Mutagenetix > Incidental Mutation

Incidental Mutation 'R1872:Kdm5b'

210799

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

039894-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.269) question?

Stock #

R1872 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

134560171-134635285 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 134624994 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 1236 (L1236P)

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 damaging
Transcript: ENSMUST00000047714
AA Change: L1236P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207
AA Change: L1236P

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 damaging
Transcript: ENSMUST00000112198
AA Change: L1236P

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000107817
Gene: ENSMUSG00000042207
AA Change: L1236P

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

Meta Mutation Damage Score

0.9017

Coding Region Coverage

1x: 97.3%
3x: 96.8%
10x: 95.4%
20x: 93.0%

Validation Efficiency

97% (113/117)

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: 108 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700003H04Rik	C	T	3: 124,556,844	C133Y	unknown	Het
8430408G22Rik	G	A	6: 116,651,722	V9M	possibly damaging	Het
Abce1	A	G	8: 79,690,251	M377T	possibly damaging	Het
Adam25	A	T	8: 40,755,226	R510*	probably null	Het
Adamts12	G	T	15: 11,217,880	E308*	probably null	Het
Adgrg3	C	A	8: 95,033,442	N96K	possibly damaging	Het
Afdn	T	C	17: 13,881,316	V1022A	probably damaging	Het
Akap9	T	C	5: 4,001,406	V1391A	probably damaging	Het
Akip1	A	G	7: 109,711,775	Y174C	probably damaging	Het
Ap3b2	T	C	7: 81,464,150	T830A	unknown	Het
Aph1a	A	G	3: 95,895,564	T159A	probably damaging	Het
Ccdc146	T	C	5: 21,301,290	T718A	probably benign	Het
Cdk5r2	T	C	1: 74,855,822	L242P	probably damaging	Het
Cep97	T	A	16: 55,927,866	N67I	probably damaging	Het
Chic2	A	T	5: 75,011,479	W121R	possibly damaging	Het
Clock	A	G	5: 76,248,462	S147P	possibly damaging	Het
Cntnap5a	T	G	1: 116,089,210	S178A	probably benign	Het
Col11a2	C	A	17: 34,062,555		probably benign	Het
Col6a3	T	A	1: 90,830,214	H6L	probably damaging	Het
Cpne5	T	C	17: 29,204,693	N154D	probably benign	Het
Ctsz	T	G	2: 174,427,976	K273Q	probably benign	Het
Cybrd1	G	A	2: 71,129,760	V101M	probably benign	Het
Cyp2c23	T	A	19: 44,005,551	K459*	probably null	Het
Cyp4a31	A	T	4: 115,574,736	H419L	probably damaging	Het
D930020B18Rik	G	A	10: 121,641,974	V35M	probably damaging	Het
Dnah9	C	T	11: 66,037,490	V2118M	probably benign	Het
Doxl2	A	G	6: 48,975,620	I160V	probably benign	Het
Dtna	T	C	18: 23,597,560		probably null	Het
Ednra	C	T	8: 77,720,396	V18I	possibly damaging	Het
Elac1	T	C	18: 73,742,646	R105G	probably benign	Het
Exoc2	A	G	13: 30,822,661	S844P	probably benign	Het
Fam185a	A	T	5: 21,480,330		probably null	Het
Fam204a	A	G	19: 60,199,449	M233T	possibly damaging	Het
Fat1	C	A	8: 44,953,304	H1031N	probably benign	Het
Fat1	T	A	8: 45,038,349	Y3816N	probably damaging	Het
Fbxo38	C	T	18: 62,517,023	R621Q	probably benign	Het
Fhod3	C	A	18: 25,130,610	R1524S	probably damaging	Het
Fnip1	A	T	11: 54,487,735	R192W	probably damaging	Het
Frem3	T	A	8: 80,612,576	H499Q	probably damaging	Het
Gab2	C	T	7: 97,299,043	T280I	probably damaging	Het
Gdpgp1	A	G	7: 80,238,424	R68G	probably benign	Het
Gm10382	C	T	5: 125,389,560		probably benign	Het
Gm4858	T	A	3: 93,074,422	L249H	probably damaging	Het
Gmps	A	G	3: 64,001,517	H480R	probably benign	Het
Hecw1	G	A	13: 14,280,449	R674*	probably null	Het
Herc2	T	A	7: 56,157,509	F2478L	probably benign	Het
Homer2	C	T	7: 81,636,402	V21M	probably damaging	Het
Ifna9	A	G	4: 88,592,255	M44T	probably damaging	Het
Igfl3	A	G	7: 18,179,896	D57G	possibly damaging	Het
Jcad	T	C	18: 4,673,048	M270T	probably benign	Het
Kif14	T	A	1: 136,486,358	L724Q	probably damaging	Het
Lhb	T	C	7: 45,421,333	V45A	probably damaging	Het
Lhpp	A	G	7: 132,634,087	N134D	probably benign	Het
Mas1	T	C	17: 12,842,191	Y115C	probably damaging	Het
Mb21d1	T	C	9: 78,433,202	D416G	probably benign	Het
Mgam	A	T	6: 40,661,300	K395*	probably null	Het
Mms22l	A	G	4: 24,598,807	N1134S	probably damaging	Het
Mrc1	A	G	2: 14,325,381		probably null	Het
Mrgprg	G	A	7: 143,764,544	S277L	probably damaging	Het
Mrpl49	G	T	19: 6,056,980	P60T	possibly damaging	Het
Mrps10	G	A	17: 47,372,452	G104D	possibly damaging	Het
Msantd3	A	G	4: 48,552,771	Y120C	probably damaging	Het
N4bp2	C	T	5: 65,794,518		probably benign	Het
Nbea	A	G	3: 55,642,889	V2706A	probably benign	Het
Nfic	T	A	10: 81,420,684	M71L	possibly damaging	Het
Ntn4	C	T	10: 93,707,353	R314W	probably damaging	Het
Olfr1112	A	G	2: 87,191,878	T64A	possibly damaging	Het
Olfr115	G	T	17: 37,609,912	P280T	probably damaging	Het
Olfr1202	T	A	2: 88,817,936	V255E	probably benign	Het
Olfr1234	A	G	2: 89,362,589	L280P	probably damaging	Het
Pak7	T	C	2: 136,085,588	I655V	possibly damaging	Het
Pip5k1c	A	G	10: 81,306,319	N121S	probably damaging	Het
Plce1	A	T	19: 38,760,077	I1737F	probably damaging	Het
Prrt1	T	C	17: 34,630,951	L113P	probably damaging	Het
Ptprq	T	A	10: 107,643,999	T1137S	probably benign	Het
Recql5	T	C	11: 115,923,309	I223V	probably benign	Het
Reg3g	A	T	6: 78,467,853	Y47*	probably null	Het
Rgs12	T	G	5: 34,965,821	M316R	probably damaging	Het
Ric1	T	C	19: 29,602,668	S1290P	probably benign	Het
Rpl36al	A	G	12: 69,182,923	C72R	probably damaging	Het
Rplp0	T	A	5: 115,563,315	F275L	possibly damaging	Het
Rpp30	G	A	19: 36,087,393	V89I	probably benign	Het
Ryr3	A	G	2: 112,709,137	F3253L	possibly damaging	Het
Serpina3n	A	T	12: 104,408,944	N92Y	probably benign	Het
Setd7	G	T	3: 51,542,831	T58N	probably benign	Het
Sh3tc2	T	A	18: 62,011,883	L1136Q	probably damaging	Het
Slc35b4	G	A	6: 34,158,505	Q291*	probably null	Het
Soga1	A	G	2: 157,040,261	C624R	possibly damaging	Het
Sort1	A	G	3: 108,340,695	N452S	probably benign	Het
Sympk	A	G	7: 19,029,145	I46V	probably benign	Het
Syngr2	T	C	11: 117,812,538	V60A	probably damaging	Het
Syt17	A	T	7: 118,408,118	F318I	probably benign	Het
Tgfb1	T	A	7: 25,692,466	L149M	probably damaging	Het
Ticam1	A	T	17: 56,271,897	M66K	probably benign	Het
Tmem131	G	T	1: 36,807,927	D1363E	probably benign	Het
Tns4	A	C	11: 99,080,100	D261E	probably damaging	Het
Trim30a	T	C	7: 104,429,210	N220D	probably benign	Het
Trmt10a	T	C	3: 138,156,720	L257P	probably damaging	Het
Troap	G	T	15: 99,075,352		probably benign	Het
Ttc6	T	C	12: 57,704,552		probably null	Het
Ttn	A	T	2: 76,811,243	L5176Q	possibly damaging	Het
Vav1	A	C	17: 57,324,750	K775T	probably damaging	Het
Vmn1r236	A	G	17: 21,287,411	K264E	possibly damaging	Het
Vmn1r84	A	G	7: 12,362,628	V46A	probably benign	Het
Wdr59	A	T	8: 111,459,017	W835R	probably damaging	Het
Zfp513	T	G	5: 31,200,423	K202T	probably damaging	Het
Zfp7	T	G	15: 76,891,777	I673S	probably benign	Het
Zmynd11	A	G	13: 9,698,701	I108T	possibly 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
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
R4791:Kdm5b	UTSW	1	134630800	missense	possibly damaging	0.82
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
R8527:Kdm5b	UTSW	1	134605774	missense	possibly damaging	0.78
R8542:Kdm5b	UTSW	1	134605774	missense	possibly damaging	0.78
R8930:Kdm5b	UTSW	1	134616272	missense	probably damaging	1.00
R8932:Kdm5b	UTSW	1	134616272	missense	probably damaging	1.00
R8950:Kdm5b	UTSW	1	134613926	missense	possibly damaging	0.84
R9089:Kdm5b	UTSW	1	134607768	missense	probably damaging	0.98
R9109:Kdm5b	UTSW	1	134600755	critical splice donor site	probably null
R9133:Kdm5b	UTSW	1	134602585	missense	probably benign
R9298:Kdm5b	UTSW	1	134600755	critical splice donor site	probably null
R9423:Kdm5b	UTSW	1	134587967	missense	possibly damaging	0.85
R9630:Kdm5b	UTSW	1	134585233	critical splice donor site	probably null
R9670:Kdm5b	UTSW	1	134630502	nonsense	probably null
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'- CTGCTTGTGTCAGAAGACTCC -3'
(R):5'- GTATCCCACAAAGTGCAGGC -3'

Sequencing Primer
(F):5'- TTGTGTCAGAAGACTCCAGCCAC -3'
(R):5'- CTGATGCCTGTCCTGCTGAG -3'

Posted On

2014-06-30