Mutagenetix > Incidental Mutation

Incidental Mutation 'R1809:Kdm6a'

203756

Institutional Source

Beutler Lab

Gene Symbol

Kdm6a

Ensembl Gene

ENSMUSG00000037369

Gene Name

lysine (K)-specific demethylase 6A

Synonyms

Utx

MMRRC Submission

039838-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1809 (G1)

Quality Score

222

Status

Validated

Chromosome

Chromosomal Location

18028814-18146175 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 18102923 bp (GRCm39)

Zygosity

Heterozygous

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]

AlphaFold

O70546

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

Domain	Start	End	E-Value	Type
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

Domain	Start	End	E-Value	Type
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

0.5969

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
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ablim2	A	G	5: 36,000,614 (GRCm39)		probably benign	Het
Adamts20	C	T	15: 94,238,968 (GRCm39)	S750N	probably damaging	Het
Adh6a	G	A	3: 138,036,722 (GRCm39)	R370H	possibly damaging	Het
Akr1b7	A	G	6: 34,396,046 (GRCm39)	N183D	probably damaging	Het
Aktip	A	T	8: 91,856,348 (GRCm39)	I43N	probably damaging	Het
Ankrd26	A	T	6: 118,502,883 (GRCm39)		probably benign	Het
Ano9	G	A	7: 140,688,717 (GRCm39)	T144I	possibly damaging	Het
Anpep	G	T	7: 79,491,571 (GRCm39)	D143E	probably benign	Het
Aox1	C	A	1: 58,333,484 (GRCm39)	Q234K	probably benign	Het
Ap1g1	C	G	8: 110,559,814 (GRCm39)		probably benign	Het
Arhgef4	G	A	1: 34,849,636 (GRCm39)		probably null	Het
Arsj	A	G	3: 126,231,944 (GRCm39)	Y230C	possibly damaging	Het
Asmt	C	T	X: 169,109,480 (GRCm39)		probably benign	Het
Astl	A	T	2: 127,187,405 (GRCm39)	K72N	probably damaging	Het
Atp2b2	G	A	6: 113,780,704 (GRCm39)		probably benign	Het
Baiap2l1	A	C	5: 144,261,365 (GRCm39)		probably null	Het
C7	A	T	15: 5,063,821 (GRCm39)	N193K	probably damaging	Het
Cacna2d4	G	T	6: 119,247,785 (GRCm39)	R362L	probably damaging	Het
Cct4	T	A	11: 22,947,615 (GRCm39)	D189E	probably benign	Het
Cd300lg	G	A	11: 101,933,938 (GRCm39)	G62S	probably benign	Het
Cdk14	T	A	5: 5,060,901 (GRCm39)	M307L	probably damaging	Het
Cfi	G	A	3: 129,666,768 (GRCm39)		probably null	Het
Clec2g	G	T	6: 128,957,273 (GRCm39)		probably null	Het
Cntnap2	T	C	6: 46,965,609 (GRCm39)	S807P	probably damaging	Het
Col6a3	T	A	1: 90,755,671 (GRCm39)	H206L	probably damaging	Het
Ct55	A	G	X: 52,735,716 (GRCm39)	E99G	probably benign	Het
Cyp2c23	A	T	19: 44,009,997 (GRCm39)		probably benign	Het
Degs1l	T	C	1: 180,887,252 (GRCm39)	I279T	probably damaging	Het
Dlec1	T	C	9: 118,965,767 (GRCm39)	V1058A	probably benign	Het
Dpp9	A	G	17: 56,506,038 (GRCm39)	Y454H	probably damaging	Het
Drosha	G	A	15: 12,890,198 (GRCm39)	G920R	probably null	Het
Duox2	A	G	2: 122,114,378 (GRCm39)	S1142P	possibly damaging	Het
Fam13a	C	T	6: 58,942,045 (GRCm39)		probably null	Het
Filip1l	A	G	16: 57,327,023 (GRCm39)	R18G	probably benign	Het
Foxa1	A	G	12: 57,589,527 (GRCm39)	V231A	probably damaging	Het
Gm4787	A	T	12: 81,425,303 (GRCm39)	M285K	possibly damaging	Het
Gm5084	T	A	13: 60,360,320 (GRCm39)		noncoding transcript	Het
Gm6788	G	A	19: 28,740,586 (GRCm39)		noncoding transcript	Het
Gm9922	G	T	14: 101,966,841 (GRCm39)		probably benign	Het
Gtf3c4	A	T	2: 28,723,988 (GRCm39)	Y440*	probably null	Het
Helq	A	G	5: 100,921,820 (GRCm39)	S795P	probably damaging	Het
Helz	T	A	11: 107,489,997 (GRCm39)	S151T	possibly damaging	Het
Irgm1	T	C	11: 48,757,440 (GRCm39)	T124A	probably benign	Het
Itgam	C	T	7: 127,670,109 (GRCm39)	P134S	possibly damaging	Het
Kif6	T	C	17: 50,208,812 (GRCm39)	L744P	probably benign	Het
Kmt2c	C	T	5: 25,489,190 (GRCm39)	R1203H	probably damaging	Het
Ksr2	A	G	5: 117,693,535 (GRCm39)	T328A	probably damaging	Het
Lig1	T	C	7: 13,034,281 (GRCm39)		probably benign	Het
Lpar3	G	A	3: 145,946,303 (GRCm39)		probably benign	Het
Lrrk2	T	C	15: 91,584,095 (GRCm39)	F285S	possibly damaging	Het
Marchf7	A	G	2: 60,062,637 (GRCm39)	D148G	probably benign	Het
Mcee	T	C	7: 64,050,049 (GRCm39)	L60S	probably damaging	Het
Mob2	A	G	7: 141,570,111 (GRCm39)	I81T	probably damaging	Het
Mphosph8	T	A	14: 56,909,909 (GRCm39)	D87E	probably damaging	Het
Msantd5f9	A	G	4: 73,835,754 (GRCm39)	F237L	probably benign	Het
Myo1g	T	C	11: 6,462,283 (GRCm39)	T560A	probably benign	Het
Nagk	C	T	6: 83,774,169 (GRCm39)	T42I	probably benign	Het
Naip1	G	T	13: 100,562,747 (GRCm39)	T806K	probably benign	Het
Ncor2	A	G	5: 125,195,857 (GRCm39)		probably benign	Het
Ocln	G	T	13: 100,647,967 (GRCm39)	Y401*	probably null	Het
Odad2	T	A	18: 7,211,630 (GRCm39)	Y748F	probably benign	Het
Oma1	T	A	4: 103,182,374 (GRCm39)	N292K	probably damaging	Het
Or8b55	G	A	9: 38,727,443 (GRCm39)	V215I	probably benign	Het
Ovch2	T	A	7: 107,389,412 (GRCm39)		probably null	Het
Pcdhb16	T	C	18: 37,611,441 (GRCm39)	F134L	probably damaging	Het
Pipox	A	T	11: 77,772,360 (GRCm39)	Y337N	probably benign	Het
Polr3b	A	G	10: 84,528,865 (GRCm39)	D763G	probably damaging	Het
Pygo1	T	A	9: 72,852,078 (GRCm39)	N88K	probably damaging	Het
Rab3gap1	T	C	1: 127,862,251 (GRCm39)	M674T	probably damaging	Het
Rbm25	T	C	12: 83,719,501 (GRCm39)		probably benign	Het
Rbm26	C	T	14: 105,354,542 (GRCm39)		probably benign	Het
Rbms2	G	A	10: 127,974,055 (GRCm39)	T187I	possibly damaging	Het
Rnase11	T	A	14: 51,287,184 (GRCm39)	R123S	probably benign	Het
Rngtt	A	G	4: 33,443,614 (GRCm39)	N485D	probably benign	Het
Rp1l1	A	T	14: 64,265,415 (GRCm39)	M334L	probably benign	Het
Rps9	T	A	7: 3,707,726 (GRCm39)	L56Q	probably damaging	Het
Saysd1	C	A	14: 20,133,170 (GRCm39)		probably benign	Het
Sema4d	C	T	13: 51,867,727 (GRCm39)		probably null	Het
Shisa5	A	T	9: 108,869,998 (GRCm39)	D34V	probably damaging	Het
Skil	A	G	3: 31,171,655 (GRCm39)	D547G	probably damaging	Het
Slc2a5	T	A	4: 150,227,514 (GRCm39)	F444L	probably damaging	Het
Slc9b2	T	G	3: 135,022,892 (GRCm39)	C10G	possibly damaging	Het
Sorcs2	G	T	5: 36,386,564 (GRCm39)		probably benign	Het
Stk17b	T	G	1: 53,805,140 (GRCm39)	K140N	possibly damaging	Het
Stradb	T	A	1: 59,033,549 (GRCm39)	L404Q	possibly damaging	Het
Synj2	T	C	17: 6,076,826 (GRCm39)	M432T	possibly damaging	Het
Tanc1	G	T	2: 59,630,441 (GRCm39)	R800L	probably damaging	Het
Tenm4	A	G	7: 96,522,987 (GRCm39)	M1473V	probably benign	Het
Tesc	A	G	5: 118,199,667 (GRCm39)	I190V	probably benign	Het
Tex15	T	C	8: 34,064,262 (GRCm39)	F1231L	probably benign	Het
Thrsp	T	C	7: 97,066,332 (GRCm39)	I127V	probably benign	Het
Tlr6	A	T	5: 65,111,055 (GRCm39)	C617*	probably null	Het
Trank1	A	T	9: 111,221,893 (GRCm39)	I2877F	probably benign	Het
Tut4	T	A	4: 108,406,552 (GRCm39)	H1373Q	probably damaging	Het
Ucp1	T	C	8: 84,024,496 (GRCm39)	S274P	probably damaging	Het
Ucp2	T	A	7: 100,147,606 (GRCm39)	V195E	probably damaging	Het
Vars2	T	C	17: 35,973,108 (GRCm39)	T394A	probably damaging	Het
Vmn1r1	A	G	1: 181,985,371 (GRCm39)	V98A	possibly damaging	Het
Vmn1r225	A	G	17: 20,722,918 (GRCm39)	I120V	probably benign	Het
Vmn2r102	A	T	17: 19,897,881 (GRCm39)	M299L	probably benign	Het
Vmn2r25	A	G	6: 123,802,337 (GRCm39)	V522A	probably benign	Het
Vmn2r70	T	C	7: 85,215,130 (GRCm39)	I135V	probably benign	Het
Vwf	T	C	6: 125,567,138 (GRCm39)		probably benign	Het
Zfp446	T	C	7: 12,713,048 (GRCm39)	F29L	probably damaging	Het

Other mutations in Kdm6a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
R2238:Kdm6a	UTSW	X	18,065,476 (GRCm39)	missense	probably damaging	0.99
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'- ACACATTTGACTTAACCTCAAGTAC -3'
(R):5'- GCATCTACAAGAGATTAAAGCATTCAC -3'

Sequencing Primer
(F):5'- ATCCTATTTGTTCTTTAGTGTGACTG -3'
(R):5'- GCAAGTTATAAGTGATTCTTCTCTGG -3'

Posted On

2014-06-23