Mutagenetix > Incidental Mutation

Incidental Mutation 'R1345:Kdm5b'

156447

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

039410-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.268) question?

Stock #

R1345 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

134560171-134635285 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 134630550 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Proline at position 1432 (T1432P)

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

possibly damaging
Transcript: ENSMUST00000047714
AA Change: T1432P

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207
AA Change: T1432P

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: T1432P

PolyPhen 2 Score 0.937 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000107817
Gene: ENSMUSG00000042207
AA Change: T1432P

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

Meta Mutation Damage Score

0.0712

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 95.9%
20x: 92.3%

Validation Efficiency

100% (45/45)

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: 43 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700001K19Rik	C	T	12: 110,668,718 (GRCm38)	V129I	probably damaging	Het
Akr1c18	T	C	13: 4,145,214 (GRCm38)	T82A	possibly damaging	Het
Alx1	A	G	10: 103,028,492 (GRCm38)	S39P	possibly damaging	Het
Atr	A	G	9: 95,920,355 (GRCm38)	T1767A	probably benign	Het
Brf1	A	T	12: 112,961,108 (GRCm38)		probably null	Het
Cd86	A	G	16: 36,618,324 (GRCm38)		probably null	Het
Cdan1	A	G	2: 120,719,139 (GRCm38)		probably null	Het
Cntln	A	G	4: 84,973,991 (GRCm38)	D371G	probably damaging	Het
Cypt4	A	G	9: 24,625,219 (GRCm38)	T2A	possibly damaging	Het
Dll1	G	T	17: 15,373,555 (GRCm38)	Y183*	probably null	Het
Dnmt1	G	T	9: 20,908,518 (GRCm38)	P1444Q	probably damaging	Het
Ern2	A	G	7: 122,177,770 (GRCm38)	L309P	probably damaging	Het
Fam151a	A	G	4: 106,742,294 (GRCm38)	K142E	probably damaging	Het
Fbn1	T	C	2: 125,314,671 (GRCm38)	E2378G	probably damaging	Het
Gm9573	T	A	17: 35,621,597 (GRCm38)		probably benign	Het
Hsh2d	G	A	8: 72,200,460 (GRCm38)	D229N	probably benign	Het
Kif2a	G	A	13: 106,993,915 (GRCm38)	S15F	probably damaging	Het
Lzic	A	G	4: 149,486,851 (GRCm38)	E31G	probably damaging	Het
Mmp16	A	G	4: 18,112,021 (GRCm38)	M466V	probably benign	Het
Mtm1	T	C	X: 71,287,231 (GRCm38)	V203A	probably benign	Het
Neurl4	A	G	11: 69,903,876 (GRCm38)	M249V	probably benign	Het
Olfr813	T	C	10: 129,856,890 (GRCm38)	I124T	probably damaging	Het
Plxna2	T	C	1: 194,644,486 (GRCm38)	Y243H	probably damaging	Het
Rbm44	A	G	1: 91,152,759 (GRCm38)	N223S	probably damaging	Het
Sel1l3	G	T	5: 53,200,217 (GRCm38)	H144Q	possibly damaging	Het
Simc1	A	ANNNNNNNNNNNNNNNNNNNNN	13: 54,525,247 (GRCm38)		probably benign	Het
Snrpb2	A	G	2: 143,065,166 (GRCm38)		probably benign	Het
Spata31d1d	T	G	13: 59,726,024 (GRCm38)	K1232N	possibly damaging	Het
Spink5	A	T	18: 43,990,682 (GRCm38)	E345D	possibly damaging	Het
Sucla2	C	T	14: 73,560,634 (GRCm38)		probably benign	Het
Tarbp1	T	C	8: 126,448,330 (GRCm38)	D789G	probably benign	Het
Tedc2	C	A	17: 24,216,318 (GRCm38)	E366*	probably null	Het
Tedc2	T	A	17: 24,216,317 (GRCm38)	E366V	probably damaging	Het
Tmem232	T	C	17: 65,450,406 (GRCm38)	N264S	possibly damaging	Het
Trim43b	G	C	9: 89,085,672 (GRCm38)	L303V	possibly damaging	Het
Tulp2	C	A	7: 45,518,721 (GRCm38)	R298S	probably benign	Het
Usp42	A	G	5: 143,717,333 (GRCm38)	V511A	probably damaging	Het
Vav1	A	T	17: 57,301,214 (GRCm38)	T321S	probably benign	Het
Vmn1r169	A	C	7: 23,577,822 (GRCm38)	H213P	probably damaging	Het
Vmn1r170	C	T	7: 23,606,362 (GRCm38)	T63I	probably benign	Het
Vmn2r103	T	G	17: 19,794,247 (GRCm38)	W434G	probably damaging	Het
Zfp407	C	T	18: 84,559,773 (GRCm38)	A1072T	probably benign	Het
Zfp7	T	C	15: 76,890,708 (GRCm38)	S317P	probably damaging	Het

Other mutations in Kdm5b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00230:Kdm5b	APN	1	134,620,955 (GRCm38)	missense	probably damaging	1.00
IGL01458:Kdm5b	APN	1	134,621,986 (GRCm38)	missense	possibly damaging	0.53
IGL01567:Kdm5b	APN	1	134,602,540 (GRCm38)	missense	probably damaging	1.00
IGL01625:Kdm5b	APN	1	134,617,968 (GRCm38)	missense	possibly damaging	0.74
IGL01970:Kdm5b	APN	1	134,600,727 (GRCm38)	missense	probably damaging	1.00
IGL02183:Kdm5b	APN	1	134,624,931 (GRCm38)	missense	probably benign	0.09
IGL02592:Kdm5b	APN	1	134,624,853 (GRCm38)	missense	probably damaging	0.99
IGL02695:Kdm5b	APN	1	134,604,485 (GRCm38)	missense	possibly damaging	0.94
IGL02697:Kdm5b	APN	1	134,588,773 (GRCm38)	splice site	probably benign
IGL03036:Kdm5b	APN	1	134,608,937 (GRCm38)	missense	probably damaging	1.00
IGL03056:Kdm5b	APN	1	134,587,979 (GRCm38)	missense	probably damaging	0.99
IGL03206:Kdm5b	APN	1	134,627,317 (GRCm38)	missense	probably benign
IGL03342:Kdm5b	APN	1	134,602,576 (GRCm38)	missense	probably benign	0.00
IGL03388:Kdm5b	APN	1	134,627,322 (GRCm38)	missense	probably benign
amaryllis	UTSW	1	134,609,061 (GRCm38)	critical splice donor site	probably null
PIT4486001:Kdm5b	UTSW	1	134,628,685 (GRCm38)	missense	probably damaging	1.00
R0233:Kdm5b	UTSW	1	134,604,634 (GRCm38)	splice site	probably benign
R0334:Kdm5b	UTSW	1	134,604,522 (GRCm38)	missense	probably damaging	0.99
R0504:Kdm5b	UTSW	1	134,621,023 (GRCm38)	critical splice donor site	probably null
R0505:Kdm5b	UTSW	1	134,602,571 (GRCm38)	missense	probably damaging	0.96
R0521:Kdm5b	UTSW	1	134,618,033 (GRCm38)	missense	possibly damaging	0.65
R1004:Kdm5b	UTSW	1	134,588,904 (GRCm38)	missense	possibly damaging	0.71
R1087:Kdm5b	UTSW	1	134,600,637 (GRCm38)	missense	probably damaging	1.00
R1126:Kdm5b	UTSW	1	134,613,991 (GRCm38)	missense	possibly damaging	0.90
R1221:Kdm5b	UTSW	1	134,599,091 (GRCm38)	missense	probably damaging	0.98
R1230:Kdm5b	UTSW	1	134,613,254 (GRCm38)	missense	probably damaging	1.00
R1482:Kdm5b	UTSW	1	134,624,897 (GRCm38)	missense	probably damaging	1.00
R1582:Kdm5b	UTSW	1	134,624,853 (GRCm38)	missense	probably damaging	0.99
R1653:Kdm5b	UTSW	1	134,602,481 (GRCm38)	missense	probably damaging	1.00
R1693:Kdm5b	UTSW	1	134,597,576 (GRCm38)	splice site	probably benign
R1721:Kdm5b	UTSW	1	134,613,181 (GRCm38)	splice site	probably benign
R1741:Kdm5b	UTSW	1	134,618,017 (GRCm38)	missense	possibly damaging	0.82
R1762:Kdm5b	UTSW	1	134,604,467 (GRCm38)	nonsense	probably null
R1820:Kdm5b	UTSW	1	134,597,670 (GRCm38)	missense	possibly damaging	0.87
R1872:Kdm5b	UTSW	1	134,624,994 (GRCm38)	missense	probably damaging	1.00
R1966:Kdm5b	UTSW	1	134,613,873 (GRCm38)	splice site	probably null
R2056:Kdm5b	UTSW	1	134,613,214 (GRCm38)	missense	probably benign	0.05
R2059:Kdm5b	UTSW	1	134,613,214 (GRCm38)	missense	probably benign	0.05
R2405:Kdm5b	UTSW	1	134,609,016 (GRCm38)	missense	probably damaging	0.97
R3417:Kdm5b	UTSW	1	134,587,977 (GRCm38)	missense	probably damaging	1.00
R3771:Kdm5b	UTSW	1	134,613,345 (GRCm38)	missense	probably damaging	1.00
R3783:Kdm5b	UTSW	1	134,630,542 (GRCm38)	missense	probably benign
R3803:Kdm5b	UTSW	1	134,615,941 (GRCm38)	missense	probably benign	0.07
R3980:Kdm5b	UTSW	1	134,619,670 (GRCm38)	missense	probably benign	0.11
R3983:Kdm5b	UTSW	1	134,631,304 (GRCm38)	missense	possibly damaging	0.91
R4013:Kdm5b	UTSW	1	134,627,329 (GRCm38)	missense	possibly damaging	0.86
R4162:Kdm5b	UTSW	1	134,625,161 (GRCm38)	missense	probably benign	0.01
R4701:Kdm5b	UTSW	1	134,606,012 (GRCm38)	intron	probably benign
R4791:Kdm5b	UTSW	1	134,630,800 (GRCm38)	missense	possibly damaging	0.82
R4836:Kdm5b	UTSW	1	134,593,315 (GRCm38)	splice site	probably null
R4924:Kdm5b	UTSW	1	134,631,351 (GRCm38)	missense	probably benign	0.00
R5135:Kdm5b	UTSW	1	134,588,746 (GRCm38)	intron	probably benign
R5248:Kdm5b	UTSW	1	134,620,997 (GRCm38)	missense	probably benign	0.11
R5290:Kdm5b	UTSW	1	134,622,099 (GRCm38)	splice site	probably null
R5358:Kdm5b	UTSW	1	134,607,694 (GRCm38)	nonsense	probably null
R5388:Kdm5b	UTSW	1	134,608,897 (GRCm38)	nonsense	probably null
R5396:Kdm5b	UTSW	1	134,622,098 (GRCm38)	splice site	probably null
R5397:Kdm5b	UTSW	1	134,622,098 (GRCm38)	splice site	probably null
R5398:Kdm5b	UTSW	1	134,622,098 (GRCm38)	splice site	probably null
R5399:Kdm5b	UTSW	1	134,622,098 (GRCm38)	splice site	probably null
R5529:Kdm5b	UTSW	1	134,588,003 (GRCm38)	missense	probably damaging	1.00
R5540:Kdm5b	UTSW	1	134,631,241 (GRCm38)	missense	probably damaging	0.98
R5661:Kdm5b	UTSW	1	134,599,073 (GRCm38)	missense	probably benign	0.01
R5663:Kdm5b	UTSW	1	134,630,635 (GRCm38)	missense	probably benign
R5822:Kdm5b	UTSW	1	134,588,773 (GRCm38)	splice site	probably benign
R6226:Kdm5b	UTSW	1	134,608,878 (GRCm38)	missense	probably damaging	0.99
R6368:Kdm5b	UTSW	1	134,599,207 (GRCm38)	missense	probably damaging	1.00
R6681:Kdm5b	UTSW	1	134,613,269 (GRCm38)	missense	possibly damaging	0.90
R6715:Kdm5b	UTSW	1	134,609,061 (GRCm38)	critical splice donor site	probably null
R7132:Kdm5b	UTSW	1	134,599,106 (GRCm38)	missense	probably damaging	1.00
R7202:Kdm5b	UTSW	1	134,624,759 (GRCm38)	missense	probably benign
R7258:Kdm5b	UTSW	1	134,621,021 (GRCm38)	missense	probably damaging	1.00
R7335:Kdm5b	UTSW	1	134,560,439 (GRCm38)	missense	probably damaging	1.00
R7420:Kdm5b	UTSW	1	134,604,497 (GRCm38)	missense	probably benign	0.14
R7426:Kdm5b	UTSW	1	134,595,833 (GRCm38)	missense	probably benign	0.02
R7452:Kdm5b	UTSW	1	134,624,948 (GRCm38)	missense	probably damaging	1.00
R7595:Kdm5b	UTSW	1	134,608,966 (GRCm38)	missense	probably benign	0.00
R7612:Kdm5b	UTSW	1	134,624,918 (GRCm38)	nonsense	probably null
R7704:Kdm5b	UTSW	1	134,587,931 (GRCm38)	missense	probably damaging	1.00
R7846:Kdm5b	UTSW	1	134,617,840 (GRCm38)	missense	probably damaging	1.00
R8115:Kdm5b	UTSW	1	134,619,673 (GRCm38)	missense	possibly damaging	0.83
R8146:Kdm5b	UTSW	1	134,625,126 (GRCm38)	missense	probably benign	0.05
R8160:Kdm5b	UTSW	1	134,613,919 (GRCm38)	missense	probably damaging	1.00
R8527:Kdm5b	UTSW	1	134,605,774 (GRCm38)	missense	possibly damaging	0.78
R8542:Kdm5b	UTSW	1	134,605,774 (GRCm38)	missense	possibly damaging	0.78
R8930:Kdm5b	UTSW	1	134,616,272 (GRCm38)	missense	probably damaging	1.00
R8932:Kdm5b	UTSW	1	134,616,272 (GRCm38)	missense	probably damaging	1.00
R8950:Kdm5b	UTSW	1	134,613,926 (GRCm38)	missense	possibly damaging	0.84
R9089:Kdm5b	UTSW	1	134,607,768 (GRCm38)	missense	probably damaging	0.98
R9109:Kdm5b	UTSW	1	134,600,755 (GRCm38)	critical splice donor site	probably null
R9133:Kdm5b	UTSW	1	134,602,585 (GRCm38)	missense	probably benign
R9298:Kdm5b	UTSW	1	134,600,755 (GRCm38)	critical splice donor site	probably null
R9423:Kdm5b	UTSW	1	134,587,967 (GRCm38)	missense	possibly damaging	0.85
R9630:Kdm5b	UTSW	1	134,585,233 (GRCm38)	critical splice donor site	probably null
R9670:Kdm5b	UTSW	1	134,630,502 (GRCm38)	nonsense	probably null
X0063:Kdm5b	UTSW	1	134,588,876 (GRCm38)	missense	probably benign	0.07
Z1176:Kdm5b	UTSW	1	134,625,035 (GRCm38)	missense	probably damaging	1.00
Z1177:Kdm5b	UTSW	1	134,595,798 (GRCm38)	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- ATTGAAGTTTGGTATCCCCAGCTCG -3'
(R):5'- CTGGACAGATGGCATCTTCATCCTC -3'

Sequencing Primer
(F):5'- ATGCAGGGTTCTCATTTGCAC -3'
(R):5'- GATGGCATCTTCATCCTCAGAGTC -3'

Posted On

2014-02-11