Incidental Mutation 'R2259:Jmjd6'
ID 243670
Institutional Source Beutler Lab
Gene Symbol Jmjd6
Ensembl Gene ENSMUSG00000056962
Gene Name jumonji domain containing 6
Synonyms Ptdsr, 5730436I23Rik, PtdSerR, PSR
MMRRC Submission 040259-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2259 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 116837432-116843449 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) T to C at 116841314 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Histidine to Arginine at position 187 (H187R)
Ref Sequence ENSEMBL: ENSMUSP00000117922 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047616] [ENSMUST00000106370] [ENSMUST00000140349] [ENSMUST00000140513] [ENSMUST00000142495]
AlphaFold Q9ERI5
Predicted Effect probably damaging
Transcript: ENSMUST00000047616
AA Change: H187R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000047570
Gene: ENSMUSG00000056962
AA Change: H187R

JmjC 141 305 6.09e-48 SMART
low complexity region 340 369 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000106370
SMART Domains Protein: ENSMUSP00000101978
Gene: ENSMUSG00000090266

low complexity region 5 22 N/A INTRINSIC
Pfam:Methyltransf_16 48 203 9.9e-20 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000124831
SMART Domains Protein: ENSMUSP00000122867
Gene: ENSMUSG00000056962

Pfam:JmjC 1 81 6.3e-20 PFAM
low complexity region 150 179 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128784
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130120
Predicted Effect probably benign
Transcript: ENSMUST00000132593
Predicted Effect probably damaging
Transcript: ENSMUST00000140349
AA Change: H139R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000120850
Gene: ENSMUSG00000056962
AA Change: H139R

JmjC 93 257 6.09e-48 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000140513
AA Change: H144R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000115086
Gene: ENSMUSG00000056962
AA Change: H144R

JmjC 98 262 6.09e-48 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000140869
Predicted Effect noncoding transcript
Transcript: ENSMUST00000141735
Predicted Effect probably damaging
Transcript: ENSMUST00000142495
AA Change: H187R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000117922
Gene: ENSMUSG00000056962
AA Change: H187R

JmjC 141 270 4.17e-14 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000175930
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176799
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176765
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184052
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 94.9%
Validation Efficiency
MGI Phenotype FUNCTION: This gene encodes a nuclear protein with a JmjC domain. JmjC domain-containing proteins are predicted to function as protein hydroxylases or histone demethylases. This protein functions in differentiation of multiple tissues during development, and in anti-inflammatory cytokine signaling. It was first identified as a putative phosphatidylserine receptor involved in phagocytosis of apoptotic cells; however, subsequent studies have indicated that this protein does not directly function in the clearance of apoptotic cells, and questioned whether it is a true phosphatidylserine receptor. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for disruptions in this gene show perinatal lethality. Abnormalities are observed in the nervous. respiratory, cardiovascular, digestive, renal, hematopoietic, and immune systems. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 87 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrd1 T G 5: 129,112,311 S91A possibly damaging Het
Ankrd13b T G 11: 77,476,342 N247T probably damaging Het
Atp10b A G 11: 43,172,745 D169G probably damaging Het
Atp10b G A 11: 43,189,613 V239M probably damaging Het
Cflar C T 1: 58,729,121 T121I probably benign Het
Clca3b T C 3: 144,846,381 N180D possibly damaging Het
Cnbd2 T A 2: 156,335,272 I62N probably damaging Het
Col11a2 A G 17: 34,039,677 H8R probably benign Het
Cyp2a4 C T 7: 26,309,035 L201F probably damaging Het
D630003M21Rik A T 2: 158,204,711 L782Q probably damaging Het
Dctn1 C A 6: 83,197,586 H1065N possibly damaging Het
Dgcr2 A T 16: 17,844,977 probably null Het
Dlg4 T C 11: 70,031,370 I143T probably damaging Het
E2f7 T G 10: 110,746,343 N4K probably damaging Het
Eef2kmt C T 16: 5,245,308 V323I probably benign Het
Eif2ak4 A C 2: 118,455,783 I1017L probably damaging Het
Eln C A 5: 134,729,654 A126S unknown Het
Exoc7 T C 11: 116,306,411 S35G probably damaging Het
Fam187a A G 11: 102,885,298 probably benign Het
Fam196a T A 7: 134,917,667 E378V probably damaging Het
Fkbp6 C T 5: 135,337,614 probably null Het
Flnc G A 6: 29,438,666 W186* probably null Het
Fmn2 T A 1: 174,502,932 L296H unknown Het
Galnt14 C A 17: 73,494,266 M520I probably benign Het
Gba2 A G 4: 43,570,107 C396R probably benign Het
Gigyf1 C A 5: 137,520,332 A215E possibly damaging Het
Glb1 C T 9: 114,443,032 Q246* probably null Het
Gm11565 T G 11: 99,915,018 C79G possibly damaging Het
Gpr160 A G 3: 30,896,295 Y172C probably damaging Het
Ift52 A G 2: 163,028,093 N159S probably benign Het
Insrr A G 3: 87,800,452 D67G probably damaging Het
Irf2 A G 8: 46,837,833 Y230C probably benign Het
Kdm2b C T 5: 122,882,416 G90S probably damaging Het
Kif7 C T 7: 79,711,589 G118D probably damaging Het
Klhl38 G C 15: 58,314,978 T532S possibly damaging Het
Kmt2a G T 9: 44,881,142 probably benign Het
Lama2 A G 10: 27,031,127 L2346S probably benign Het
Marveld2 A G 13: 100,612,470 S34P probably benign Het
Mettl7a1 A T 15: 100,313,168 I174F probably benign Het
Mllt6 T C 11: 97,664,976 V44A probably damaging Het
Muc5ac A G 7: 141,791,008 N72S probably benign Het
Myo7a T G 7: 98,069,499 D1388A probably damaging Het
Ncapd3 A G 9: 27,056,072 D568G probably benign Het
Ncoa1 A C 12: 4,315,819 H82Q probably damaging Het
Npbwr1 C A 1: 5,916,658 L212F probably damaging Het
Nptx1 T G 11: 119,543,316 I315L probably benign Het
Npy2r G T 3: 82,541,354 P38Q possibly damaging Het
Ocln A T 13: 100,535,029 D24E probably damaging Het
Olfr1350 A T 7: 6,570,023 I11F probably damaging Het
Olfr295 T A 7: 86,585,884 V203D possibly damaging Het
Olfr933 T C 9: 38,976,000 V108A probably benign Het
Pde2a A T 7: 101,484,567 D85V probably damaging Het
Phf3 A G 1: 30,804,343 V1845A probably benign Het
Plch1 T A 3: 63,697,977 Q1493L possibly damaging Het
Pold1 T C 7: 44,541,484 probably benign Het
Polq T C 16: 37,062,097 V1541A probably benign Het
Psmd3 T A 11: 98,690,964 M305K probably benign Het
Pura T C 18: 36,287,750 F197L possibly damaging Het
Rab3gap2 T A 1: 185,221,859 W43R probably damaging Het
Repin1 A G 6: 48,596,530 Q128R probably benign Het
Rnf208 G A 2: 25,243,644 V117I probably damaging Het
Rpe65 A G 3: 159,615,571 Y340C probably damaging Het
Ryr1 C A 7: 29,019,741 V4414L unknown Het
Sephs2 T C 7: 127,273,477 E148G possibly damaging Het
Spns2 T A 11: 72,457,268 Q291L probably benign Het
Ssc5d C T 7: 4,943,916 P1090S probably benign Het
Tasp1 A T 2: 139,951,506 V250D probably damaging Het
Tcaf3 A G 6: 42,591,430 I664T possibly damaging Het
Tg T C 15: 66,683,898 V813A probably benign Het
Tmem132c T C 5: 127,504,924 L401P probably benign Het
Tmem138 T C 19: 10,571,603 N101S probably benign Het
Tmem242 G T 17: 5,433,470 A99E probably damaging Het
Tmem30a C T 9: 79,774,164 R277H probably benign Het
Tnni3 T A 7: 4,519,406 I182F probably benign Het
Trim30a T A 7: 104,411,504 D355V probably damaging Het
Trim35 C T 14: 66,309,262 R493* probably null Het
Trip10 G C 17: 57,255,135 V254L probably benign Het
Tshz2 A T 2: 169,886,406 Q505L probably benign Het
Ttyh1 T C 7: 4,128,184 V218A probably damaging Het
Unc13b A T 4: 43,182,780 E3163V possibly damaging Het
Unc45b T A 11: 82,917,799 M237K probably benign Het
Usp8 A G 2: 126,758,568 T1080A probably benign Het
Vmn2r65 T A 7: 84,940,911 H599L possibly damaging Het
Vps13c A G 9: 67,953,860 N2891S probably benign Het
Xpo5 C T 17: 46,240,896 Q1050* probably null Het
Zfp407 G T 18: 84,209,793 T1897K probably damaging Het
Zzef1 C T 11: 72,900,633 R2188* probably null Het
Other mutations in Jmjd6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00959:Jmjd6 APN 11 116842376 missense possibly damaging 0.68
IGL01877:Jmjd6 APN 11 116842693 missense probably benign
IGL01941:Jmjd6 APN 11 116841358 splice site probably null
IGL02316:Jmjd6 APN 11 116843102 missense possibly damaging 0.50
IGL03396:Jmjd6 APN 11 116841251 missense probably damaging 1.00
jumanji UTSW 11 116842500 missense probably damaging 1.00
R0675:Jmjd6 UTSW 11 116840527 missense probably damaging 1.00
R1531:Jmjd6 UTSW 11 116842440 missense probably benign
R3937:Jmjd6 UTSW 11 116841165 missense probably benign
R4284:Jmjd6 UTSW 11 116842708 missense probably damaging 1.00
R5534:Jmjd6 UTSW 11 116840426 missense probably damaging 1.00
R5881:Jmjd6 UTSW 11 116839856 nonsense probably null
R6546:Jmjd6 UTSW 11 116842500 missense probably damaging 1.00
R7468:Jmjd6 UTSW 11 116842449 missense probably damaging 1.00
R7940:Jmjd6 UTSW 11 116843229 start gained probably benign
R9370:Jmjd6 UTSW 11 116839126 missense probably benign 0.00
R9790:Jmjd6 UTSW 11 116842612 missense probably benign
R9791:Jmjd6 UTSW 11 116842612 missense probably benign
Predicted Primers PCR Primer

Sequencing Primer
Posted On 2014-10-16