Mutagenetix > Incidental Mutation

Incidental Mutation 'R2029:Kdm6b'

221026

Institutional Source

Beutler Lab

Gene Symbol

Kdm6b

Ensembl Gene

ENSMUSG00000018476

Gene Name

KDM1 lysine (K)-specific demethylase 6B

Synonyms

Jmjd3

MMRRC Submission

040036-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2029 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

69289334-69304501 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 69294418 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Aspartic acid at position 1218 (G1218D)

Ref Sequence

ENSEMBL: ENSMUSP00000091620 (fasta)

Gene Model

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

AlphaFold

Q5NCY0

PDB Structure

The free structure of the mouse C-terminal domain of KDM6B [X-RAY DIFFRACTION]
free KDM6B structure [X-RAY DIFFRACTION]
the crystal structure of KDM6B bound with H3K27me3 peptide [X-RAY DIFFRACTION]

Predicted Effect

unknown
Transcript: ENSMUST00000094077
AA Change: G1218D

SMART Domains

Protein: ENSMUSP00000091620
Gene: ENSMUSG00000018476
AA Change: G1218D

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: ENSMUST00000129924

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156562

Meta Mutation Damage Score

0.6545

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 93.8%

Validation Efficiency

98% (97/99)

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: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam18	C	G	8: 25,140,893 (GRCm39)	G286A	probably damaging	Het
Adcy1	G	A	11: 7,089,142 (GRCm39)	A519T	probably benign	Het
Anxa2	T	A	9: 69,371,762 (GRCm39)	S2T	possibly damaging	Het
Ap3m1	G	A	14: 21,089,217 (GRCm39)	S261L	possibly damaging	Het
Baz2b	A	T	2: 59,743,067 (GRCm39)		probably benign	Het
Brdt	T	A	5: 107,507,090 (GRCm39)	S497T	probably benign	Het
Cdh11	A	G	8: 103,406,404 (GRCm39)	F23S	probably benign	Het
Cdh16	A	C	8: 105,344,434 (GRCm39)	L540R	probably damaging	Het
Ces5a	A	T	8: 94,261,205 (GRCm39)	L74Q	probably damaging	Het
Cfap69	A	G	5: 5,654,306 (GRCm39)	S543P	probably damaging	Het
Cfap74	T	C	4: 155,526,538 (GRCm39)	I763T	possibly damaging	Het
Cma1	T	A	14: 56,181,191 (GRCm39)	R58S	possibly damaging	Het
Csmd3	C	T	15: 47,701,975 (GRCm39)	D1599N	probably damaging	Het
Cyld	A	G	8: 89,471,940 (GRCm39)	K857R	probably benign	Het
Cyp3a16	T	C	5: 145,388,667 (GRCm39)	D270G	probably damaging	Het
D1Pas1	T	C	1: 186,700,286 (GRCm39)	S72P	possibly damaging	Het
Ddx3y	T	C	Y: 1,266,389 (GRCm39)	E331G	probably benign	Het
Degs1l	T	A	1: 180,882,496 (GRCm39)	I86K	probably benign	Het
Dis3l2	T	C	1: 86,782,189 (GRCm39)		probably benign	Het
Dop1a	G	T	9: 86,403,418 (GRCm39)	W1539C	probably damaging	Het
Dop1b	A	G	16: 93,566,323 (GRCm39)	K917E	probably benign	Het
Ecpas	G	A	4: 58,844,165 (GRCm39)	R534*	probably null	Het
Efcab3	T	C	11: 104,990,851 (GRCm39)	I5462T	probably damaging	Het
Eif1ad15	A	T	12: 88,288,191 (GRCm39)	S21T	unknown	Het
Epo	A	G	5: 137,483,447 (GRCm39)		probably benign	Het
Figla	T	A	6: 85,997,624 (GRCm39)		probably benign	Het
Flvcr1	T	C	1: 190,753,353 (GRCm39)	D273G	probably benign	Het
Fryl	T	A	5: 73,179,465 (GRCm39)	R304*	probably null	Het
Gcm1	T	G	9: 77,972,326 (GRCm39)	D422E	possibly damaging	Het
Get3	A	T	8: 85,746,403 (GRCm39)	Y148*	probably null	Het
Ggt6	A	G	11: 72,328,367 (GRCm39)	D251G	possibly damaging	Het
Git2	A	G	5: 114,904,511 (GRCm39)		probably null	Het
Gm18856	A	T	13: 14,139,376 (GRCm39)		probably benign	Het
Gm20939	T	A	17: 95,183,252 (GRCm39)		probably benign	Het
Gpr176	A	G	2: 118,109,913 (GRCm39)	Y449H	probably benign	Het
H2-Eb1	A	G	17: 34,533,366 (GRCm39)	E196G	probably damaging	Het
H2-M10.6	A	G	17: 37,124,799 (GRCm39)	T239A	possibly damaging	Het
Haus5	T	C	7: 30,358,825 (GRCm39)	N237S	possibly damaging	Het
Hectd3	T	C	4: 116,857,882 (GRCm39)	M605T	probably damaging	Het
Hps3	T	C	3: 20,084,691 (GRCm39)	I166V	probably benign	Het
Ighv5-21	A	T	12: 114,286,434 (GRCm39)		probably benign	Het
Klhl30	A	G	1: 91,285,636 (GRCm39)		probably null	Het
Kmt2a	A	T	9: 44,729,747 (GRCm39)	S3523R	probably benign	Het
Lnpep	A	T	17: 17,788,661 (GRCm39)	N481K	probably damaging	Het
Lrp1b	T	C	2: 41,231,861 (GRCm39)	H1203R	probably benign	Het
Lrrc8a	C	T	2: 30,146,661 (GRCm39)	R492W	probably damaging	Het
Magel2	T	A	7: 62,030,342 (GRCm39)	V1082D	unknown	Het
Memo1	A	C	17: 74,552,049 (GRCm39)	H82Q	probably null	Het
Myh13	A	T	11: 67,252,115 (GRCm39)	T1408S	probably benign	Het
Myh2	A	T	11: 67,085,451 (GRCm39)	N1792Y	possibly damaging	Het
Myo1e	A	T	9: 70,275,969 (GRCm39)	N728I	possibly damaging	Het
Myo1e	T	C	9: 70,285,997 (GRCm39)		probably benign	Het
Myo5c	T	C	9: 75,196,337 (GRCm39)		probably benign	Het
Or11l3	T	A	11: 58,516,319 (GRCm39)	L184F	probably damaging	Het
Or1e19	A	G	11: 73,316,188 (GRCm39)	V207A	probably benign	Het
Or2d2b	T	C	7: 106,705,643 (GRCm39)	I142V	probably benign	Het
Or4c11c	T	A	2: 88,661,749 (GRCm39)	M96K	possibly damaging	Het
Or51g1	T	A	7: 102,633,478 (GRCm39)	T298S	probably damaging	Het
Or52e3	T	C	7: 102,868,967 (GRCm39)	F14S	probably damaging	Het
Parp2	C	T	14: 51,047,543 (GRCm39)	A18V	probably benign	Het
Peli1	T	A	11: 21,098,110 (GRCm39)	C282S	probably damaging	Het
Phf8-ps	G	T	17: 33,286,598 (GRCm39)	S68*	probably null	Het
Piezo2	T	C	18: 63,252,006 (GRCm39)	M404V	possibly damaging	Het
Pkn1	T	A	8: 84,404,592 (GRCm39)	Q496L	possibly damaging	Het
Pla2r1	A	T	2: 60,262,317 (GRCm39)	F1093L	probably damaging	Het
Ppp2r3d	A	G	9: 101,022,680 (GRCm39)	V323A	probably damaging	Het
Pramel16	T	A	4: 143,676,453 (GRCm39)	Y217F	probably benign	Het
Prg2	C	T	2: 84,812,342 (GRCm39)		probably benign	Het
Ptprb	G	A	10: 116,182,958 (GRCm39)	G1545S	probably benign	Het
Rbm19	A	G	5: 120,258,307 (GRCm39)	D174G	possibly damaging	Het
Rhbdf2	T	A	11: 116,491,974 (GRCm39)	T526S	probably damaging	Het
Rpusd4	A	G	9: 35,179,310 (GRCm39)	N42S	probably benign	Het
Ryr3	T	A	2: 112,477,361 (GRCm39)	Q4455L	possibly damaging	Het
Sema4a	G	T	3: 88,358,668 (GRCm39)	H30Q	probably damaging	Het
Skint1	G	A	4: 111,878,653 (GRCm39)		probably null	Het
Slc1a3	A	G	15: 8,675,153 (GRCm39)	V284A	probably benign	Het
Slc30a9	A	T	5: 67,497,318 (GRCm39)	K288*	probably null	Het
Slc36a1	G	T	11: 55,119,164 (GRCm39)	A380S	probably benign	Het
Slc47a1	G	A	11: 61,268,833 (GRCm39)		probably benign	Het
Snx19	A	T	9: 30,340,296 (GRCm39)	E478V	probably benign	Het
Spag6	T	C	2: 18,738,916 (GRCm39)		probably benign	Het
Stag1	A	T	9: 100,668,740 (GRCm39)	T223S	probably damaging	Het
Terb1	A	T	8: 105,224,732 (GRCm39)		probably benign	Het
Terf1	A	G	1: 15,876,170 (GRCm39)	D90G	possibly damaging	Het
Tex15	A	G	8: 34,061,302 (GRCm39)	D518G	probably damaging	Het
Tmem174	T	A	13: 98,773,546 (GRCm39)	M95L	possibly damaging	Het
Tnnt3	GTCCAGGCATCTC	GTC	7: 142,066,364 (GRCm39)		probably benign	Het
Usp28	A	G	9: 48,896,803 (GRCm39)	D8G	probably benign	Het
Vmn2r105	T	C	17: 20,444,840 (GRCm39)	T551A	probably damaging	Het
Vmn2r107	A	G	17: 20,595,549 (GRCm39)	I701V	probably benign	Het
Vmn2r13	A	C	5: 109,339,943 (GRCm39)	F11V	probably benign	Het
Vmn2r85	G	C	10: 130,261,443 (GRCm39)	S298*	probably null	Het
Wdr6	C	G	9: 108,452,554 (GRCm39)	W443S	probably damaging	Het
Wipi1	A	G	11: 109,474,016 (GRCm39)	V210A	probably damaging	Het
Zfp317	A	G	9: 19,556,532 (GRCm39)	T47A	probably benign	Het
Zfp61	T	C	7: 23,991,714 (GRCm39)	T146A	probably benign	Het
Zfp964	A	G	8: 70,116,567 (GRCm39)	E389G	unknown	Het
Zfyve16	T	C	13: 92,640,985 (GRCm39)	D1253G	probably damaging	Het
Zpld2	T	C	4: 133,929,669 (GRCm39)	K212R	possibly damaging	Het
Zswim7	G	A	11: 62,158,299 (GRCm39)		probably benign	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
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
R5386:Kdm6b	UTSW	11	69,291,636 (GRCm39)	unclassified	probably benign
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'- GAGGTCTATTTCCCATGTGTCCAC -3'
(R):5'- AGAGCCACCCTTTCCAGAAG -3'

Sequencing Primer
(F):5'- AACACCTCAAGGCTGGTTG -3'
(R):5'- CTTTCCAGAAGGGTTGAATTGG -3'

Posted On

2014-08-25