Incidental Mutation 'R4284:Jmjd6'
ID 322004
Institutional Source Beutler Lab
Gene Symbol Jmjd6
Ensembl Gene ENSMUSG00000056962
Gene Name jumonji domain containing 6
Synonyms 5730436I23Rik, Ptdsr, PSR, PtdSerR
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4284 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 116728258-116734275 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 116733534 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Glycine at position 48 (R48G)
Ref Sequence ENSEMBL: ENSMUSP00000117922 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047616] [ENSMUST00000106370] [ENSMUST00000140513] [ENSMUST00000140349] [ENSMUST00000142495]
AlphaFold Q9ERI5
Predicted Effect probably damaging
Transcript: ENSMUST00000047616
AA Change: R48G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000047570
Gene: ENSMUSG00000056962
AA Change: R48G

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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: ENSMUST00000140513
AA Change: R5G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000115086
Gene: ENSMUSG00000056962
AA Change: R5G

DomainStartEndE-ValueType
JmjC 98 262 6.09e-48 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000140349
SMART Domains Protein: ENSMUSP00000120850
Gene: ENSMUSG00000056962

DomainStartEndE-ValueType
JmjC 93 257 6.09e-48 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000141735
Predicted Effect probably damaging
Transcript: ENSMUST00000142495
AA Change: R48G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000117922
Gene: ENSMUSG00000056962
AA Change: R48G

DomainStartEndE-ValueType
JmjC 141 270 4.17e-14 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000184052
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176799
Predicted Effect noncoding transcript
Transcript: ENSMUST00000175930
Predicted Effect noncoding transcript
Transcript: ENSMUST00000176765
Predicted Effect probably benign
Transcript: ENSMUST00000140869
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.8%
  • 10x: 97.5%
  • 20x: 95.7%
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: 32 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Agl G A 3: 116,545,827 (GRCm39) S1323L possibly damaging Het
Capg T C 6: 72,538,082 (GRCm39) Y323H probably damaging Het
Cdh23 T C 10: 60,139,272 (GRCm39) T3314A possibly damaging Het
Cilp A T 9: 65,185,560 (GRCm39) T552S probably damaging Het
Cox16 T C 12: 81,521,293 (GRCm39) probably null Het
Ctu2 G A 8: 123,204,978 (GRCm39) V88I probably benign Het
Elfn1 A T 5: 139,958,069 (GRCm39) K358* probably null Het
Enpp6 T C 8: 47,522,050 (GRCm39) F328S probably damaging Het
Galnt12 T C 4: 47,104,231 (GRCm39) L163P probably damaging Het
Gcfc2 G A 6: 81,918,372 (GRCm39) R354H probably damaging Het
Hcn1 ACAGCAGCAGCAGCAGCAGCAGCAACAGCAACAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGC ACAGCAGCAGCAGCAGCAGCAACAGCAACAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGC 13: 118,112,269 (GRCm39) probably benign Het
Ikbke C T 1: 131,203,515 (GRCm39) probably null Het
Il1rn T C 2: 24,239,557 (GRCm39) L151P probably damaging Het
Klk14 G A 7: 43,341,501 (GRCm39) C51Y probably damaging Het
Lilra6 T C 7: 3,911,803 (GRCm39) H285R possibly damaging Het
Lrp2 G A 2: 69,310,438 (GRCm39) R2712C possibly damaging Het
Magi3 C A 3: 103,923,184 (GRCm39) G1178* probably null Het
Memo1 T C 17: 74,562,293 (GRCm39) probably null Het
Mug2 T A 6: 122,040,632 (GRCm39) D727E probably benign Het
Relch A G 1: 105,649,012 (GRCm39) D717G probably damaging Het
Sema3c A G 5: 17,883,345 (GRCm39) T318A probably benign Het
Shroom3 G T 5: 93,090,945 (GRCm39) V1151F probably damaging Het
Slc20a2 G A 8: 23,051,365 (GRCm39) R466Q probably benign Het
Slc25a51 C T 4: 45,399,768 (GRCm39) V141M probably benign Het
Sox5 T C 6: 143,781,055 (GRCm39) K570E probably damaging Het
Ssbp1 T G 6: 40,454,851 (GRCm39) probably null Het
Sult5a1 A G 8: 123,875,969 (GRCm39) S116P probably damaging Het
Tktl2 T A 8: 66,965,808 (GRCm39) D455E probably damaging Het
Tm9sf1 T C 14: 55,878,780 (GRCm39) Y204C probably damaging Het
Tmem161a A G 8: 70,630,076 (GRCm39) probably benign Het
Ttn T A 2: 76,623,211 (GRCm39) K13663* probably null Het
Unc5c T C 3: 141,420,435 (GRCm39) I52T probably damaging Het
Other mutations in Jmjd6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00959:Jmjd6 APN 11 116,733,202 (GRCm39) missense possibly damaging 0.68
IGL01877:Jmjd6 APN 11 116,733,519 (GRCm39) missense probably benign
IGL01941:Jmjd6 APN 11 116,732,184 (GRCm39) splice site probably null
IGL02316:Jmjd6 APN 11 116,733,928 (GRCm39) missense possibly damaging 0.50
IGL03396:Jmjd6 APN 11 116,732,077 (GRCm39) missense probably damaging 1.00
jumanji UTSW 11 116,733,326 (GRCm39) missense probably damaging 1.00
R0675:Jmjd6 UTSW 11 116,731,353 (GRCm39) missense probably damaging 1.00
R1531:Jmjd6 UTSW 11 116,733,266 (GRCm39) missense probably benign
R2259:Jmjd6 UTSW 11 116,732,140 (GRCm39) missense probably damaging 1.00
R3937:Jmjd6 UTSW 11 116,731,991 (GRCm39) missense probably benign
R5534:Jmjd6 UTSW 11 116,731,252 (GRCm39) missense probably damaging 1.00
R5881:Jmjd6 UTSW 11 116,730,682 (GRCm39) nonsense probably null
R6546:Jmjd6 UTSW 11 116,733,326 (GRCm39) missense probably damaging 1.00
R7468:Jmjd6 UTSW 11 116,733,275 (GRCm39) missense probably damaging 1.00
R7940:Jmjd6 UTSW 11 116,734,055 (GRCm39) start gained probably benign
R9370:Jmjd6 UTSW 11 116,729,952 (GRCm39) missense probably benign 0.00
R9790:Jmjd6 UTSW 11 116,733,438 (GRCm39) missense probably benign
R9791:Jmjd6 UTSW 11 116,733,438 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- ATTATCCTCGCCGCACTTGAAC -3'
(R):5'- TGTCAAAACTCGCTCGGTCG -3'

Sequencing Primer
(F):5'- GCCGCACTTGAACTTCTGG -3'
(R):5'- CTCGGTCGTGGGAGCTTC -3'
Posted On 2015-06-20