Mutagenetix > Incidental Mutation

Incidental Mutation 'R5386:Kdm6b'

425251

Institutional Source

Beutler Lab

Gene Symbol

Kdm6b

Ensembl Gene

ENSMUSG00000018476

Gene Name

KDM1 lysine (K)-specific demethylase 6B

Synonyms

Jmjd3

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5386 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

69289334-69304501 bp(-) (GRCm39)

Type of Mutation

unclassified

DNA Base Change (assembly)

T to C at 69291636 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000123155 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000050140] [ENSMUST00000094077] [ENSMUST00000144531]

AlphaFold

Q5NCY0

Predicted Effect

probably benign
Transcript: ENSMUST00000050140

SMART Domains

Protein: ENSMUSP00000055528
Gene: ENSMUSG00000045377

Domain	Start	End	E-Value	Type
transmembrane domain	44	66	N/A	INTRINSIC
transmembrane domain	86	108	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000082283

Predicted Effect

unknown
Transcript: ENSMUST00000094077
AA Change: N1501D

SMART Domains

Protein: ENSMUSP00000091620
Gene: ENSMUSG00000018476
AA Change: N1501D

Domain	Start	End	E-Value	Type
low complexity region	29	43	N/A	INTRINSIC
low complexity region	54	71	N/A	INTRINSIC
SCOP:d1elwa_	91	152	9e-5	SMART
low complexity region	214	227	N/A	INTRINSIC
low complexity region	239	270	N/A	INTRINSIC
low complexity region	312	329	N/A	INTRINSIC
low complexity region	333	345	N/A	INTRINSIC
low complexity region	389	415	N/A	INTRINSIC
low complexity region	461	487	N/A	INTRINSIC
low complexity region	515	524	N/A	INTRINSIC
low complexity region	544	577	N/A	INTRINSIC
low complexity region	585	615	N/A	INTRINSIC
low complexity region	643	650	N/A	INTRINSIC
low complexity region	711	719	N/A	INTRINSIC
low complexity region	743	766	N/A	INTRINSIC
low complexity region	771	811	N/A	INTRINSIC
low complexity region	840	879	N/A	INTRINSIC
low complexity region	890	909	N/A	INTRINSIC
low complexity region	950	989	N/A	INTRINSIC
low complexity region	993	1011	N/A	INTRINSIC
low complexity region	1044	1068	N/A	INTRINSIC
low complexity region	1284	1317	N/A	INTRINSIC
JmjC	1337	1500	1.61e-47	SMART
Blast:JmjC	1536	1600	1e-18	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124932

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000129924

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142126

Predicted Effect

probably benign
Transcript: ENSMUST00000144531

SMART Domains

Protein: ENSMUSP00000123155
Gene: ENSMUSG00000059278

Domain	Start	End	E-Value	Type
low complexity region	18	36	N/A	INTRINSIC
Sm	43	114	4.26e-15	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156562

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.3%
20x: 95.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a lysine-specific demethylase that specifically demethylates di- or tri-methylated lysine 27 of histone H3 (H3K27me2 or H3K27me3). H3K27 trimethylation is a repressive epigenetic mark controlling chromatin organization and gene silencing. This protein can also demethylate non-histone proteins such as retinoblastoma protein. Through its demethylation actvity this gene influences cellular differentiation and development, tumorigenesis, inflammatory diseases, and neurodegenerative diseases. This protein has two classical nuclear localization signals at its N-terminus. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2017]
PHENOTYPE: Mice homozygous for a null allele show perinatal death, thick alveolar septum, and absence of air space in the lungs. Mice homozygous for a different null allele die neonatally displaying abnormal lung development, dwarfism, kyphosis, short limbs, and a severe delay in endochondral ossification. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 134 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc12	T	G	8: 87,244,118 (GRCm39)	K1012Q	possibly damaging	Het
Afmid	G	A	11: 117,718,968 (GRCm39)	G33R	probably benign	Het
Agbl3	G	T	6: 34,776,131 (GRCm39)	W207C	probably damaging	Het
Ajuba	T	C	14: 54,807,855 (GRCm39)	Y459C	probably damaging	Het
Ak2	T	C	4: 128,901,965 (GRCm39)	S213P	probably benign	Het
Alk	T	A	17: 72,182,007 (GRCm39)	N1339Y	probably damaging	Het
Angpt1	T	C	15: 42,301,761 (GRCm39)	S416G	probably damaging	Het
Ank2	C	T	3: 126,775,582 (GRCm39)	V854M	probably benign	Het
Ankrd61	G	T	5: 143,828,482 (GRCm39)	N122K	possibly damaging	Het
Armc9	T	A	1: 86,126,011 (GRCm39)	L34Q	probably null	Het
Aspg	T	A	12: 112,089,466 (GRCm39)	V418E	probably benign	Het
Baz1b	C	T	5: 135,266,913 (GRCm39)	R1241C	probably damaging	Het
Bclaf1	T	C	10: 20,201,338 (GRCm39)	V201A	possibly damaging	Het
C1ql3	A	T	2: 13,009,169 (GRCm39)	D225E	probably damaging	Het
Capn9	A	G	8: 125,332,279 (GRCm39)	T417A	possibly damaging	Het
Card14	C	T	11: 119,208,115 (GRCm39)	R62C	probably damaging	Het
Cc2d2a	A	G	5: 43,887,383 (GRCm39)	N1271S	probably benign	Het
Ccpg1	G	A	9: 72,920,326 (GRCm39)	S647N	probably benign	Het
Cdv3	T	C	9: 103,232,429 (GRCm39)	K133R	possibly damaging	Het
Cep128	A	C	12: 90,966,345 (GRCm39)	S1087R	probably benign	Het
Cep70	T	A	9: 99,163,128 (GRCm39)	L325Q	probably damaging	Het
Chit1	T	G	1: 134,077,192 (GRCm39)	F332V	probably damaging	Het
Chodl	C	A	16: 78,743,585 (GRCm39)	T219K	probably damaging	Het
Cntn4	T	C	6: 106,158,765 (GRCm39)	L10P	possibly damaging	Het
Copg1	G	T	6: 87,867,189 (GRCm39)	M87I	possibly damaging	Het
Cplane1	G	A	15: 8,223,897 (GRCm39)	G887R	probably damaging	Het
Cyp3a59	A	G	5: 146,022,578 (GRCm39)	Y28C	probably benign	Het
Dchs1	A	C	7: 105,407,236 (GRCm39)	V2119G	probably damaging	Het
Dedd	T	C	1: 171,165,951 (GRCm39)	L23P	probably damaging	Het
Dmxl2	A	G	9: 54,286,041 (GRCm39)	S2715P	probably benign	Het
Dnah9	T	C	11: 65,920,182 (GRCm39)	N2237S	probably damaging	Het
Drosha	A	G	15: 12,842,207 (GRCm39)	I337V	probably benign	Het
Duox2	A	G	2: 122,125,617 (GRCm39)	V330A	probably benign	Het
Dusp11	T	C	6: 85,924,587 (GRCm39)	*322W	probably null	Het
Dusp8	T	A	7: 141,643,730 (GRCm39)	Q61L	possibly damaging	Het
Ears2	G	C	7: 121,643,600 (GRCm39)	T426S	probably benign	Het
Elmo1	T	C	13: 20,784,380 (GRCm39)	Y646H	probably benign	Het
Eps15	T	A	4: 109,178,422 (GRCm39)	I220K	possibly damaging	Het
Faap100	T	A	11: 120,268,458 (GRCm39)	E105V	possibly damaging	Het
Fam171a2	C	A	11: 102,328,693 (GRCm39)	V689L	possibly damaging	Het
Fam91a1	G	A	15: 58,320,243 (GRCm39)	S645N	probably benign	Het
Fancg	G	A	4: 43,007,076 (GRCm39)	Q234*	probably null	Het
Garre1	A	G	7: 33,941,813 (GRCm39)	F120L	probably damaging	Het
Gid4	T	A	11: 60,323,268 (GRCm39)		probably null	Het
Gm7361	A	C	5: 26,463,903 (GRCm39)	T53P	probably benign	Het
Golgb1	T	A	16: 36,732,677 (GRCm39)	C641*	probably null	Het
Gon4l	T	A	3: 88,765,803 (GRCm39)	M409K	probably benign	Het
Gpatch8	A	T	11: 102,399,053 (GRCm39)		probably null	Het
Gpr156	T	A	16: 37,768,671 (GRCm39)	V64E	possibly damaging	Het
Grid2	T	A	6: 63,908,089 (GRCm39)	I243K	probably damaging	Het
Gucy2g	G	A	19: 55,203,548 (GRCm39)	A750V	probably damaging	Het
Hdac5	T	C	11: 102,092,967 (GRCm39)	E590G	possibly damaging	Het
Herc3	T	A	6: 58,851,263 (GRCm39)	M504K	probably damaging	Het
Hif1a	A	G	12: 73,990,867 (GRCm39)	E713G	probably benign	Het
Hmx3	A	G	7: 131,146,033 (GRCm39)	D247G	probably damaging	Het
Hoxd11	G	T	2: 74,513,163 (GRCm39)	E143*	probably null	Het
Ifitm3	T	C	7: 140,590,554 (GRCm39)	N2S	probably benign	Het
Il17f	T	C	1: 20,848,181 (GRCm39)	Q99R	probably benign	Het
Itga6	T	A	2: 71,671,494 (GRCm39)	S341R	probably damaging	Het
Itgam	A	G	7: 127,707,152 (GRCm39)	N661S	probably benign	Het
Jag1	A	T	2: 136,937,464 (GRCm39)	H303Q	possibly damaging	Het
Kcnh8	T	A	17: 53,033,023 (GRCm39)	N103K	probably benign	Het
Keg1	A	C	19: 12,691,902 (GRCm39)	N63T	probably damaging	Het
Klf12	T	A	14: 100,137,595 (GRCm39)	H317L	probably damaging	Het
Lrp1	A	T	10: 127,427,983 (GRCm39)	V530E	probably damaging	Het
Mrgpra6	A	G	7: 46,838,629 (GRCm39)	C190R	probably damaging	Het
Myo1a	G	T	10: 127,541,766 (GRCm39)	E102*	probably null	Het
Napa	A	T	7: 15,850,397 (GRCm39)	E265D	probably benign	Het
Ncam1	A	C	9: 49,476,174 (GRCm39)	V305G	probably damaging	Het
Nek8	T	C	11: 78,061,263 (GRCm39)		probably null	Het
Or10ag53	C	T	2: 87,082,827 (GRCm39)	P182L	probably benign	Het
Or11g24	T	A	14: 50,662,846 (GRCm39)	V290E	possibly damaging	Het
Or4a70	G	T	2: 89,324,481 (GRCm39)	Y58*	probably null	Het
Or4f52	T	C	2: 111,061,539 (GRCm39)	T200A	probably benign	Het
Or52a20	T	C	7: 103,366,562 (GRCm39)	F254L	probably benign	Het
Or5ak4	T	C	2: 85,161,979 (GRCm39)	T88A	probably benign	Het
Or5h23	T	A	16: 58,906,253 (GRCm39)	M198L	probably benign	Het
Or8c11	A	T	9: 38,289,281 (GRCm39)	I29F	probably benign	Het
Or8g2b	A	G	9: 39,751,126 (GRCm39)	Y132C	possibly damaging	Het
Pabpc4	A	G	4: 123,188,790 (GRCm39)	Q417R	probably benign	Het
Panx3	A	T	9: 37,580,320 (GRCm39)	M11K	probably damaging	Het
Pcbp1	C	T	6: 86,502,471 (GRCm39)	E143K	probably damaging	Het
Pdcd7	G	A	9: 65,265,974 (GRCm39)	W477*	probably null	Het
Pi4k2a	G	A	19: 42,078,954 (GRCm39)	S5N	probably damaging	Het
Plag1	T	A	4: 3,904,075 (GRCm39)	Q372L	probably benign	Het
Plce1	C	A	19: 38,748,535 (GRCm39)	N1755K	probably damaging	Het
Pld4	G	T	12: 112,730,422 (GRCm39)	E102*	probably null	Het
Pnlip	A	G	19: 58,668,039 (GRCm39)	N345S	probably benign	Het
Ppm1e	A	T	11: 87,249,377 (GRCm39)	L118Q	possibly damaging	Het
Prkra	T	G	2: 76,469,622 (GRCm39)	T146P	probably damaging	Het
Prpf8	A	G	11: 75,386,625 (GRCm39)	D1038G	probably damaging	Het
Prss51	T	A	14: 64,334,543 (GRCm39)	V108E	probably damaging	Het
Prxl2b	T	A	4: 154,983,462 (GRCm39)	M1L	probably benign	Het
Ptch1	A	G	13: 63,692,857 (GRCm39)	Y181H	probably damaging	Het
Reln	A	G	5: 22,244,527 (GRCm39)	V817A	probably benign	Het
Rictor	C	A	15: 6,818,985 (GRCm39)	Q1403K	probably benign	Het
Rims1	T	A	1: 22,482,469 (GRCm39)	I882F	probably damaging	Het
Rnf19a	A	G	15: 36,242,185 (GRCm39)	V618A	probably benign	Het
Ryr1	A	T	7: 28,816,841 (GRCm39)	I65N	probably damaging	Het
S1pr2	T	C	9: 20,878,890 (GRCm39)	T313A	probably benign	Het
Serpine2	A	T	1: 79,799,004 (GRCm39)	Y83*	probably null	Het
Sfi1	A	ATCTTCCCAAAGCCAGTGC	11: 3,103,384 (GRCm39)		probably benign	Het
Sgip1	T	C	4: 102,772,256 (GRCm39)	V215A	probably benign	Het
Sgsm3	T	C	15: 80,892,200 (GRCm39)	V256A	probably benign	Het
Shroom4	T	A	X: 6,497,523 (GRCm39)	C894*	probably null	Het
Slc14a2	T	A	18: 78,229,055 (GRCm39)	D306V	possibly damaging	Het
Slc28a2b	C	A	2: 122,353,259 (GRCm39)	L480I	probably benign	Het
Slc4a10	A	T	2: 62,120,402 (GRCm39)	E843V	probably damaging	Het
Smyd4	T	A	11: 75,280,982 (GRCm39)	C152S	probably damaging	Het
Snx10	T	C	6: 51,552,952 (GRCm39)	Y32H	probably damaging	Het
Sorl1	T	C	9: 41,968,580 (GRCm39)	T558A	possibly damaging	Het
Spata31d1b	G	A	13: 59,866,866 (GRCm39)	C1338Y	possibly damaging	Het
Sppl2c	T	A	11: 104,078,127 (GRCm39)	I309K	possibly damaging	Het
Stard9	A	G	2: 120,531,111 (GRCm39)	E2456G	probably damaging	Het
Stx1b	A	T	7: 127,414,575 (GRCm39)	D16E	probably benign	Het
Tecpr2	T	C	12: 110,881,887 (GRCm39)	V152A	probably damaging	Het
Tedc1	T	C	12: 113,120,302 (GRCm39)	V47A	probably benign	Het
Tep1	A	T	14: 51,105,774 (GRCm39)	L82Q	probably damaging	Het
Tgm4	A	G	9: 122,885,559 (GRCm39)	Y367C	probably damaging	Het
Tle1	C	T	4: 72,060,081 (GRCm39)	V258M	probably damaging	Het
Tm9sf1	C	T	14: 55,880,301 (GRCm39)	G32D	possibly damaging	Het
Tmco2	A	G	4: 120,963,181 (GRCm39)	L106P	probably damaging	Het
Tmem131	A	T	1: 36,911,639 (GRCm39)	C103S	possibly damaging	Het
Tmprss7	T	A	16: 45,489,891 (GRCm39)	I444F	possibly damaging	Het
Trank1	T	C	9: 111,191,470 (GRCm39)	V493A	probably benign	Het
Trim80	A	T	11: 115,338,843 (GRCm39)	T558S	probably benign	Het
Trmt6	C	A	2: 132,650,703 (GRCm39)	A302S	probably benign	Het
Ttc17	A	T	2: 94,133,985 (GRCm39)	W1067R	probably damaging	Het
Tulp4	T	A	17: 6,286,568 (GRCm39)	V1532D	probably damaging	Het
Ubqlnl	T	G	7: 103,798,424 (GRCm39)	I358L	probably benign	Het
Ulk3	T	A	9: 57,498,023 (GRCm39)	I108N	possibly damaging	Het
Vps13b	A	T	15: 35,640,674 (GRCm39)		probably null	Het
Vwa3a	A	G	7: 120,389,365 (GRCm39)	K68E	possibly damaging	Het
Zfp746	G	T	6: 48,041,110 (GRCm39)	H538N	possibly damaging	Het

Other mutations in Kdm6b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00484:Kdm6b	APN	11	69,297,132 (GRCm39)	missense	possibly damaging	0.85
IGL02271:Kdm6b	APN	11	69,296,893 (GRCm39)	missense	possibly damaging	0.65
beine	UTSW	11	69,294,418 (GRCm39)	missense	unknown
Gaudy	UTSW	11	69,291,032 (GRCm39)	missense	unknown
Hypocrisy	UTSW	11	69,292,977 (GRCm39)	nonsense	probably null
Knochen	UTSW	11	69,290,881 (GRCm39)	unclassified	probably benign
Ostentatious	UTSW	11	69,294,424 (GRCm39)	missense	unknown
Piquant	UTSW	11	69,294,620 (GRCm39)	missense	unknown
preen	UTSW	11	69,292,919 (GRCm39)	missense	unknown
Tart	UTSW	11	69,297,192 (GRCm39)	missense	probably damaging	1.00
BB007:Kdm6b	UTSW	11	69,290,778 (GRCm39)	missense	unknown
BB017:Kdm6b	UTSW	11	69,290,778 (GRCm39)	missense	unknown
PIT4458001:Kdm6b	UTSW	11	69,290,778 (GRCm39)	missense	unknown
R0455:Kdm6b	UTSW	11	69,297,822 (GRCm39)	nonsense	probably null
R0645:Kdm6b	UTSW	11	69,295,844 (GRCm39)	missense	unknown
R1659:Kdm6b	UTSW	11	69,298,414 (GRCm39)	missense	possibly damaging	0.88
R1855:Kdm6b	UTSW	11	69,298,112 (GRCm39)	missense	probably damaging	0.99
R1962:Kdm6b	UTSW	11	69,292,191 (GRCm39)	unclassified	probably benign
R1993:Kdm6b	UTSW	11	69,297,129 (GRCm39)	missense	probably null	0.85
R2029:Kdm6b	UTSW	11	69,294,418 (GRCm39)	missense	unknown
R2181:Kdm6b	UTSW	11	69,291,952 (GRCm39)	nonsense	probably null
R2215:Kdm6b	UTSW	11	69,295,870 (GRCm39)	missense	unknown
R2904:Kdm6b	UTSW	11	69,296,611 (GRCm39)	missense	possibly damaging	0.63
R2992:Kdm6b	UTSW	11	69,297,133 (GRCm39)	small deletion	probably benign
R3236:Kdm6b	UTSW	11	69,297,192 (GRCm39)	missense	probably damaging	1.00
R3950:Kdm6b	UTSW	11	69,296,441 (GRCm39)	missense	probably damaging	1.00
R4027:Kdm6b	UTSW	11	69,297,094 (GRCm39)	missense	possibly damaging	0.92
R4830:Kdm6b	UTSW	11	69,294,620 (GRCm39)	missense	unknown
R4996:Kdm6b	UTSW	11	69,296,557 (GRCm39)	missense	probably damaging	1.00
R5034:Kdm6b	UTSW	11	69,292,736 (GRCm39)	splice site	probably benign
R5140:Kdm6b	UTSW	11	69,290,881 (GRCm39)	unclassified	probably benign
R5160:Kdm6b	UTSW	11	69,291,594 (GRCm39)	unclassified	probably benign
R5240:Kdm6b	UTSW	11	69,292,730 (GRCm39)	splice site	probably benign
R5273:Kdm6b	UTSW	11	69,295,027 (GRCm39)	missense	unknown
R5597:Kdm6b	UTSW	11	69,296,900 (GRCm39)	missense	probably damaging	0.96
R5598:Kdm6b	UTSW	11	69,296,900 (GRCm39)	missense	probably damaging	0.96
R5812:Kdm6b	UTSW	11	69,296,755 (GRCm39)	missense	probably damaging	0.98
R5976:Kdm6b	UTSW	11	69,294,614 (GRCm39)	critical splice donor site	probably null
R6000:Kdm6b	UTSW	11	69,294,424 (GRCm39)	missense	unknown
R6145:Kdm6b	UTSW	11	69,295,852 (GRCm39)	missense	unknown
R6191:Kdm6b	UTSW	11	69,297,584 (GRCm39)	missense	probably benign	0.01
R6256:Kdm6b	UTSW	11	69,297,555 (GRCm39)	missense	probably damaging	0.96
R6304:Kdm6b	UTSW	11	69,295,084 (GRCm39)	missense	unknown
R6917:Kdm6b	UTSW	11	69,297,419 (GRCm39)	missense	probably benign	0.04
R6939:Kdm6b	UTSW	11	69,297,588 (GRCm39)	missense	probably damaging	0.99
R7356:Kdm6b	UTSW	11	69,292,991 (GRCm39)	nonsense	probably null
R7644:Kdm6b	UTSW	11	69,291,032 (GRCm39)	missense	unknown
R7673:Kdm6b	UTSW	11	69,296,568 (GRCm39)	missense	probably damaging	0.98
R7698:Kdm6b	UTSW	11	69,296,807 (GRCm39)	missense	probably benign	0.14
R7776:Kdm6b	UTSW	11	69,296,960 (GRCm39)	missense	possibly damaging	0.84
R7930:Kdm6b	UTSW	11	69,290,778 (GRCm39)	missense	unknown
R8383:Kdm6b	UTSW	11	69,296,876 (GRCm39)	missense	probably benign
R8725:Kdm6b	UTSW	11	69,292,919 (GRCm39)	missense	unknown
R8727:Kdm6b	UTSW	11	69,292,919 (GRCm39)	missense	unknown
R8813:Kdm6b	UTSW	11	69,297,658 (GRCm39)	small insertion	probably benign
R8813:Kdm6b	UTSW	11	69,297,655 (GRCm39)	small insertion	probably benign
R8851:Kdm6b	UTSW	11	69,291,993 (GRCm39)	missense	unknown
R9074:Kdm6b	UTSW	11	69,292,977 (GRCm39)	nonsense	probably null
R9130:Kdm6b	UTSW	11	69,295,424 (GRCm39)	missense	unknown
R9179:Kdm6b	UTSW	11	69,297,521 (GRCm39)	critical splice donor site	probably null
R9535:Kdm6b	UTSW	11	69,297,276 (GRCm39)	nonsense	probably null
Z1177:Kdm6b	UTSW	11	69,294,692 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- TAAGGACATGCTGCAGACG -3'
(R):5'- ACAACATTGCCTGGAACGTGG -3'

Sequencing Primer
(F):5'- TGCAGACGCAGGGGAAGAATG -3'
(R):5'- TCACCGGTAAGAGGCTGG -3'

Posted On

2016-08-04