,934 (GRCm39) T144M probably damaging Het
Haus6 A T 4: 86,501,751 (GRCm39) F707I possibly damaging Het
Hmcn1 T A 1: 150,469,767 (GRCm39) T4971S probably benign Het
Ints6 A T 14: 62,934,208 (GRCm39) F766L probably benign Het
Kif21b T C 1: 136,087,166 (GRCm39) F881S possibly damaging Het
Klrk1 C A 6: 129,591,598 (GRCm39) Q176H possibly damaging Het
Ky T C 9: 102,414,820 (GRCm39) V244A probably benign Het
Mia2 T A 12: 59,201,205 (GRCm39) L191M possibly damaging Het
Miga2 T A 2: 30,271,756 (GRCm39) probably benign Het
Mtss2 C T 8: 111,464,580 (GRCm39) P322S probably damaging Het
Nalcn A G 14: 123,536,553 (GRCm39) probably benign Het
Ncbp3 T A 11: 72,940,671 (GRCm39) probably benign Het
Nprl3 G A 11: 32,184,876 (GRCm39) L378F probably damaging Het
Ntrk2 A T 13: 58,994,635 (GRCm39) M184L probably benign Het
Or11g1 G T 14: 50,651,154 (GRCm39) C51F probably benign Het
Or9e1 T G 11: 58,732,269 (GRCm39) C110G probably damaging Het
Osbpl9 T C 4: 108,940,325 (GRCm39) E287G probably damaging Het
Parva T C 7: 112,175,618 (GRCm39) F250L probably damaging Het
Pcdhb11 C T 18: 37,554,864 (GRCm39) Q65* probably null Het
Phtf1 A G 3: 103,901,081 (GRCm39) T377A probably damaging Het
Pkp4 G A 2: 59,152,987 (GRCm39) V612I possibly damaging Het
Plscr2 C A 9: 92,169,707 (GRCm39) S52R probably benign Het
Pnisr C T 4: 21,874,092 (GRCm39) probably benign Het
Pole2 A C 12: 69,256,653 (GRCm39) S291A probably damaging Het
Ppp2r5d A G 17: 46,994,944 (GRCm39) F586L probably benign Het
Prrx1 G A 1: 163,085,385 (GRCm39) R182C probably damaging Het
Ptprs A G 17: 56,736,103 (GRCm39) I110T possibly damaging Het
Rasgrf2 G A 13: 92,067,936 (GRCm39) probably benign Het
Resf1 A T 6: 149,229,873 (GRCm39) Q973L probably damaging Het
Riox2 T C 16: 59,312,255 (GRCm39) V464A probably benign Het
Robo2 A G 16: 73,764,690 (GRCm39) V646A possibly damaging Het
Ros1 T A 10: 51,994,444 (GRCm39) I1279F probably damaging Het
Siglec1 G A 2: 130,916,188 (GRCm39) T1254M probably benign Het
Snx7 T C 3: 117,640,324 (GRCm39) N62D probably damaging Het
Sp100 G A 1: 85,587,588 (GRCm39) probably null Het
Stil A T 4: 114,864,356 (GRCm39) I86L possibly damaging Het
Tbc1d16 T A 11: 119,099,864 (GRCm39) D170V probably benign Het
Trappc13 G A 13: 104,297,589 (GRCm39) T105M probably damaging Het
Trhr T A 15: 44,092,896 (GRCm39) S378T probably benign Het
Ttc7b T C 12: 100,466,332 (GRCm39) probably null Het
Vegfc A T 8: 54,610,174 (GRCm39) Y110F probably benign Het
Vmn1r184 C A 7: 25,966,602 (GRCm39) P116H possibly damaging Het
Vmn2r5 A T 3: 64,411,235 (GRCm39) C444* probably null Het
Zfp341 A G 2: 154,476,193 (GRCm39) E460G possibly damaging Het
Zfp819 T A 7: 43,265,868 (GRCm39) V41E probably benign 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
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'- CGTGCTTACCACAGTGGCTTTAACC -3'
(R):5'- ACTAGGAGCAGTGTTCTGGACACC -3'

Sequencing Primer
(F):5'- CAAGGCTATAACTTTGCTGAGGC -3'
(R):5'- AATACTGAGCCCTGCTGTG -3'
Posted On 2013-07-11