Incidental Mutation 'R7014:Kdm4d'
ID 545194
Institutional Source Beutler Lab
Gene Symbol Kdm4d
Ensembl Gene ENSMUSG00000053914
Gene Name lysine (K)-specific demethylase 4D
Synonyms Jmjd2d
MMRRC Submission 045115-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R7014 (G1)
Quality Score 225.009
Status Validated
Chromosome 9
Chromosomal Location 14373844-14411778 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 14375475 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 128 (Y128H)
Ref Sequence ENSEMBL: ENSMUSP00000111311 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000058796] [ENSMUST00000115647]
AlphaFold Q3U2K5
Predicted Effect probably damaging
Transcript: ENSMUST00000058796
AA Change: Y128H

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000061632
Gene: ENSMUSG00000053914
AA Change: Y128H

DomainStartEndE-ValueType
Pfam:JmjN 16 50 3.3e-15 PFAM
JmjC 143 309 2.3e-57 SMART
low complexity region 370 383 N/A INTRINSIC
low complexity region 417 434 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000115647
AA Change: Y128H

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000111311
Gene: ENSMUSG00000053914
AA Change: Y128H

DomainStartEndE-ValueType
Pfam:JmjN 16 50 1.1e-16 PFAM
JmjC 143 309 2.3e-57 SMART
low complexity region 370 383 N/A INTRINSIC
low complexity region 417 434 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.2%
Validation Efficiency 99% (80/81)
MGI Phenotype PHENOTYPE: Mice homozygous for a knock-out allele exhibit accumulation of histone 3 methylation in spermatids, a transient increase in testes size, wider tubules, occasional male germ cell apoptosis, and decreased body weight. However, fertility is normal. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 80 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310022A10Rik C T 7: 27,278,198 (GRCm39) Q156* probably null Het
2700097O09Rik A G 12: 55,092,727 (GRCm39) I264T probably benign Het
Arid3a G T 10: 79,786,718 (GRCm39) M488I possibly damaging Het
Auts2 A G 5: 131,494,961 (GRCm39) F331S probably damaging Het
Axdnd1 T C 1: 156,158,532 (GRCm39) probably null Het
Bpifb5 C A 2: 154,066,876 (GRCm39) S43* probably null Het
Carhsp1 A G 16: 8,478,869 (GRCm39) V128A probably benign Het
Ccdc141 A G 2: 76,962,641 (GRCm39) V101A probably damaging Het
Cdk6 C G 5: 3,523,152 (GRCm39) L191V probably damaging Het
Cgnl1 T G 9: 71,632,416 (GRCm39) K312Q possibly damaging Het
Col6a1 T C 10: 76,557,277 (GRCm39) E225G probably damaging Het
Copg1 T A 6: 87,879,322 (GRCm39) L456Q probably damaging Het
Ctif T A 18: 75,570,279 (GRCm39) D540V possibly damaging Het
Cyfip1 T C 7: 55,569,241 (GRCm39) I917T probably benign Het
Cyth1 T C 11: 118,103,477 (GRCm39) D9G probably benign Het
Dnajb1 T C 8: 84,336,884 (GRCm39) I118T probably damaging Het
Ebna1bp2 T A 4: 118,480,575 (GRCm39) Y139* probably null Het
Efcab3 A G 11: 104,584,248 (GRCm39) T100A probably benign Het
Fam162a A T 16: 35,870,302 (GRCm39) V59E probably damaging Het
Fhad1 CGG CG 4: 141,645,602 (GRCm39) probably null Het
Fmo6 C G 1: 162,753,877 (GRCm39) R112T probably benign Het
Gm17087 T A 17: 8,785,304 (GRCm39) D133V probably benign Het
Gm42669 A G 5: 107,656,142 (GRCm39) I802V probably benign Het
Gp2 T C 7: 119,050,868 (GRCm39) N288D probably damaging Het
Gstm7 C T 3: 107,834,278 (GRCm39) D196N probably benign Het
Hsph1 A T 5: 149,553,865 (GRCm39) V201D probably damaging Het
Il20ra T C 10: 19,588,458 (GRCm39) L26P unknown Het
Itpr1 T A 6: 108,408,459 (GRCm39) probably null Het
Kcns3 A T 12: 11,141,688 (GRCm39) I337N probably damaging Het
Kirrel2 A G 7: 30,153,999 (GRCm39) I200T probably benign Het
Klhdc10 T A 6: 30,450,502 (GRCm39) I294N probably damaging Het
Map1a A C 2: 121,130,720 (GRCm39) N512T probably damaging Het
Marchf8 C G 6: 116,380,504 (GRCm39) C118W probably damaging Het
Marchf8 T G 6: 116,380,505 (GRCm39) C119G probably damaging Het
Mrpl38 G T 11: 116,025,741 (GRCm39) P195Q probably damaging Het
Ms4a4d A T 19: 11,525,947 (GRCm39) Q27L probably benign Het
Muc16 T A 9: 18,569,532 (GRCm39) T996S unknown Het
Mug1 C T 6: 121,838,084 (GRCm39) A438V probably benign Het
Mup7 T A 4: 60,069,866 (GRCm39) I33F probably damaging Het
Ndufa5 C T 6: 24,519,190 (GRCm39) probably null Het
Or2b7 A G 13: 21,740,108 (GRCm39) F28S probably benign Het
Or2l5 A T 16: 19,334,206 (GRCm39) F60Y probably benign Het
Or5w17 T C 2: 87,584,215 (GRCm39) I41V probably benign Het
Or5w1b A T 2: 87,476,320 (GRCm39) L49Q probably damaging Het
Or7e177 T A 9: 20,211,959 (GRCm39) C154* probably null Het
Parp9 T A 16: 35,780,433 (GRCm39) probably null Het
Pate8 C A 9: 36,493,854 (GRCm39) W26C unknown Het
Pbx1 T A 1: 168,258,949 (GRCm39) D42V probably damaging Het
Pde4dip G T 3: 97,622,738 (GRCm39) N1490K possibly damaging Het
Pdzd2 T C 15: 12,372,647 (GRCm39) N2496S probably benign Het
Pdzd2 A G 15: 12,373,061 (GRCm39) M2358T probably benign Het
Pglyrp2 C A 17: 32,634,904 (GRCm39) C486F probably damaging Het
Pi4ka A G 16: 17,114,931 (GRCm39) probably benign Het
Pknox2 T A 9: 36,820,963 (GRCm39) T300S probably damaging Het
Plekhm3 A G 1: 64,922,429 (GRCm39) I582T probably damaging Het
Prtg T C 9: 72,799,267 (GRCm39) Y766H possibly damaging Het
Prxl2a T C 14: 40,724,451 (GRCm39) E71G probably benign Het
Rabgap1 A G 2: 37,450,575 (GRCm39) E901G probably benign Het
Rabgap1l A T 1: 160,169,642 (GRCm39) N60K probably damaging Het
Rnf150 C T 8: 83,769,292 (GRCm39) T359I probably benign Het
Rps6ka2 C T 17: 7,523,331 (GRCm39) H236Y probably benign Het
Rrp1b T A 17: 32,268,401 (GRCm39) L120Q probably damaging Het
Scn7a C A 2: 66,572,303 (GRCm39) G223C probably null Het
Sema6a T A 18: 47,431,284 (GRCm39) N138I probably damaging Het
Septin5 T A 16: 18,443,659 (GRCm39) I97F probably damaging Het
Shcbp1 T A 8: 4,804,234 (GRCm39) E225D probably damaging Het
Slc25a19 A G 11: 115,511,792 (GRCm39) C124R probably damaging Het
Slc37a2 C T 9: 37,145,183 (GRCm39) A428T probably damaging Het
Slc5a12 A G 2: 110,474,709 (GRCm39) I538V probably benign Het
Slco4c1 A T 1: 96,751,506 (GRCm39) probably null Het
Smarcad1 T C 6: 65,029,654 (GRCm39) S81P probably damaging Het
Smyd1 T C 6: 71,215,611 (GRCm39) D116G probably damaging Het
Themis T C 10: 28,665,703 (GRCm39) Y589H probably benign Het
Trim30d T C 7: 104,132,543 (GRCm39) K248R probably benign Het
Tspan12 C T 6: 21,772,918 (GRCm39) M210I probably benign Het
Vmn2r11 T C 5: 109,201,289 (GRCm39) Y405C probably damaging Het
Wdfy3 A G 5: 102,042,775 (GRCm39) probably null Het
Wiz C A 17: 32,580,840 (GRCm39) A83S probably damaging Het
Zfp1002 A T 2: 150,097,182 (GRCm39) C82* probably null Het
Zmym6 T A 4: 127,017,337 (GRCm39) Y947* probably null Het
Other mutations in Kdm4d
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01011:Kdm4d APN 9 14,375,515 (GRCm39) missense probably benign 0.10
IGL01114:Kdm4d APN 9 14,375,493 (GRCm39) missense probably damaging 1.00
IGL01609:Kdm4d APN 9 14,375,714 (GRCm39) missense probably damaging 0.99
IGL02342:Kdm4d APN 9 14,374,860 (GRCm39) missense probably damaging 0.99
IGL02513:Kdm4d APN 9 14,375,850 (GRCm39) missense probably benign 0.00
IGL03276:Kdm4d APN 9 14,375,838 (GRCm39) missense probably benign 0.04
IGL03379:Kdm4d APN 9 14,375,139 (GRCm39) missense probably damaging 1.00
R0220:Kdm4d UTSW 9 14,374,418 (GRCm39) missense probably benign
R0755:Kdm4d UTSW 9 14,375,591 (GRCm39) missense probably damaging 0.99
R1195:Kdm4d UTSW 9 14,374,395 (GRCm39) missense probably benign
R1195:Kdm4d UTSW 9 14,374,395 (GRCm39) missense probably benign
R1195:Kdm4d UTSW 9 14,374,395 (GRCm39) missense probably benign
R1455:Kdm4d UTSW 9 14,375,691 (GRCm39) missense probably damaging 0.98
R1552:Kdm4d UTSW 9 14,375,325 (GRCm39) missense probably damaging 1.00
R1692:Kdm4d UTSW 9 14,375,807 (GRCm39) missense probably benign 0.43
R1871:Kdm4d UTSW 9 14,375,679 (GRCm39) missense probably damaging 1.00
R1892:Kdm4d UTSW 9 14,375,613 (GRCm39) missense probably benign 0.14
R4792:Kdm4d UTSW 9 14,374,686 (GRCm39) missense probably benign
R5113:Kdm4d UTSW 9 14,375,409 (GRCm39) missense probably damaging 1.00
R5211:Kdm4d UTSW 9 14,374,400 (GRCm39) missense probably benign 0.04
R5352:Kdm4d UTSW 9 14,375,654 (GRCm39) missense probably damaging 1.00
R6692:Kdm4d UTSW 9 14,374,361 (GRCm39) missense probably benign
R7198:Kdm4d UTSW 9 14,375,316 (GRCm39) missense probably damaging 1.00
R7260:Kdm4d UTSW 9 14,374,454 (GRCm39) missense probably benign 0.05
R8116:Kdm4d UTSW 9 14,375,237 (GRCm39) missense probably damaging 1.00
R8134:Kdm4d UTSW 9 14,374,532 (GRCm39) missense probably damaging 1.00
R8354:Kdm4d UTSW 9 14,375,235 (GRCm39) missense possibly damaging 0.80
R9006:Kdm4d UTSW 9 14,374,833 (GRCm39) missense probably benign 0.01
R9197:Kdm4d UTSW 9 14,375,537 (GRCm39) missense probably damaging 1.00
R9298:Kdm4d UTSW 9 14,375,336 (GRCm39) missense probably damaging 1.00
R9300:Kdm4d UTSW 9 14,375,336 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- AGTTGATACTGTACAGGTCCATG -3'
(R):5'- TTAATAGCAACTCCCCTGCAG -3'

Sequencing Primer
(F):5'- CACGCAAAGGTGGTCTTCC -3'
(R):5'- CTGCAGCAAGTGGTCTCTG -3'
Posted On 2019-05-13