Mutagenetix > Incidental Mutations

Incidental Mutation 'R4791:Kdm5b'

368532

Institutional Source

Beutler Lab

Gene Symbol

Kdm5b

Ensembl Gene

ENSMUSG00000042207

Gene Name

lysine (K)-specific demethylase 5B

Synonyms

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

MMRRC Submission

041976-MU

Accession Numbers

Is this an essential gene?

Possibly non essential (E-score: 0.374) question?

Stock #

R4791 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

134560171-134635285 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 134630800 bp

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 1515 (E1515G)

Ref Sequence

ENSEMBL: ENSMUSP00000107817 (fasta)

Gene Model

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

PDB Structure

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

Predicted Effect

probably benign
Transcript: ENSMUST00000047714

SMART Domains

Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207

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

possibly damaging
Transcript: ENSMUST00000112198
AA Change: E1515G

PolyPhen 2 Score 0.816 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000107817
Gene: ENSMUSG00000042207
AA Change: E1515G

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: ENSMUST00000191572

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.3%

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: 97 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921507P07Rik	G	T	6: 50,595,837	P32Q	probably damaging	Het
Abcc6	C	T	7: 45,982,160	V1231M	probably benign	Het
Agl	A	G	3: 116,786,528		probably null	Het
Ak7	T	C	12: 105,710,145	F35L	probably benign	Het
Aldh1a1	A	G	19: 20,619,985	N110S	probably damaging	Het
Arhgef5	C	T	6: 43,283,183	L1368F	probably damaging	Het
Atp5j2	T	C	5: 145,184,555	Y72C	possibly damaging	Het
Atp6v0a2	T	G	5: 124,646,727	F317V	probably benign	Het
Bank1	A	T	3: 136,254,929	S56T	probably benign	Het
BC080695	A	G	4: 143,570,989		probably benign	Het
Cachd1	T	A	4: 100,918,085	C166S	probably damaging	Het
Cand1	A	G	10: 119,210,702	I961T	probably benign	Het
Ccdc73	G	A	2: 104,981,105		probably null	Het
Cct6b	A	T	11: 82,742,004		probably null	Het
Chd2	A	C	7: 73,468,577	S1098A	probably benign	Het
Col6a4	A	T	9: 106,080,202	V141E	possibly damaging	Het
Col6a5	T	C	9: 105,930,784	T1022A	unknown	Het
Cr2	A	T	1: 195,155,935	C698S	probably damaging	Het
Diexf	G	A	1: 193,128,267	H143Y	probably benign	Het
Dnaaf5	C	A	5: 139,184,650	Q786K	possibly damaging	Het
Dnah6	T	C	6: 73,095,074	D2423G	probably benign	Het
Dnhd1	T	C	7: 105,721,117	F4583S	probably damaging	Het
Duoxa2	A	T	2: 122,301,198	T123S	probably damaging	Het
Edem1	T	G	6: 108,841,634	V201G	probably damaging	Het
Eef1d	C	T	15: 75,903,682	A43T	possibly damaging	Het
Elavl3	T	C	9: 22,024,678	K249E	probably damaging	Het
Epg5	G	T	18: 77,948,996	E303*	probably null	Het
Fam83h	T	C	15: 76,002,368	D1040G	probably damaging	Het
Fndc7	A	T	3: 108,876,659	F211L	probably benign	Het
Fsip2	A	G	2: 82,982,108	T2924A	possibly damaging	Het
Gm5616	T	C	9: 48,450,683		noncoding transcript	Het
Gpr135	T	A	12: 72,069,868	D375V	probably benign	Het
Hgd	A	G	16: 37,631,825	*446W	probably null	Het
Hivep2	C	A	10: 14,128,969	T437K	probably benign	Het
Htra2	A	G	6: 83,051,817	L379P	probably damaging	Het
Hypk	G	T	2: 121,457,655		probably null	Het
Ica1l	A	G	1: 60,010,201	F198L	probably damaging	Het
Igsf11	G	A	16: 39,024,864	S319N	probably damaging	Het
Il12rb1	T	C	8: 70,813,368	S213P	possibly damaging	Het
Katnal1	C	T	5: 148,904,650	V135M	probably damaging	Het
Kcnc4	G	A	3: 107,447,543	P530S	probably benign	Het
Kcnu1	T	C	8: 25,913,752	Y24H	probably damaging	Het
Kif18a	A	T	2: 109,287,875	M12L	probably benign	Het
Klre1	T	C	6: 129,584,155	S160P	probably damaging	Het
Lama2	A	T	10: 27,467,271	H68Q	probably damaging	Het
Lgals8	T	C	13: 12,453,322	K49R	possibly damaging	Het
Lmf1	G	A	17: 25,654,471	V317M	probably damaging	Het
Lsr	T	C	7: 30,958,552	T328A	probably damaging	Het
Mark4	C	T	7: 19,451,657	E51K	probably benign	Het
Mindy2	T	C	9: 70,634,001		probably null	Het
Mkks	G	A	2: 136,876,162	T400I	probably benign	Het
Mon2	T	A	10: 123,006,057	M1544L	probably benign	Het
Mrc2	G	A	11: 105,348,431		probably null	Het
Myo5c	T	G	9: 75,290,916	L1341R	probably damaging	Het
Nin	T	C	12: 70,043,807	R945G	possibly damaging	Het
Nox4	T	C	7: 87,304,847	V120A	probably benign	Het
Olfr1196	C	T	2: 88,700,898	V144I	probably benign	Het
Olfr1496	T	A	19: 13,781,342	C243*	probably null	Het
Olfr169	G	T	16: 19,566,663	H73Q	possibly damaging	Het
Olfr30	A	T	11: 58,455,544	V135E	possibly damaging	Het
Olfr847	T	C	9: 19,375,809	E24G	probably benign	Het
Plekha2	T	A	8: 25,042,762	R398W	probably damaging	Het
Pradc1	A	G	6: 85,447,191	W58R	probably damaging	Het
Prrc2b	A	G	2: 32,217,339		probably null	Het
Psg19	T	A	7: 18,794,146	N224I	probably damaging	Het
Ranbp17	A	C	11: 33,487,746	V164G	probably benign	Het
Rasgrp3	A	G	17: 75,500,173	S211G	probably benign	Het
Rcc1l	G	A	5: 134,163,776	P270S	possibly damaging	Het
Rfx6	T	A	10: 51,719,944		probably null	Het
Rnf222	A	T	11: 68,893,019	E137D	probably damaging	Het
Selenof	T	G	3: 144,596,823	Y120D	probably damaging	Het
Sema3b	G	T	9: 107,603,813	D108E	probably damaging	Het
Shank3	T	A	15: 89,500,354	L143Q	probably damaging	Het
Shtn1	G	C	19: 59,050,873	R45G	probably damaging	Het
Sirt4	T	C	5: 115,480,314	T234A	possibly damaging	Het
Slc25a30	C	A	14: 75,763,366	W266L	probably benign	Het
Spata20	A	T	11: 94,484,586	N127K	probably damaging	Het
St14	C	T	9: 31,095,622	G636D	probably benign	Het
Stat5a	G	A	11: 100,865,463	E170K	probably damaging	Het
Sugp2	C	T	8: 70,242,790	R138C	probably damaging	Het
Sult1e1	C	A	5: 87,586,730	W119L	possibly damaging	Het
Sv2a	T	C	3: 96,192,558	V608A	possibly damaging	Het
Syne2	T	C	12: 75,909,244	Y575H	possibly damaging	Het
Taok2	G	A	7: 126,868,132	S167L	possibly damaging	Het
Thoc6	T	C	17: 23,670,067	H151R	possibly damaging	Het
Tm9sf2	T	C	14: 122,139,650	S197P	probably benign	Het
Tmem260	CAGGGACCGGCATAG	CAG	14: 48,511,994		probably benign	Het
Tmx2	G	A	2: 84,677,996	P15L	probably damaging	Het
Top1mt	C	T	15: 75,668,625		probably null	Het
Trpm6	T	A	19: 18,867,981	S1682T	probably benign	Het
Trrap	C	T	5: 144,803,277	R1171W	probably damaging	Het
Ugt3a2	A	G	15: 9,361,579	D147G	probably damaging	Het
Vnn3	A	G	10: 23,864,621	H274R	probably benign	Het
Vwf	C	A	6: 125,643,363	T1668K		Het
Zfp568	T	C	7: 30,015,183	S162P	probably damaging	Het
Zfp658	T	A	7: 43,574,466	C722S	possibly damaging	Het
Zfp808	T	A	13: 62,171,231	H91Q	probably damaging	Het

Other mutations in Kdm5b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00230:Kdm5b	APN	1	134620955	missense	probably damaging	1.00
IGL01458:Kdm5b	APN	1	134621986	missense	possibly damaging	0.53
IGL01567:Kdm5b	APN	1	134602540	missense	probably damaging	1.00
IGL01625:Kdm5b	APN	1	134617968	missense	possibly damaging	0.74
IGL01970:Kdm5b	APN	1	134600727	missense	probably damaging	1.00
IGL02183:Kdm5b	APN	1	134624931	missense	probably benign	0.09
IGL02592:Kdm5b	APN	1	134624853	missense	probably damaging	0.99
IGL02695:Kdm5b	APN	1	134604485	missense	possibly damaging	0.94
IGL02697:Kdm5b	APN	1	134588773	splice site	probably benign
IGL03036:Kdm5b	APN	1	134608937	missense	probably damaging	1.00
IGL03056:Kdm5b	APN	1	134587979	missense	probably damaging	0.99
IGL03206:Kdm5b	APN	1	134627317	missense	probably benign
IGL03342:Kdm5b	APN	1	134602576	missense	probably benign	0.00
IGL03388:Kdm5b	APN	1	134627322	missense	probably benign
amaryllis	UTSW	1	134609061	critical splice donor site	probably null
PIT4486001:Kdm5b	UTSW	1	134628685	missense	probably damaging	1.00
R0233:Kdm5b	UTSW	1	134604634	splice site	probably benign
R0334:Kdm5b	UTSW	1	134604522	missense	probably damaging	0.99
R0504:Kdm5b	UTSW	1	134621023	critical splice donor site	probably null
R0505:Kdm5b	UTSW	1	134602571	missense	probably damaging	0.96
R0521:Kdm5b	UTSW	1	134618033	missense	possibly damaging	0.65
R1004:Kdm5b	UTSW	1	134588904	missense	possibly damaging	0.71
R1087:Kdm5b	UTSW	1	134600637	missense	probably damaging	1.00
R1126:Kdm5b	UTSW	1	134613991	missense	possibly damaging	0.90
R1221:Kdm5b	UTSW	1	134599091	missense	probably damaging	0.98
R1230:Kdm5b	UTSW	1	134613254	missense	probably damaging	1.00
R1345:Kdm5b	UTSW	1	134630550	missense	possibly damaging	0.94
R1482:Kdm5b	UTSW	1	134624897	missense	probably damaging	1.00
R1582:Kdm5b	UTSW	1	134624853	missense	probably damaging	0.99
R1653:Kdm5b	UTSW	1	134602481	missense	probably damaging	1.00
R1693:Kdm5b	UTSW	1	134597576	splice site	probably benign
R1721:Kdm5b	UTSW	1	134613181	splice site	probably benign
R1741:Kdm5b	UTSW	1	134618017	missense	possibly damaging	0.82
R1762:Kdm5b	UTSW	1	134604467	nonsense	probably null
R1820:Kdm5b	UTSW	1	134597670	missense	possibly damaging	0.87
R1872:Kdm5b	UTSW	1	134624994	missense	probably damaging	1.00
R1966:Kdm5b	UTSW	1	134613873	splice site	probably null
R2056:Kdm5b	UTSW	1	134613214	missense	probably benign	0.05
R2059:Kdm5b	UTSW	1	134613214	missense	probably benign	0.05
R2405:Kdm5b	UTSW	1	134609016	missense	probably damaging	0.97
R3417:Kdm5b	UTSW	1	134587977	missense	probably damaging	1.00
R3771:Kdm5b	UTSW	1	134613345	missense	probably damaging	1.00
R3783:Kdm5b	UTSW	1	134630542	missense	probably benign
R3803:Kdm5b	UTSW	1	134615941	missense	probably benign	0.07
R3980:Kdm5b	UTSW	1	134619670	missense	probably benign	0.11
R3983:Kdm5b	UTSW	1	134631304	missense	possibly damaging	0.91
R4013:Kdm5b	UTSW	1	134627329	missense	possibly damaging	0.86
R4162:Kdm5b	UTSW	1	134625161	missense	probably benign	0.01
R4701:Kdm5b	UTSW	1	134606012	intron	probably benign
R4836:Kdm5b	UTSW	1	134593315	splice site	probably null
R4924:Kdm5b	UTSW	1	134631351	missense	probably benign	0.00
R5135:Kdm5b	UTSW	1	134588746	intron	probably benign
R5248:Kdm5b	UTSW	1	134620997	missense	probably benign	0.11
R5290:Kdm5b	UTSW	1	134622099	splice site	probably null
R5358:Kdm5b	UTSW	1	134607694	nonsense	probably null
R5388:Kdm5b	UTSW	1	134608897	nonsense	probably null
R5396:Kdm5b	UTSW	1	134622098	splice site	probably null
R5397:Kdm5b	UTSW	1	134622098	splice site	probably null
R5398:Kdm5b	UTSW	1	134622098	splice site	probably null
R5399:Kdm5b	UTSW	1	134622098	splice site	probably null
R5529:Kdm5b	UTSW	1	134588003	missense	probably damaging	1.00
R5540:Kdm5b	UTSW	1	134631241	missense	probably damaging	0.98
R5661:Kdm5b	UTSW	1	134599073	missense	probably benign	0.01
R5663:Kdm5b	UTSW	1	134630635	missense	probably benign
R5822:Kdm5b	UTSW	1	134588773	splice site	probably benign
R6226:Kdm5b	UTSW	1	134608878	missense	probably damaging	0.99
R6368:Kdm5b	UTSW	1	134599207	missense	probably damaging	1.00
R6681:Kdm5b	UTSW	1	134613269	missense	possibly damaging	0.90
R6715:Kdm5b	UTSW	1	134609061	critical splice donor site	probably null
R7132:Kdm5b	UTSW	1	134599106	missense	probably damaging	1.00
R7202:Kdm5b	UTSW	1	134624759	missense	probably benign
R7258:Kdm5b	UTSW	1	134621021	missense	probably damaging	1.00
R7335:Kdm5b	UTSW	1	134560439	missense	probably damaging	1.00
R7420:Kdm5b	UTSW	1	134604497	missense	probably benign	0.14
R7426:Kdm5b	UTSW	1	134595833	missense	probably benign	0.02
R7452:Kdm5b	UTSW	1	134624948	missense	probably damaging	1.00
R7595:Kdm5b	UTSW	1	134608966	missense	probably benign	0.00
R7612:Kdm5b	UTSW	1	134624918	nonsense	probably null
R7704:Kdm5b	UTSW	1	134587931	missense	probably damaging	1.00
R7846:Kdm5b	UTSW	1	134617840	missense	probably damaging	1.00
R8115:Kdm5b	UTSW	1	134619673	missense	possibly damaging	0.83
R8146:Kdm5b	UTSW	1	134625126	missense	probably benign	0.05
R8160:Kdm5b	UTSW	1	134613919	missense	probably damaging	1.00
X0063:Kdm5b	UTSW	1	134588876	missense	probably benign	0.07
Z1176:Kdm5b	UTSW	1	134625035	missense	probably damaging	1.00
Z1177:Kdm5b	UTSW	1	134595798	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- CTATGACTTAGTGCGTAATGCTG -3'
(R):5'- AAGGGCACTCACTCCATCAG -3'

Sequencing Primer
(F):5'- GTGCGTAATGCTGAAACTCATTCC -3'
(R):5'- CCACCTTCTGAGCGCCG -3'

Posted On

2016-02-04