Incidental Mutation 'R2238:Kdm6a'
ID 240274
Institutional Source Beutler Lab
Gene Symbol Kdm6a
Ensembl Gene ENSMUSG00000037369
Gene Name lysine (K)-specific demethylase 6A
Synonyms Utx
MMRRC Submission 040238-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R2238 (G1)
Quality Score 222
Status Validated
Chromosome X
Chromosomal Location 18028814-18146175 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 18065476 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Serine at position 104 (F104S)
Ref Sequence ENSEMBL: ENSMUSP00000153609 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000044484] [ENSMUST00000052368] [ENSMUST00000223885]
AlphaFold O70546
Predicted Effect possibly damaging
Transcript: ENSMUST00000044484
AA Change: F104S

PolyPhen 2 Score 0.611 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000045862
Gene: ENSMUSG00000037369
AA Change: F104S

DomainStartEndE-ValueType
low complexity region 9 19 N/A INTRINSIC
low complexity region 28 42 N/A INTRINSIC
TPR 95 128 4.2e-2 SMART
TPR 132 165 6.1e-6 SMART
TPR 207 240 3.3e-2 SMART
TPR 286 319 2.3e-3 SMART
TPR 320 353 2e-5 SMART
TPR 354 387 7.7e-2 SMART
low complexity region 814 833 N/A INTRINSIC
low complexity region 919 932 N/A INTRINSIC
low complexity region 972 983 N/A INTRINSIC
low complexity region 1055 1071 N/A INTRINSIC
JmjC 1095 1258 3.9e-51 SMART
Blast:JmjC 1294 1358 7e-35 BLAST
Predicted Effect possibly damaging
Transcript: ENSMUST00000052368
AA Change: F104S

PolyPhen 2 Score 0.611 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000061539
Gene: ENSMUSG00000037369
AA Change: F104S

DomainStartEndE-ValueType
low complexity region 9 19 N/A INTRINSIC
low complexity region 28 42 N/A INTRINSIC
TPR 95 128 8.74e0 SMART
TPR 132 165 1.3e-3 SMART
TPR 207 240 7.01e0 SMART
TPR 286 319 4.69e-1 SMART
TPR 320 353 4.21e-3 SMART
TPR 354 387 1.6e1 SMART
low complexity region 814 833 N/A INTRINSIC
low complexity region 919 932 N/A INTRINSIC
low complexity region 972 983 N/A INTRINSIC
low complexity region 1055 1071 N/A INTRINSIC
JmjC 1095 1258 1.08e-48 SMART
Blast:JmjC 1294 1358 9e-35 BLAST
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130978
Predicted Effect probably damaging
Transcript: ENSMUST00000223885
AA Change: F104S

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
Predicted Effect noncoding transcript
Transcript: ENSMUST00000225738
Meta Mutation Damage Score 0.7252 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.0%
Validation Efficiency 98% (59/60)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is located on the X chromosome and is the corresponding locus to a Y-linked gene which encodes a tetratricopeptide repeat (TPR) protein. The encoded protein of this gene contains a JmjC-domain and catalyzes the demethylation of tri/dimethylated histone H3. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Apr 2014]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality, caudal body truncation, abnormal neural tube closure and abnormal heart development. Mice hemizygous for this allele exhibit perinatal lethality, abnormal neural tube closure, inability to breath, exencephaly and atelectasis. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aadacl4fm1 T A 4: 144,246,469 (GRCm39) V5E possibly damaging Het
Acaca T C 11: 84,282,331 (GRCm39) probably benign Het
Adam18 T C 8: 25,136,303 (GRCm39) E406G probably benign Het
Adgrl4 A T 3: 151,205,779 (GRCm39) I164F probably damaging Het
Arhgap36 G T X: 48,582,282 (GRCm39) V60L possibly damaging Het
Bmi1 T C 2: 18,688,225 (GRCm39) probably benign Het
Carf T C 1: 60,187,193 (GRCm39) S599P probably benign Het
Cdc37 G A 9: 21,053,829 (GRCm39) Q176* probably null Het
Clca3a1 T A 3: 144,457,766 (GRCm39) I373F possibly damaging Het
Clnk A G 5: 38,921,694 (GRCm39) probably benign Het
Cnot1 T C 8: 96,496,149 (GRCm39) I342V probably benign Het
Dact2 A T 17: 14,417,312 (GRCm39) L296Q probably damaging Het
Dctn2 C T 10: 127,112,257 (GRCm39) T123I probably damaging Het
Deup1 A C 9: 15,486,597 (GRCm39) I455S probably damaging Het
Dnmbp A G 19: 43,857,303 (GRCm39) V957A possibly damaging Het
Emilin2 T C 17: 71,581,734 (GRCm39) R331G possibly damaging Het
Eomes A G 9: 118,311,359 (GRCm39) D394G probably damaging Het
Epn1 A G 7: 5,100,601 (GRCm39) N518S probably damaging Het
Gbf1 T C 19: 46,152,057 (GRCm39) I30T probably benign Het
Gcc1 A G 6: 28,420,462 (GRCm39) V285A probably benign Het
Gopc T C 10: 52,229,499 (GRCm39) H188R probably damaging Het
Herc6 A G 6: 57,631,386 (GRCm39) N693D probably benign Het
Hipk2 A G 6: 38,706,850 (GRCm39) probably benign Het
Htatsf1 G T X: 56,111,864 (GRCm39) D642Y unknown Het
Ints1 G A 5: 139,750,955 (GRCm39) T814M possibly damaging Het
Kdr T A 5: 76,110,179 (GRCm39) Y936F possibly damaging Het
Ly6k T C 15: 74,669,018 (GRCm39) E87G probably benign Het
Lyst A G 13: 13,917,848 (GRCm39) N3303D probably benign Het
Mindy4 T C 6: 55,278,055 (GRCm39) F633S probably damaging Het
Msl2 T A 9: 100,978,569 (GRCm39) N314K probably benign Het
Ncapd3 A G 9: 26,978,320 (GRCm39) T840A probably benign Het
Neil3 T C 8: 54,052,311 (GRCm39) D429G possibly damaging Het
Nt5c1b C A 12: 10,425,558 (GRCm39) T309K probably damaging Het
Nt5c1b A G 12: 10,440,108 (GRCm39) Y550C probably damaging Het
Or10v5 T C 19: 11,805,814 (GRCm39) D192G probably damaging Het
Pabpc4l A C 3: 46,401,137 (GRCm39) V169G probably damaging Het
Pcgf5 A T 19: 36,414,754 (GRCm39) N105I probably damaging Het
Phka2 A G X: 159,324,408 (GRCm39) E254G probably damaging Het
Pik3cb A G 9: 98,923,081 (GRCm39) Y984H probably damaging Het
Ptprz1 A T 6: 22,987,376 (GRCm39) Q387L probably damaging Het
Rassf8 T C 6: 145,762,910 (GRCm39) V419A probably damaging Het
Rnf148 T C 6: 23,654,345 (GRCm39) Y217C probably benign Het
Sec24d T A 3: 123,143,543 (GRCm39) probably null Het
Sesn3 T C 9: 14,219,761 (GRCm39) V50A probably benign Het
Sgcd T C 11: 47,023,509 (GRCm39) N99D possibly damaging Het
Sncaip T C 18: 53,001,619 (GRCm39) S47P probably damaging Het
Sp2 C T 11: 96,846,762 (GRCm39) C527Y probably damaging Het
Spata4 A C 8: 55,055,664 (GRCm39) K185T probably benign Het
Spin2c A G X: 152,616,672 (GRCm39) I162V probably damaging Het
Srcin1 T C 11: 97,425,645 (GRCm39) T471A probably benign Het
Stac G A 9: 111,519,190 (GRCm39) probably benign Het
Tcaf3 A G 6: 42,570,262 (GRCm39) Y497H probably benign Het
Tmem40 C T 6: 115,708,038 (GRCm39) W150* probably null Het
Tmem59l T C 8: 70,937,772 (GRCm39) T203A probably damaging Het
Tnfsf11 A T 14: 78,537,421 (GRCm39) S81T possibly damaging Het
Topaz1 C T 9: 122,600,212 (GRCm39) T984I probably benign Het
Vmn1r204 A G 13: 22,740,993 (GRCm39) H208R probably benign Het
Vmn2r98 T A 17: 19,286,213 (GRCm39) M237K probably damaging Het
Other mutations in Kdm6a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00908:Kdm6a APN X 18,102,905 (GRCm39) missense possibly damaging 0.94
IGL00963:Kdm6a APN X 18,112,665 (GRCm39) splice site probably benign
IGL02072:Kdm6a APN X 18,120,528 (GRCm39) missense probably benign 0.00
IGL02426:Kdm6a APN X 18,112,549 (GRCm39) missense probably damaging 1.00
IGL03351:Kdm6a APN X 18,113,343 (GRCm39) nonsense probably null
R0539:Kdm6a UTSW X 18,128,664 (GRCm39) missense probably damaging 0.99
R1387:Kdm6a UTSW X 18,120,235 (GRCm39) splice site probably benign
R1809:Kdm6a UTSW X 18,102,923 (GRCm39) missense probably benign 0.44
R2239:Kdm6a UTSW X 18,065,476 (GRCm39) missense probably damaging 0.99
R4062:Kdm6a UTSW X 18,117,114 (GRCm39) missense probably benign
R4063:Kdm6a UTSW X 18,117,114 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- TGTCTTGAAGAATGATATGCTGAGA -3'
(R):5'- ACTTGCCTTTCCAGTAACAAGA -3'

Sequencing Primer
(F):5'- TATTGATTTCCTGGAGAGAGAGAG -3'
(R):5'- CTGGCCCACAAAAATCTGT -3'
Posted On 2014-10-15