Mutagenetix > Incidental Mutation

Incidental Mutation 'R5248:Kdm5b'

398608

Institutional Source

Beutler Lab

Gene Symbol

Kdm5b

Ensembl Gene

ENSMUSG00000042207

Gene Name

lysine demethylase 5B

Synonyms

2010009J12Rik, PLU-1, Rb-Bp2, Jarid1b, D1Ertd202e, Plu1, 2210016I17Rik

MMRRC Submission

042819-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.451) question?

Stock #

R5248 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

134487916-134560621 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 134548735 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 1080 (E1080G)

Ref Sequence

ENSEMBL: ENSMUSP00000107817 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047714] [ENSMUST00000112198]

AlphaFold

Q80Y84

PDB Structure

Solution structure of the ARID domain of Jarid1b protein [SOLUTION NMR]

Predicted Effect

probably benign
Transcript: ENSMUST00000047714
AA Change: E1080G

PolyPhen 2 Score 0.112 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207
AA Change: E1080G

Domain	Start	End	E-Value	Type
low complexity region	7	30	N/A	INTRINSIC
JmjN	31	72	2.87e-20	SMART
ARID	94	183	7.39e-32	SMART
BRIGHT	98	188	1.51e-35	SMART
low complexity region	228	239	N/A	INTRINSIC
PHD	311	357	6.15e-14	SMART
JmjC	453	619	2.33e-67	SMART
Pfam:zf-C5HC2	692	744	2.2e-17	PFAM
Pfam:PLU-1	757	1088	5.6e-92	PFAM
low complexity region	1097	1109	N/A	INTRINSIC
PHD	1178	1222	6.2e-10	SMART
low complexity region	1225	1236	N/A	INTRINSIC
low complexity region	1406	1417	N/A	INTRINSIC
low complexity region	1470	1484	N/A	INTRINSIC
PHD	1486	1536	1.18e-6	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000112198
AA Change: E1080G

PolyPhen 2 Score 0.112 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000107817
Gene: ENSMUSG00000042207
AA Change: E1080G

Domain	Start	End	E-Value	Type
low complexity region	7	30	N/A	INTRINSIC
JmjN	31	72	2.87e-20	SMART
ARID	94	183	7.39e-32	SMART
BRIGHT	98	188	1.51e-35	SMART
low complexity region	228	239	N/A	INTRINSIC
PHD	311	357	6.15e-14	SMART
JmjC	453	619	2.33e-67	SMART
Pfam:zf-C5HC2	692	745	6.7e-21	PFAM
Pfam:PLU-1	756	1088	6e-94	PFAM
low complexity region	1097	1109	N/A	INTRINSIC
PHD	1178	1222	6.2e-10	SMART
low complexity region	1225	1236	N/A	INTRINSIC
low complexity region	1406	1417	N/A	INTRINSIC
low complexity region	1470	1484	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133725

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000191572

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.1%
20x: 94.9%

Validation Efficiency

MGI Phenotype

FUNCTION: This gene encodes a lysine-specific histone demethylase that belongs to the jumonji/ARID domain-containing family of histone demethylases. The encoded protein is capable of demethylating tri-, di- and monomethylated lysine 4 of histone H3. This protein plays a role in the transcriptional repression or certain tumor suppressor genes and is upregulated in certain cancer cells. This protein may also play a role in genome stability and DNA repair. Homozygous mutant mice display decreased body weight, decreased female fertility, lower uterine weight, and a delay in mammary development. Knockout of this gene has also been associated with embryonic lethality. [provided by RefSeq, Dec 2016]
PHENOTYPE: Mice homozygous for a gene trapped allele exhibit decreased body weight, background-sensitive premature mortality, decreased female fertility, delayed mammary gland development, decreased serum estradiol levels, and reduced mammary epithelial cell proliferation in early puberty. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aass	T	A	6: 23,109,437 (GRCm39)	E344D	probably benign	Het
Acoxl	G	A	2: 127,917,855 (GRCm39)		probably null	Het
Adora1	A	T	1: 134,131,224 (GRCm39)	L149Q	possibly damaging	Het
Aebp1	C	A	11: 5,818,501 (GRCm39)	D115E	possibly damaging	Het
Ank3	A	G	10: 69,822,938 (GRCm39)	I1819V	probably benign	Het
Ankrd44	T	C	1: 54,706,539 (GRCm39)	H454R	probably damaging	Het
Ap4e1	C	T	2: 126,906,842 (GRCm39)	A1034V	possibly damaging	Het
B3galt2	T	A	1: 143,522,849 (GRCm39)	F328L	probably benign	Het
Bbip1	G	A	19: 53,919,786 (GRCm39)		probably benign	Het
Brsk1	G	A	7: 4,711,865 (GRCm39)	E572K	possibly damaging	Het
Clca3a1	G	T	3: 144,442,897 (GRCm39)	P716T	possibly damaging	Het
Clpx	T	C	9: 65,228,132 (GRCm39)	V380A	probably damaging	Het
Epha3	T	A	16: 63,418,620 (GRCm39)	Q608H	probably damaging	Het
Gprc6a	G	T	10: 51,491,089 (GRCm39)	P712T	probably damaging	Het
Itpr1	C	A	6: 108,519,023 (GRCm39)	Q2720K	probably damaging	Het
Macf1	G	A	4: 123,295,567 (GRCm39)	R3163*	probably null	Het
Map4k5	T	C	12: 69,888,755 (GRCm39)	D292G	probably benign	Het
Mau2	A	T	8: 70,481,373 (GRCm39)	C217S	probably benign	Het
Mtf1	T	C	4: 124,714,220 (GRCm39)	F210L	probably damaging	Het
Mtif2	G	A	11: 29,486,889 (GRCm39)	V300M	probably damaging	Het
Mtmr2	T	C	9: 13,694,905 (GRCm39)		probably benign	Het
Mybpc3	C	A	2: 90,955,573 (GRCm39)		probably null	Het
Ncmap	T	C	4: 135,107,430 (GRCm39)		probably null	Het
Nek9	A	G	12: 85,355,751 (GRCm39)	F672S	probably damaging	Het
Nuak1	A	T	10: 84,245,542 (GRCm39)	I101N	probably damaging	Het
Or8s16	T	C	15: 98,211,311 (GRCm39)	N40S	probably damaging	Het
Pcdh7	T	A	5: 58,286,515 (GRCm39)	M1197K	probably damaging	Het
Pcdhb17	A	C	18: 37,618,939 (GRCm39)	Q243P	probably benign	Het
Pcf11	T	G	7: 92,310,699 (GRCm39)	K221Q	probably damaging	Het
Pkhd1	C	T	1: 20,604,769 (GRCm39)	R1182H	probably benign	Het
Ptprz1	C	A	6: 23,001,900 (GRCm39)	P1330Q	probably benign	Het
Rbm33	T	G	5: 28,542,050 (GRCm39)		probably null	Het
Rhobtb1	A	G	10: 69,084,615 (GRCm39)	D2G	probably damaging	Het
Rngtt	T	A	4: 33,325,110 (GRCm39)	C110*	probably null	Het
Setx	T	A	2: 29,038,430 (GRCm39)	N1638K	probably benign	Het
Slc24a3	A	T	2: 145,446,437 (GRCm39)	M282L	probably benign	Het
Slc7a1	A	T	5: 148,270,798 (GRCm39)	V556D	possibly damaging	Het
Sppl2c	A	T	11: 104,077,407 (GRCm39)	D69V	possibly damaging	Het
Srpk3	C	T	X: 72,818,555 (GRCm39)	R82*	probably null	Het
Tas2r120	A	T	6: 132,634,110 (GRCm39)	N64I	probably damaging	Het
Tcf25	G	T	8: 124,100,678 (GRCm39)	A23S	probably damaging	Het
Tigd2	A	T	6: 59,188,138 (GRCm39)	K335I	probably damaging	Het
Tlr6	A	G	5: 65,112,647 (GRCm39)	S87P	probably benign	Het
Tmem135	T	A	7: 88,797,200 (GRCm39)	Y352F	probably damaging	Het
Tob2	T	C	15: 81,735,918 (GRCm39)	Y17C	probably damaging	Het
Tymp	GC	GCC	15: 89,258,567 (GRCm39)		probably null	Het
Vmn1r179	T	C	7: 23,628,478 (GRCm39)	V223A	probably damaging	Het
Zfp946	T	C	17: 22,673,447 (GRCm39)	V67A	probably benign	Het
Zswim4	G	T	8: 84,946,561 (GRCm39)	N698K	probably benign	Het
Zzz3	A	G	3: 152,133,182 (GRCm39)	Q80R	probably damaging	Het

Other mutations in Kdm5b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00230:Kdm5b	APN	1	134,548,693 (GRCm39)	missense	probably damaging	1.00
IGL01458:Kdm5b	APN	1	134,549,724 (GRCm39)	missense	possibly damaging	0.53
IGL01567:Kdm5b	APN	1	134,530,278 (GRCm39)	missense	probably damaging	1.00
IGL01625:Kdm5b	APN	1	134,545,706 (GRCm39)	missense	possibly damaging	0.74
IGL01970:Kdm5b	APN	1	134,528,465 (GRCm39)	missense	probably damaging	1.00
IGL02183:Kdm5b	APN	1	134,552,669 (GRCm39)	missense	probably benign	0.09
IGL02592:Kdm5b	APN	1	134,552,591 (GRCm39)	missense	probably damaging	0.99
IGL02695:Kdm5b	APN	1	134,532,223 (GRCm39)	missense	possibly damaging	0.94
IGL02697:Kdm5b	APN	1	134,516,511 (GRCm39)	splice site	probably benign
IGL03036:Kdm5b	APN	1	134,536,675 (GRCm39)	missense	probably damaging	1.00
IGL03056:Kdm5b	APN	1	134,515,717 (GRCm39)	missense	probably damaging	0.99
IGL03206:Kdm5b	APN	1	134,555,055 (GRCm39)	missense	probably benign
IGL03342:Kdm5b	APN	1	134,530,314 (GRCm39)	missense	probably benign	0.00
IGL03388:Kdm5b	APN	1	134,555,060 (GRCm39)	missense	probably benign
amaryllis	UTSW	1	134,536,799 (GRCm39)	critical splice donor site	probably null
PIT4486001:Kdm5b	UTSW	1	134,556,423 (GRCm39)	missense	probably damaging	1.00
R0233:Kdm5b	UTSW	1	134,532,372 (GRCm39)	splice site	probably benign
R0334:Kdm5b	UTSW	1	134,532,260 (GRCm39)	missense	probably damaging	0.99
R0504:Kdm5b	UTSW	1	134,548,761 (GRCm39)	critical splice donor site	probably null
R0505:Kdm5b	UTSW	1	134,530,309 (GRCm39)	missense	probably damaging	0.96
R0521:Kdm5b	UTSW	1	134,545,771 (GRCm39)	missense	possibly damaging	0.65
R1004:Kdm5b	UTSW	1	134,516,642 (GRCm39)	missense	possibly damaging	0.71
R1087:Kdm5b	UTSW	1	134,528,375 (GRCm39)	missense	probably damaging	1.00
R1126:Kdm5b	UTSW	1	134,541,729 (GRCm39)	missense	possibly damaging	0.90
R1221:Kdm5b	UTSW	1	134,526,829 (GRCm39)	missense	probably damaging	0.98
R1230:Kdm5b	UTSW	1	134,540,992 (GRCm39)	missense	probably damaging	1.00
R1345:Kdm5b	UTSW	1	134,558,288 (GRCm39)	missense	possibly damaging	0.94
R1482:Kdm5b	UTSW	1	134,552,635 (GRCm39)	missense	probably damaging	1.00
R1582:Kdm5b	UTSW	1	134,552,591 (GRCm39)	missense	probably damaging	0.99
R1653:Kdm5b	UTSW	1	134,530,219 (GRCm39)	missense	probably damaging	1.00
R1693:Kdm5b	UTSW	1	134,525,314 (GRCm39)	splice site	probably benign
R1721:Kdm5b	UTSW	1	134,540,919 (GRCm39)	splice site	probably benign
R1741:Kdm5b	UTSW	1	134,545,755 (GRCm39)	missense	possibly damaging	0.82
R1762:Kdm5b	UTSW	1	134,532,205 (GRCm39)	nonsense	probably null
R1820:Kdm5b	UTSW	1	134,525,408 (GRCm39)	missense	possibly damaging	0.87
R1872:Kdm5b	UTSW	1	134,552,732 (GRCm39)	missense	probably damaging	1.00
R1966:Kdm5b	UTSW	1	134,541,611 (GRCm39)	splice site	probably null
R2056:Kdm5b	UTSW	1	134,540,952 (GRCm39)	missense	probably benign	0.05
R2059:Kdm5b	UTSW	1	134,540,952 (GRCm39)	missense	probably benign	0.05
R2405:Kdm5b	UTSW	1	134,536,754 (GRCm39)	missense	probably damaging	0.97
R3417:Kdm5b	UTSW	1	134,515,715 (GRCm39)	missense	probably damaging	1.00
R3771:Kdm5b	UTSW	1	134,541,083 (GRCm39)	missense	probably damaging	1.00
R3783:Kdm5b	UTSW	1	134,558,280 (GRCm39)	missense	probably benign
R3803:Kdm5b	UTSW	1	134,543,679 (GRCm39)	missense	probably benign	0.07
R3980:Kdm5b	UTSW	1	134,547,408 (GRCm39)	missense	probably benign	0.11
R3983:Kdm5b	UTSW	1	134,559,042 (GRCm39)	missense	possibly damaging	0.91
R4013:Kdm5b	UTSW	1	134,555,067 (GRCm39)	missense	possibly damaging	0.86
R4162:Kdm5b	UTSW	1	134,552,899 (GRCm39)	missense	probably benign	0.01
R4701:Kdm5b	UTSW	1	134,533,750 (GRCm39)	intron	probably benign
R4791:Kdm5b	UTSW	1	134,558,538 (GRCm39)	missense	possibly damaging	0.82
R4836:Kdm5b	UTSW	1	134,521,053 (GRCm39)	splice site	probably null
R4924:Kdm5b	UTSW	1	134,559,089 (GRCm39)	missense	probably benign	0.00
R5135:Kdm5b	UTSW	1	134,516,484 (GRCm39)	intron	probably benign
R5290:Kdm5b	UTSW	1	134,549,837 (GRCm39)	splice site	probably null
R5358:Kdm5b	UTSW	1	134,535,432 (GRCm39)	nonsense	probably null
R5388:Kdm5b	UTSW	1	134,536,635 (GRCm39)	nonsense	probably null
R5396:Kdm5b	UTSW	1	134,549,836 (GRCm39)	splice site	probably null
R5397:Kdm5b	UTSW	1	134,549,836 (GRCm39)	splice site	probably null
R5398:Kdm5b	UTSW	1	134,549,836 (GRCm39)	splice site	probably null
R5399:Kdm5b	UTSW	1	134,549,836 (GRCm39)	splice site	probably null
R5529:Kdm5b	UTSW	1	134,515,741 (GRCm39)	missense	probably damaging	1.00
R5540:Kdm5b	UTSW	1	134,558,979 (GRCm39)	missense	probably damaging	0.98
R5661:Kdm5b	UTSW	1	134,526,811 (GRCm39)	missense	probably benign	0.01
R5663:Kdm5b	UTSW	1	134,558,373 (GRCm39)	missense	probably benign
R5822:Kdm5b	UTSW	1	134,516,511 (GRCm39)	splice site	probably benign
R6226:Kdm5b	UTSW	1	134,536,616 (GRCm39)	missense	probably damaging	0.99
R6368:Kdm5b	UTSW	1	134,526,945 (GRCm39)	missense	probably damaging	1.00
R6681:Kdm5b	UTSW	1	134,541,007 (GRCm39)	missense	possibly damaging	0.90
R6715:Kdm5b	UTSW	1	134,536,799 (GRCm39)	critical splice donor site	probably null
R7132:Kdm5b	UTSW	1	134,526,844 (GRCm39)	missense	probably damaging	1.00
R7202:Kdm5b	UTSW	1	134,552,497 (GRCm39)	missense	probably benign
R7258:Kdm5b	UTSW	1	134,548,759 (GRCm39)	missense	probably damaging	1.00
R7335:Kdm5b	UTSW	1	134,488,177 (GRCm39)	missense	probably damaging	1.00
R7420:Kdm5b	UTSW	1	134,532,235 (GRCm39)	missense	probably benign	0.14
R7426:Kdm5b	UTSW	1	134,523,571 (GRCm39)	missense	probably benign	0.02
R7452:Kdm5b	UTSW	1	134,552,686 (GRCm39)	missense	probably damaging	1.00
R7595:Kdm5b	UTSW	1	134,536,704 (GRCm39)	missense	probably benign	0.00
R7612:Kdm5b	UTSW	1	134,552,656 (GRCm39)	nonsense	probably null
R7704:Kdm5b	UTSW	1	134,515,669 (GRCm39)	missense	probably damaging	1.00
R7846:Kdm5b	UTSW	1	134,545,578 (GRCm39)	missense	probably damaging	1.00
R8115:Kdm5b	UTSW	1	134,547,411 (GRCm39)	missense	possibly damaging	0.83
R8146:Kdm5b	UTSW	1	134,552,864 (GRCm39)	missense	probably benign	0.05
R8160:Kdm5b	UTSW	1	134,541,657 (GRCm39)	missense	probably damaging	1.00
R8527:Kdm5b	UTSW	1	134,533,512 (GRCm39)	missense	possibly damaging	0.78
R8542:Kdm5b	UTSW	1	134,533,512 (GRCm39)	missense	possibly damaging	0.78
R8930:Kdm5b	UTSW	1	134,544,010 (GRCm39)	missense	probably damaging	1.00
R8932:Kdm5b	UTSW	1	134,544,010 (GRCm39)	missense	probably damaging	1.00
R8950:Kdm5b	UTSW	1	134,541,664 (GRCm39)	missense	possibly damaging	0.84
R9089:Kdm5b	UTSW	1	134,535,506 (GRCm39)	missense	probably damaging	0.98
R9109:Kdm5b	UTSW	1	134,528,493 (GRCm39)	critical splice donor site	probably null
R9133:Kdm5b	UTSW	1	134,530,323 (GRCm39)	missense	probably benign
R9298:Kdm5b	UTSW	1	134,528,493 (GRCm39)	critical splice donor site	probably null
R9423:Kdm5b	UTSW	1	134,515,705 (GRCm39)	missense	possibly damaging	0.85
R9630:Kdm5b	UTSW	1	134,512,971 (GRCm39)	critical splice donor site	probably null
R9670:Kdm5b	UTSW	1	134,558,240 (GRCm39)	nonsense	probably null
X0063:Kdm5b	UTSW	1	134,516,614 (GRCm39)	missense	probably benign	0.07
Z1176:Kdm5b	UTSW	1	134,552,773 (GRCm39)	missense	probably damaging	1.00
Z1177:Kdm5b	UTSW	1	134,523,536 (GRCm39)	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- TGGAGTCATTGACCATGAGC -3'
(R):5'- CCCTGAGAACAGAGAGACTTATC -3'

Sequencing Primer
(F):5'- GAGTCATTGACCATGAGCTACACTG -3'
(R):5'- TGAGAACAGAGAGACTTATCTTACAC -3'

Posted On

2016-07-06