Mutagenetix > Incidental Mutation

Incidental Mutation 'R5388:Kdm5b'

425386

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

042960-MU

Accession Numbers

Essential gene?

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

Stock #

R5388 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

134560171-134635285 bp(+) (GRCm38)

Type of Mutation

nonsense

DNA Base Change (assembly)

T to A at 134608897 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Stop codon at position 618 (Y618*)

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 null
Transcript: ENSMUST00000047714
AA Change: Y618*

SMART Domains

Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207
AA Change: Y618*

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

noncoding transcript
Transcript: ENSMUST00000112197

SMART Domains

Protein: ENSMUSP00000107816
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	225	236	N/A	INTRINSIC
PHD	308	354	6.15e-14	SMART
JmjC	450	595	2.6e-24	SMART

Predicted Effect

probably null
Transcript: ENSMUST00000112198
AA Change: Y618*

SMART Domains

Protein: ENSMUSP00000107817
Gene: ENSMUSG00000042207
AA Change: Y618*

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

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.3%
3x: 98.8%
10x: 97.5%
20x: 95.9%

Validation Efficiency

98% (57/58)

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: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932415D10Rik	T	C	10: 82,283,727 (GRCm38)	Q4483R	probably damaging	Het
Abca16	T	C	7: 120,540,746 (GRCm38)		probably null	Het
Acap2	C	A	16: 31,109,725 (GRCm38)	C475F	probably damaging	Het
Ace	C	A	11: 105,988,458 (GRCm38)	P603Q	possibly damaging	Het
Adamts20	C	G	15: 94,345,778 (GRCm38)	V657L	possibly damaging	Het
Antxr2	A	G	5: 97,977,599 (GRCm38)		probably null	Het
Atp6v1b2	G	A	8: 69,101,437 (GRCm38)	V89I	probably benign	Het
Cacna1e	G	A	1: 154,477,796 (GRCm38)	P676L	probably damaging	Het
Camsap3	A	T	8: 3,604,276 (GRCm38)	I649F	probably damaging	Het
Camta1	G	T	4: 151,075,238 (GRCm38)	S490R	probably damaging	Het
Celsr1	A	G	15: 85,925,518 (GRCm38)	I2221T	probably damaging	Het
Cfd	A	T	10: 79,892,125 (GRCm38)	D164V	probably damaging	Het
Cfdp1	T	C	8: 111,768,752 (GRCm38)	D278G	probably damaging	Het
Cntn6	A	T	6: 104,832,562 (GRCm38)	L519F	probably damaging	Het
Col4a4	C	T	1: 82,493,591 (GRCm38)	G681E	unknown	Het
Cybrd1	T	C	2: 71,137,645 (GRCm38)		probably null	Het
Cyp2e1	T	C	7: 140,763,993 (GRCm38)	L48P	probably damaging	Het
Ep400	G	A	5: 110,701,728 (GRCm38)	T1409I	unknown	Het
Epp13	T	C	7: 6,266,347 (GRCm38)		probably null	Het
Exosc7	A	T	9: 123,118,907 (GRCm38)	D47V	probably damaging	Het
Fgr	T	C	4: 132,995,031 (GRCm38)	F204L	probably damaging	Het
Gm10100	G	A	10: 77,726,726 (GRCm38)	V81M	probably benign	Het
Gm12367	T	C	4: 35,235,690 (GRCm38)		noncoding transcript	Het
Gm15922	T	C	7: 3,738,857 (GRCm38)	T175A	possibly damaging	Het
Grxcr1	C	A	5: 68,166,195 (GRCm38)	T272K	probably damaging	Het
Kcna5	C	T	6: 126,534,896 (GRCm38)	D90N	probably benign	Het
Lama5	T	A	2: 180,190,746 (GRCm38)	H1670L	possibly damaging	Het
Mtus2	C	T	5: 148,306,708 (GRCm38)	Q113*	probably null	Het
Ncam1	A	C	9: 49,544,754 (GRCm38)	D521E	probably benign	Het
Nkapl	T	C	13: 21,467,570 (GRCm38)	H291R	possibly damaging	Het
Nlrp1b	T	G	11: 71,172,141 (GRCm38)	N695H	probably damaging	Het
Npc1l1	T	A	11: 6,214,733 (GRCm38)	Q1105H	probably damaging	Het
Paxip1	C	G	5: 27,781,455 (GRCm38)		probably benign	Het
Pign	A	T	1: 105,655,970 (GRCm38)	W136R	probably damaging	Het
Pkn3	T	A	2: 30,081,074 (GRCm38)	S222T	probably damaging	Het
Polr3a	T	C	14: 24,454,941 (GRCm38)	I1084V	possibly damaging	Het
Ppfibp1	T	A	6: 146,996,840 (GRCm38)	I98N	probably damaging	Het
Ppfibp1	T	G	6: 147,016,330 (GRCm38)	S484A	probably damaging	Het
Ppp1r7	T	C	1: 93,352,590 (GRCm38)	F127L	probably damaging	Het
Pramel1	T	C	4: 143,397,384 (GRCm38)	Y210H	probably benign	Het
Rad21l	C	T	2: 151,653,483 (GRCm38)	V427I	probably benign	Het
Ripply1	TTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCT	TTCCTCCTCCTCCTCCTCCTCCTCCTCCT	X: 139,779,850 (GRCm38)		probably benign	Het
Rnf225	A	G	7: 12,928,005 (GRCm38)	D37G	probably damaging	Het
Smpd2	A	G	10: 41,487,971 (GRCm38)		probably null	Het
Tmem38b	C	T	4: 53,859,945 (GRCm38)	R242W	probably benign	Het
Topaz1	A	T	9: 122,774,093 (GRCm38)	K1035I	possibly damaging	Het
Trhr	T	C	15: 44,197,477 (GRCm38)	I131T	possibly damaging	Het
Usp1	A	G	4: 98,931,057 (GRCm38)	D252G	probably benign	Het
Usp14	C	T	18: 10,018,023 (GRCm38)	E90K	probably damaging	Het
Yme1l1	T	G	2: 23,162,557 (GRCm38)	D74E	probably benign	Het
Ythdc2	T	A	18: 44,857,025 (GRCm38)	L732Q	possibly damaging	Het
Zbbx	G	T	3: 75,083,670 (GRCm38)	A289D	probably damaging	Het
Zfhx3	G	A	8: 108,946,814 (GRCm38)	V1499I	possibly damaging	Het
Zfp622	T	C	15: 25,996,199 (GRCm38)	V184A	possibly 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
R1345:Kdm5b	UTSW	1	134,630,550 (GRCm38)	missense	possibly damaging	0.94
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
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'- ACCTAATGTGATAGACCTTTAGAGCAC -3'
(R):5'- GGACTTCCAGAAATCTTACCAATTTCC -3'

Sequencing Primer
(F):5'- ACAATAGACCCAGGGCTCTG -3'
(R):5'- TCCGAACAGTTTCCCTTAAAGC -3'

Posted On

2016-08-04