Incidental Mutation 'R1195:Kdm4d'
ID 164508
Institutional Source Beutler Lab
Gene Symbol Kdm4d
Ensembl Gene ENSMUSG00000053914
Gene Name lysine (K)-specific demethylase 4D
Synonyms Jmjd2d
MMRRC Submission 039267-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R1195 (G1)
Quality Score 180
Status Not validated
Chromosome 9
Chromosomal Location 14373844-14411778 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 14374395 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 488 (S488P)
Ref Sequence ENSEMBL: ENSMUSP00000061632 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000058796] [ENSMUST00000115647]
AlphaFold Q3U2K5
Predicted Effect probably benign
Transcript: ENSMUST00000058796
AA Change: S488P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000061632
Gene: ENSMUSG00000053914
AA Change: S488P

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 benign
Transcript: ENSMUST00000115647
SMART Domains Protein: ENSMUSP00000111311
Gene: ENSMUSG00000053914

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
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.7%
  • 3x: 98.6%
  • 10x: 92.8%
  • 20x: 76.0%
Validation Efficiency
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: 35 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Agtr1a C A 13: 30,565,901 (GRCm39) P322Q probably damaging Het
Brd1 T C 15: 88,585,014 (GRCm39) E940G probably benign Het
Cd163 T A 6: 124,302,209 (GRCm39) probably benign Het
Cd28 C T 1: 60,802,303 (GRCm39) T74I possibly damaging Het
Cntnap2 T A 6: 46,460,902 (GRCm39) M646K probably benign Het
Cyb5d1 C T 11: 69,285,797 (GRCm39) probably null Het
D6Ertd527e C G 6: 87,088,506 (GRCm39) T223S unknown Het
Dab2ip T C 2: 35,608,757 (GRCm39) probably benign Het
Dst A G 1: 34,250,235 (GRCm39) D4063G probably damaging Het
Elmod1 T C 9: 53,843,052 (GRCm39) Y42C probably damaging Het
Hdac5 T C 11: 102,096,332 (GRCm39) I310V probably damaging Het
Hpx A G 7: 105,248,856 (GRCm39) probably benign Het
Ighv10-1 A T 12: 114,443,015 (GRCm39) probably benign Het
Igsf3 A G 3: 101,365,419 (GRCm39) D1130G probably benign Het
Katnip A G 7: 125,465,654 (GRCm39) R1343G probably damaging Het
Lingo2 A G 4: 35,708,538 (GRCm39) Y481H probably damaging Het
Ltbp1 A G 17: 75,532,280 (GRCm39) Q118R possibly damaging Het
Map3k20 C T 2: 72,268,562 (GRCm39) P523L probably damaging Het
Myo9a A G 9: 59,802,483 (GRCm39) D1990G probably damaging Het
Niban2 T C 2: 32,809,815 (GRCm39) V304A probably benign Het
Perp C A 10: 18,731,483 (GRCm39) Y147* probably null Het
Prr16 A T 18: 51,435,755 (GRCm39) D78V probably damaging Het
Rfx7 C T 9: 72,525,228 (GRCm39) T806M probably damaging Het
Robo2 T C 16: 73,713,016 (GRCm39) probably null Het
Spdl1 T C 11: 34,710,644 (GRCm39) Y368C probably damaging Het
Sptbn2 G C 19: 4,795,921 (GRCm39) R1700P possibly damaging Het
Tenm2 C T 11: 35,954,004 (GRCm39) G1236R possibly damaging Het
Tln2 T G 9: 67,165,848 (GRCm39) K1000Q probably damaging Het
Tmbim7 A G 5: 3,711,943 (GRCm39) T63A probably benign Het
Tmed11 T C 5: 108,926,885 (GRCm39) D129G possibly damaging Het
Ttc28 G A 5: 111,373,543 (GRCm39) S962N probably damaging Het
Ttll6 T C 11: 96,026,555 (GRCm39) I113T probably damaging Het
Uso1 T A 5: 92,318,606 (GRCm39) F210L probably damaging Het
Uspl1 T A 5: 149,131,131 (GRCm39) V224E probably benign Het
Zfp639 G A 3: 32,573,345 (GRCm39) V86I possibly damaging 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
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
R7014:Kdm4d UTSW 9 14,375,475 (GRCm39) missense probably damaging 0.99
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'- GGCCAATGTCCTGCAAACTCAGTC -3'
(R):5'- TCCAGGCAACCATCAGATGTGAAAG -3'

Sequencing Primer
(F):5'- CTCAGTCAAAACTATGAGGTAATGG -3'
(R):5'- GATGATGTCCAGAAGTCTGACTC -3'
Posted On 2014-03-28