Incidental Mutation 'R1809:Kdm6a'
ID203756
Institutional Source Beutler Lab
Gene Symbol Kdm6a
Ensembl Gene ENSMUSG00000037369
Gene Namelysine (K)-specific demethylase 6A
SynonymsUtx
MMRRC Submission 039838-MU
Accession Numbers
Is this an essential gene? Essential (E-score: 1.000) question?
Stock #R1809 (G1)
Quality Score222
Status Validated
ChromosomeX
Chromosomal Location18162575-18279936 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to C at 18236684 bp
ZygosityHeterozygous
Amino Acid Change Tyrosine to Histidine at position 217 (Y217H)
Ref Sequence ENSEMBL: ENSMUSP00000061539 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000044484] [ENSMUST00000052368] [ENSMUST00000223885]
Predicted Effect probably benign
Transcript: ENSMUST00000044484
AA Change: Y217H

PolyPhen 2 Score 0.439 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000045862
Gene: ENSMUSG00000037369
AA Change: Y217H

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 probably benign
Transcript: ENSMUST00000052368
AA Change: Y217H

PolyPhen 2 Score 0.439 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000061539
Gene: ENSMUSG00000037369
AA Change: Y217H

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 silent
Transcript: ENSMUST00000223885
Predicted Effect noncoding transcript
Transcript: ENSMUST00000225738
Meta Mutation Damage Score 0.1664 question?
Coding Region Coverage
  • 1x: 97.5%
  • 3x: 96.8%
  • 10x: 94.9%
  • 20x: 91.2%
Validation Efficiency 96% (107/111)
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: 104 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930502E18Rik A G X: 53,733,749 E99G probably benign Het
9130409I23Rik T C 1: 181,059,687 I279T probably damaging Het
Ablim2 A G 5: 35,843,270 probably benign Het
Adamts20 C T 15: 94,341,087 S750N probably damaging Het
Adh6a G A 3: 138,330,961 R370H possibly damaging Het
Akr1b7 A G 6: 34,419,111 N183D probably damaging Het
Aktip A T 8: 91,129,720 I43N probably damaging Het
Ankrd26 A T 6: 118,525,922 probably benign Het
Ano9 G A 7: 141,108,804 T144I possibly damaging Het
Anpep G T 7: 79,841,823 D143E probably benign Het
Aox2 C A 1: 58,294,325 Q234K probably benign Het
Ap1g1 C G 8: 109,833,182 probably benign Het
Arhgef4 G A 1: 34,810,555 probably null Het
Armc4 T A 18: 7,211,630 Y748F probably benign Het
Arsj A G 3: 126,438,295 Y230C possibly damaging Het
Asmt C T X: 170,675,745 probably benign Het
Astl A T 2: 127,345,485 K72N probably damaging Het
Atp2b2 G A 6: 113,803,743 probably benign Het
Baiap2l1 A C 5: 144,324,555 probably null Het
C7 A T 15: 5,034,339 N193K probably damaging Het
Cacna2d4 G T 6: 119,270,824 R362L probably damaging Het
Cct4 T A 11: 22,997,615 D189E probably benign Het
Cd300lg G A 11: 102,043,112 G62S probably benign Het
Cdk14 T A 5: 5,010,901 M307L probably damaging Het
Cfi G A 3: 129,873,119 probably null Het
Clec2g G T 6: 128,980,310 probably null Het
Cntnap2 T C 6: 46,988,675 S807P probably damaging Het
Col6a3 T A 1: 90,827,949 H206L probably damaging Het
Cyp2c23 A T 19: 44,021,558 probably benign Het
Dlec1 T C 9: 119,136,699 V1058A probably benign Het
Dpp9 A G 17: 56,199,038 Y454H probably damaging Het
Drosha G A 15: 12,890,112 G920R probably null Het
Duox2 A G 2: 122,283,897 S1142P possibly damaging Het
Fam13a C T 6: 58,965,060 probably null Het
Filip1l A G 16: 57,506,660 R18G probably benign Het
Foxa1 A G 12: 57,542,741 V231A probably damaging Het
Gm11756 A G 4: 73,917,517 F237L probably benign Het
Gm4787 A T 12: 81,378,529 M285K possibly damaging Het
Gm5084 T A 13: 60,212,506 noncoding transcript Het
Gm6788 G A 19: 28,763,186 noncoding transcript Het
Gm9922 G T 14: 101,729,405 probably benign Het
Gtf3c4 A T 2: 28,833,976 Y440* probably null Het
Helq A G 5: 100,773,954 S795P probably damaging Het
Helz T A 11: 107,599,171 S151T possibly damaging Het
Irgm1 T C 11: 48,866,613 T124A probably benign Het
Itgam C T 7: 128,070,937 P134S possibly damaging Het
Kif6 T C 17: 49,901,784 L744P probably benign Het
Kmt2c C T 5: 25,284,192 R1203H probably damaging Het
Ksr2 A G 5: 117,555,470 T328A probably damaging Het
Lig1 T C 7: 13,300,355 probably benign Het
Lpar3 G A 3: 146,240,548 probably benign Het
Lrrk2 T C 15: 91,699,892 F285S possibly damaging Het
March7 A G 2: 60,232,293 D148G probably benign Het
Mcee T C 7: 64,400,301 L60S probably damaging Het
Mob2 A G 7: 142,016,374 I81T probably damaging Het
Mphosph8 T A 14: 56,672,452 D87E probably damaging Het
Myo1g T C 11: 6,512,283 T560A probably benign Het
Nagk C T 6: 83,797,187 T42I probably benign Het
Naip1 G T 13: 100,426,239 T806K probably benign Het
Ncor2 A G 5: 125,118,793 probably benign Het
Ocln G T 13: 100,511,459 Y401* probably null Het
Olfr922 G A 9: 38,816,147 V215I probably benign Het
Oma1 T A 4: 103,325,177 N292K probably damaging Het
Ovch2 T A 7: 107,790,205 probably null Het
Pcdhb16 T C 18: 37,478,388 F134L probably damaging Het
Pipox A T 11: 77,881,534 Y337N probably benign Het
Polr3b A G 10: 84,693,001 D763G probably damaging Het
Pygo1 T A 9: 72,944,796 N88K probably damaging Het
Rab3gap1 T C 1: 127,934,514 M674T probably damaging Het
Rbm25 T C 12: 83,672,727 probably benign Het
Rbm26 C T 14: 105,117,106 probably benign Het
Rbms2 G A 10: 128,138,186 T187I possibly damaging Het
Rnase11 T A 14: 51,049,727 R123S probably benign Het
Rngtt A G 4: 33,443,614 N485D probably benign Het
Rp1l1 A T 14: 64,027,966 M334L probably benign Het
Rps9 T A 7: 3,704,727 L56Q probably damaging Het
Saysd1 C A 14: 20,083,102 probably benign Het
Sema4d C T 13: 51,713,691 probably null Het
Shisa5 A T 9: 109,040,930 D34V probably damaging Het
Skil A G 3: 31,117,506 D547G probably damaging Het
Slc2a5 T A 4: 150,143,057 F444L probably damaging Het
Slc9b2 T G 3: 135,317,131 C10G possibly damaging Het
Sorcs2 G T 5: 36,229,220 probably benign Het
Stk17b T G 1: 53,765,981 K140N possibly damaging Het
Stradb T A 1: 58,994,390 L404Q possibly damaging Het
Synj2 T C 17: 6,026,551 M432T possibly damaging Het
Tanc1 G T 2: 59,800,097 R800L probably damaging Het
Tenm4 A G 7: 96,873,780 M1473V probably benign Het
Tesc A G 5: 118,061,602 I190V probably benign Het
Tex15 T C 8: 33,574,234 F1231L probably benign Het
Thrsp T C 7: 97,417,125 I127V probably benign Het
Tlr6 A T 5: 64,953,712 C617* probably null Het
Trank1 A T 9: 111,392,825 I2877F probably benign Het
Ucp1 T C 8: 83,297,867 S274P probably damaging Het
Ucp2 T A 7: 100,498,399 V195E probably damaging Het
Vars2 T C 17: 35,662,216 T394A probably damaging Het
Vmn1r1 A G 1: 182,157,806 V98A possibly damaging Het
Vmn1r225 A G 17: 20,502,656 I120V probably benign Het
Vmn2r102 A T 17: 19,677,619 M299L probably benign Het
Vmn2r25 A G 6: 123,825,378 V522A probably benign Het
Vmn2r70 T C 7: 85,565,922 I135V probably benign Het
Vwf T C 6: 125,590,175 probably benign Het
Zcchc11 T A 4: 108,549,355 H1373Q probably damaging Het
Zfp446 T C 7: 12,979,121 F29L probably damaging Het
Other mutations in Kdm6a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00908:Kdm6a APN X 18236666 missense possibly damaging 0.94
IGL00963:Kdm6a APN X 18246426 splice site probably benign
IGL02072:Kdm6a APN X 18254289 missense probably benign 0.00
IGL02426:Kdm6a APN X 18246310 missense probably damaging 1.00
IGL03351:Kdm6a APN X 18247104 nonsense probably null
R0539:Kdm6a UTSW X 18262425 missense probably damaging 0.99
R1387:Kdm6a UTSW X 18253996 splice site probably benign
R2238:Kdm6a UTSW X 18199237 missense probably damaging 0.99
R2239:Kdm6a UTSW X 18199237 missense probably damaging 0.99
R4062:Kdm6a UTSW X 18250875 missense probably benign
R4063:Kdm6a UTSW X 18250875 missense probably benign
Predicted Primers PCR Primer
(F):5'- ACACATTTGACTTAACCTCAAGTAC -3'
(R):5'- GCATCTACAAGAGATTAAAGCATTCAC -3'

Sequencing Primer
(F):5'- ATCCTATTTGTTCTTTAGTGTGACTG -3'
(R):5'- GCAAGTTATAAGTGATTCTTCTCTGG -3'
Posted On2014-06-23