Mutagenetix > Incidental Mutation

Incidental Mutation 'R9130:Kdm6b'

693564

Institutional Source

Beutler Lab

Gene Symbol

Kdm6b

Ensembl Gene

ENSMUSG00000018476

Gene Name

KDM1 lysine (K)-specific demethylase 6B

Synonyms

Jmjd3

MMRRC Submission

068928-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9130 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

69289334-69304501 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 69295424 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 948 (T948A)

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: T948A

SMART Domains

Protein: ENSMUSP00000091620
Gene: ENSMUSG00000018476
AA Change: T948A

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.2%

Validation Efficiency

99% (87/88)

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: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abr	A	G	11: 76,342,753 (GRCm39)	C585R	possibly damaging	Het
Acaca	T	C	11: 84,202,145 (GRCm39)	L1380S	probably damaging	Het
Aifm2	A	C	10: 61,563,505 (GRCm39)	Q125P	probably null	Het
Ak5	A	T	3: 152,178,569 (GRCm39)	L482*	probably null	Het
Aldh3a2	T	C	11: 61,139,758 (GRCm39)	Q458R	probably benign	Het
Ank2	G	A	3: 126,810,565 (GRCm39)	T524I		Het
Apoc3	A	T	9: 46,146,481 (GRCm39)	S25T	unknown	Het
Ash1l	A	T	3: 88,965,848 (GRCm39)	R2417*	probably null	Het
Bbs12	A	G	3: 37,373,205 (GRCm39)		probably benign	Het
Birc6	T	A	17: 74,919,146 (GRCm39)	I1992N		Het
Brd9	G	A	13: 74,092,906 (GRCm39)	V299M	probably damaging	Het
Brwd1	A	T	16: 95,866,130 (GRCm39)	N217K	probably damaging	Het
C3	T	C	17: 57,518,678 (GRCm39)	Y1235C	probably damaging	Het
Cacna1c	T	C	6: 118,590,907 (GRCm39)	Y1538C		Het
Ccdc172	T	A	19: 58,525,779 (GRCm39)	H212Q	possibly damaging	Het
Cdc6	A	G	11: 98,802,999 (GRCm39)	D313G	probably damaging	Het
Cyp2e1	T	C	7: 140,353,022 (GRCm39)	V353A	probably damaging	Het
Dlg2	G	T	7: 92,080,258 (GRCm39)	V711F	probably damaging	Het
Dmac2	T	C	7: 25,320,448 (GRCm39)	F49S	probably damaging	Het
Dnah7b	A	G	1: 46,173,674 (GRCm39)	K660E	probably benign	Het
Dusp8	A	T	7: 141,642,155 (GRCm39)	S106T	probably benign	Het
Dynll1	T	A	5: 115,438,604 (GRCm39)	I34F	probably benign	Het
Epb41l4b	A	G	4: 57,103,447 (GRCm39)	F130L	possibly damaging	Het
Erc2	T	C	14: 27,751,418 (GRCm39)	Y705H	probably benign	Het
Exosc8	T	A	3: 54,638,503 (GRCm39)	L160F	probably damaging	Het
F5	A	G	1: 164,001,830 (GRCm39)	T178A	probably benign	Het
F7	C	A	8: 13,085,059 (GRCm39)	P362T	probably damaging	Het
Fkbp3	T	C	12: 65,112,567 (GRCm39)	K156E	possibly damaging	Het
Folh1	G	A	7: 86,368,913 (GRCm39)	T738I	probably benign	Het
Gatad2b	C	T	3: 90,255,936 (GRCm39)	A134V	probably benign	Het
Glud1	T	A	14: 34,057,349 (GRCm39)	W338R		Het
Gm21149	T	C	5: 15,680,261 (GRCm39)	K62E	possibly damaging	Het
Gm32742	A	G	9: 51,050,049 (GRCm39)	Y1517H	probably damaging	Het
Grik5	G	A	7: 24,767,429 (GRCm39)		probably benign	Het
Gse1	A	T	8: 121,295,052 (GRCm39)	E391V	unknown	Het
Gxylt2	C	T	6: 100,710,329 (GRCm39)	Q157*	probably null	Het
Hbq1b	C	T	11: 32,237,092 (GRCm39)	T27I	probably damaging	Het
Hoxd13	T	A	2: 74,499,382 (GRCm39)	D243E	probably benign	Het
Hsd3b3	T	A	3: 98,651,211 (GRCm39)	I80F	possibly damaging	Het
Hsf2bp	A	T	17: 32,230,082 (GRCm39)		probably benign	Het
Itch	G	A	2: 155,052,045 (GRCm39)		probably benign	Het
Kat14	T	C	2: 144,215,742 (GRCm39)	F76L	probably benign	Het
Kmt2c	A	T	5: 25,516,102 (GRCm39)	H2580Q	probably benign	Het
Lrp1	T	C	10: 127,382,281 (GRCm39)	T3727A	probably benign	Het
Lrrc8a	A	G	2: 30,147,042 (GRCm39)	I619V	possibly damaging	Het
Mansc1	C	A	6: 134,586,951 (GRCm39)	G409W	probably damaging	Het
Map3k11	C	A	19: 5,746,038 (GRCm39)	L418I	possibly damaging	Het
Mettl4	T	A	17: 95,042,913 (GRCm39)	I308L	possibly damaging	Het
Myo9a	A	G	9: 59,739,514 (GRCm39)	D742G	probably damaging	Het
Mypn	T	C	10: 63,028,652 (GRCm39)	Q137R	probably benign	Het
Neurod4	A	T	10: 130,106,427 (GRCm39)	Y282*	probably null	Het
Nup210	A	G	6: 91,020,799 (GRCm39)	F965S	probably benign	Het
Oplah	T	C	15: 76,185,098 (GRCm39)	T872A	possibly damaging	Het
Or1ab2	G	T	8: 72,863,697 (GRCm39)	G96C	probably damaging	Het
Or4b12	A	G	2: 90,096,358 (GRCm39)	C139R	probably damaging	Het
Or5m8	T	G	2: 85,822,819 (GRCm39)	Y219*	probably null	Het
Or6c68	A	G	10: 129,157,897 (GRCm39)	N135S	probably benign	Het
Pkn2	A	T	3: 142,515,245 (GRCm39)	D696E	possibly damaging	Het
Pla2r1	A	T	2: 60,325,729 (GRCm39)		probably benign	Het
Plpp1	A	T	13: 112,988,038 (GRCm39)	I54L		Het
Ppp4r2	T	G	6: 100,842,113 (GRCm39)	N191K	probably damaging	Het
Ptpdc1	G	T	13: 48,739,655 (GRCm39)	P592Q	probably benign	Het
Qrich2	A	T	11: 116,347,692 (GRCm39)	L1044*	probably null	Het
Rb1cc1	A	G	1: 6,315,109 (GRCm39)	I421V	probably damaging	Het
Ripor3	A	T	2: 167,823,267 (GRCm39)	C881*	probably null	Het
Rreb1	T	C	13: 38,114,282 (GRCm39)	F547S	probably benign	Het
Scel	T	C	14: 103,770,746 (GRCm39)	V60A	probably benign	Het
Shank3	G	A	15: 89,442,419 (GRCm39)	A1771T	probably benign	Het
Slc6a20a	A	G	9: 123,469,631 (GRCm39)		probably null	Het
Slfn5	C	T	11: 82,851,446 (GRCm39)	T581I	probably damaging	Het
Ssh3	A	C	19: 4,314,113 (GRCm39)	V412G	probably damaging	Het
Stx17	T	G	4: 48,159,071 (GRCm39)		probably benign	Het
Sun3	T	G	11: 8,968,170 (GRCm39)	T274P	probably benign	Het
Tm9sf1	T	C	14: 55,875,464 (GRCm39)	T427A	probably damaging	Het
Tmem114	T	A	16: 8,229,983 (GRCm39)	I140F		Het
Tmem40	T	C	6: 115,710,980 (GRCm39)	R167G	possibly damaging	Het
Top3a	C	A	11: 60,641,401 (GRCm39)		probably null	Het
Trafd1	A	G	5: 121,516,573 (GRCm39)	V210A	probably benign	Het
Trim66	T	C	7: 109,076,896 (GRCm39)	I348V	possibly damaging	Het
Ttn	G	A	2: 76,679,172 (GRCm39)	A10850V	unknown	Het
Unc80	G	A	1: 66,677,244 (GRCm39)	A2058T	possibly damaging	Het
Upp2	T	C	2: 58,668,020 (GRCm39)	Y238H	probably damaging	Het
Vmn1r224	T	A	17: 20,640,242 (GRCm39)	I273N	probably damaging	Het
Vps13c	T	C	9: 67,836,805 (GRCm39)	S1768P	probably damaging	Het
Zfp26	G	A	9: 20,348,723 (GRCm39)	H614Y	probably damaging	Het
Zfp263	C	T	16: 3,567,701 (GRCm39)	T672I	probably benign	Het
Zfp641	T	A	15: 98,186,732 (GRCm39)	Q297L	probably benign	Het
Zfp944	T	C	17: 22,560,031 (GRCm39)	E25G	probably damaging	Het
Zfp994	T	C	17: 22,418,981 (GRCm39)	E656G	unknown	Het
Zfyve19	A	G	2: 119,045,330 (GRCm39)	D206G	probably 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
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
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'- ACTCTGCAAGTCGAGGTTCC -3'
(R):5'- TCAGTTCTCTACCTCAGGCG -3'

Sequencing Primer
(F):5'- AAGTCGAGGTTCCCCAGCAC -3'
(R):5'- GGTGAAGAGCCAGCACC -3'

Posted On

2022-01-20