Mutagenetix > Incidental Mutation

Incidental Mutation 'R9298:Kdm5b'

704706

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

068963-MU

Accession Numbers

Essential gene?

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

Stock #

R9298 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

134560171-134635285 bp(+) (GRCm38)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

T to C at 134600755 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000038138 (fasta)

Gene Model

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

AlphaFold

Q80Y84

Predicted Effect

probably null
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

probably null
Transcript: ENSMUST00000112198

SMART Domains

Protein: ENSMUSP00000107817
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	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

0.9501

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.4%

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: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700030K09Rik	C	A	8: 72,445,079 (GRCm38)	A110D	probably benign	Het
4930407I10Rik	A	G	15: 82,063,414 (GRCm38)	E504G	probably benign	Het
Apbb2	T	C	5: 66,451,675 (GRCm38)	K210E	probably benign	Het
Arhgef37	G	T	18: 61,518,001 (GRCm38)	A151D	probably damaging	Het
Btaf1	A	G	19: 36,986,714 (GRCm38)	Y895C	probably benign	Het
Catsperb	A	G	12: 101,594,341 (GRCm38)	I864V	possibly damaging	Het
Cmklr1	G	C	5: 113,613,982 (GRCm38)	H319Q	probably benign	Het
Col18a1	G	A	10: 77,057,370 (GRCm38)	T1057M	probably damaging	Het
Col1a2	T	A	6: 4,515,260 (GRCm38)		probably null	Het
Col6a4	A	G	9: 106,068,335 (GRCm38)	I860T	probably damaging	Het
Csmd3	A	C	15: 47,753,791 (GRCm38)	H1000Q		Het
Cyp4a29	T	A	4: 115,251,198 (GRCm38)	M373K	probably damaging	Het
Dnhd1	A	G	7: 105,683,966 (GRCm38)	E215G	probably damaging	Het
Dopey2	A	G	16: 93,800,199 (GRCm38)	E1972G	probably damaging	Het
Dusp19	T	C	2: 80,617,385 (GRCm38)	M1T	probably null	Het
Eif4b	A	G	15: 102,082,014 (GRCm38)	T18A	possibly damaging	Het
Exosc6	G	A	8: 111,056,881 (GRCm38)	A171T	probably damaging	Het
Fau	G	A	19: 6,058,267 (GRCm38)	R6H	probably benign	Het
Flrt3	T	C	2: 140,659,959 (GRCm38)	D583G	probably damaging	Het
Fpgt	A	T	3: 155,087,058 (GRCm38)	L444*	probably null	Het
Gm10226	A	G	17: 21,691,861 (GRCm38)	E1G	probably null	Het
Gm14443	A	T	2: 175,170,076 (GRCm38)	C192*	probably null	Het
Gm28710	T	A	5: 16,791,857 (GRCm38)	C10*	probably null	Het
Gm35060	T	C	18: 32,460,976 (GRCm38)	R110G	possibly damaging	Het
Gm4353	T	A	7: 116,083,608 (GRCm38)	N246I	probably benign	Het
Igfn1	A	G	1: 135,998,589 (GRCm38)	L41P	probably benign	Het
Iigp1	T	G	18: 60,389,991 (GRCm38)	D60E	probably benign	Het
Kcnt2	T	A	1: 140,425,297 (GRCm38)	V248D	probably damaging	Het
Kctd14	A	G	7: 97,458,036 (GRCm38)	K166R	probably benign	Het
Kdm4d	G	A	9: 14,464,040 (GRCm38)	T174M	probably damaging	Het
Maz	CGCGGCCTCGGCGGCTGGTGCGG	CGCGG	7: 127,025,903 (GRCm38)		probably benign	Het
Mkl2	A	G	16: 13,384,218 (GRCm38)	Q115R	probably benign	Het
Nox4	G	A	7: 87,376,240 (GRCm38)	R525Q	probably benign	Het
Olfr1443	T	A	19: 12,680,826 (GRCm38)	C239*	probably null	Het
Olfr713	A	T	7: 107,036,433 (GRCm38)	I93F	probably damaging	Het
Olfr93	A	T	17: 37,151,681 (GRCm38)	V97D	probably damaging	Het
Pigc	C	T	1: 161,970,463 (GRCm38)	R5C	probably benign	Het
Plekhm2	C	A	4: 141,629,518 (GRCm38)	M771I	probably benign	Het
Pqlc1	T	C	18: 80,257,085 (GRCm38)	L57P	probably damaging	Het
Runx1	T	A	16: 92,644,259 (GRCm38)	T221S	possibly damaging	Het
S100pbp	A	G	4: 129,151,054 (GRCm38)	Y363H	probably damaging	Het
Sema5a	A	G	15: 32,618,894 (GRCm38)	T523A	probably benign	Het
Slc38a8	A	G	8: 119,486,112 (GRCm38)	F270S	possibly damaging	Het
Slc4a1ap	T	C	5: 31,536,194 (GRCm38)	S491P	probably damaging	Het
Slc7a6	T	C	8: 106,195,902 (GRCm38)	V440A	probably damaging	Het
Sobp	A	T	10: 43,022,906 (GRCm38)	C228S	probably damaging	Het
Svop	G	A	5: 114,030,170 (GRCm38)	T456M	probably benign	Het
Synrg	A	G	11: 84,009,452 (GRCm38)	D750G	probably damaging	Het
Syt14	C	A	1: 192,930,636 (GRCm38)	E336*	probably null	Het
Tcp11l1	C	T	2: 104,698,552 (GRCm38)	V134I	possibly damaging	Het
Tle3	T	A	9: 61,412,280 (GRCm38)	H443Q	possibly damaging	Het
Unc13a	C	T	8: 71,655,691 (GRCm38)	R506Q	possibly damaging	Het
Vmn1r121	A	C	7: 21,098,419 (GRCm38)	V32G	probably damaging	Het
Wiz	A	G	17: 32,361,740 (GRCm38)	F246L	probably benign	Het
Zfp672	A	T	11: 58,329,764 (GRCm38)	M3K	unknown	Het
Zfp709	A	T	8: 71,890,804 (GRCm38)	E692D	possibly damaging	Het
Zglp1	A	T	9: 21,066,186 (GRCm38)	L111Q	probably benign	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
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
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'- GTCATTTGAAAGTGTCACCTGG -3'
(R):5'- AATTAGTCCATGTGTGCTAGTGGC -3'

Sequencing Primer
(F):5'- GTGTCACCTGGAAAACAGCTTTTC -3'
(R):5'- AGTGAATTCCAGGCTGACTGC -3'

Posted On

2022-03-25