Mutagenetix > Incidental Mutation

Incidental Mutation 'R9109:Kdm5b'

692113

Institutional Source

Beutler Lab

Gene Symbol

Kdm5b

Ensembl Gene

ENSMUSG00000042207

Gene Name

lysine demethylase 5B

Synonyms

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

MMRRC Submission

068918-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.356) question?

Stock #

R9109 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

134487916-134560621 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

T to C at 134528493 bp (GRCm39)

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: 99.7%
20x: 99.1%

Validation Efficiency

98% (61/62)

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700030K09Rik	C	A	8: 73,198,923 (GRCm39)	A110D	probably benign	Het
4930407I10Rik	A	G	15: 81,947,615 (GRCm39)	E504G	probably benign	Het
4931406B18Rik	C	A	7: 43,148,702 (GRCm39)	A170S		Het
Apbb2	T	C	5: 66,609,018 (GRCm39)	K210E	probably benign	Het
Arid4a	C	A	12: 71,122,129 (GRCm39)	L515I	probably damaging	Het
Atp13a3	A	G	16: 30,134,716 (GRCm39)	S1186P	possibly damaging	Het
Brf1	A	G	12: 112,927,011 (GRCm39)	Y500H	probably damaging	Het
Btaf1	A	G	19: 36,964,114 (GRCm39)	Y895C	probably benign	Het
Cdhr17	T	A	5: 16,997,909 (GRCm39)	V47E	possibly damaging	Het
Cenpf	T	C	1: 189,391,571 (GRCm39)	T737A	probably benign	Het
Cmklr1	G	C	5: 113,752,043 (GRCm39)	H319Q	probably benign	Het
Col18a1	G	A	10: 76,893,204 (GRCm39)	T1057M	probably damaging	Het
Col1a2	T	A	6: 4,515,260 (GRCm39)		probably null	Het
Csmd3	A	C	15: 47,617,187 (GRCm39)	H1000Q		Het
Cyp4a29	T	A	4: 115,108,395 (GRCm39)	M373K	probably damaging	Het
Dnhd1	A	G	7: 105,333,173 (GRCm39)	E215G	probably damaging	Het
Dusp19	T	C	2: 80,447,729 (GRCm39)	M1T	probably null	Het
Etv4	A	G	11: 101,664,492 (GRCm39)	Y253H	probably benign	Het
Exosc6	G	A	8: 111,783,513 (GRCm39)	A171T	probably damaging	Het
Fam219a	G	A	4: 41,521,870 (GRCm39)	T70M	probably damaging	Het
Fau	G	A	19: 6,108,297 (GRCm39)	R6H	probably benign	Het
Flrt3	T	C	2: 140,501,879 (GRCm39)	D583G	probably damaging	Het
Gm14443	A	T	2: 175,011,869 (GRCm39)	C192*	probably null	Het
Gm4353	T	A	7: 115,682,843 (GRCm39)	N246I	probably benign	Het
Igfn1	A	G	1: 135,926,327 (GRCm39)	L41P	probably benign	Het
Jakmip3	A	T	7: 138,622,560 (GRCm39)	I307F	probably damaging	Het
Kcnt2	T	A	1: 140,353,035 (GRCm39)	V248D	probably damaging	Het
Kctd14	A	G	7: 97,107,243 (GRCm39)	K166R	probably benign	Het
Kif5c	A	G	2: 49,620,151 (GRCm39)	D461G	probably damaging	Het
Lpin2	T	C	17: 71,538,516 (GRCm39)		probably null	Het
Mettl22	G	A	16: 8,305,231 (GRCm39)	D295N	probably damaging	Het
Nox4	G	A	7: 87,025,448 (GRCm39)	R525Q	probably benign	Het
Or10a5	A	T	7: 106,635,640 (GRCm39)	I93F	probably damaging	Het
Or5b95	T	A	19: 12,658,190 (GRCm39)	C239*	probably null	Het
Or5k8	A	T	16: 58,644,677 (GRCm39)	Y132N	probably damaging	Het
Pecam1	G	T	11: 106,586,587 (GRCm39)	N309K	probably damaging	Het
Pigc	C	T	1: 161,798,032 (GRCm39)	R5C	probably benign	Het
Pih1d1	T	C	7: 44,809,193 (GRCm39)	V259A	possibly damaging	Het
Ptpre	A	G	7: 135,271,508 (GRCm39)	I374M	probably benign	Het
Rnps1	A	G	17: 24,637,573 (GRCm39)	S72G	unknown	Het
S100pbp	A	G	4: 129,044,847 (GRCm39)	Y363H	probably damaging	Het
Sema5a	A	G	15: 32,619,040 (GRCm39)	T523A	probably benign	Het
Slc38a8	A	G	8: 120,212,851 (GRCm39)	F270S	possibly damaging	Het
Slc4a1ap	T	C	5: 31,693,538 (GRCm39)	S491P	probably damaging	Het
Slc66a2	T	C	18: 80,300,300 (GRCm39)	L57P	probably damaging	Het
Slc7a6	T	C	8: 106,922,534 (GRCm39)	V440A	probably damaging	Het
Sobp	A	T	10: 42,898,902 (GRCm39)	C228S	probably damaging	Het
Sox8	T	C	17: 25,787,813 (GRCm39)	D212G	possibly damaging	Het
Specc1	A	G	11: 62,102,464 (GRCm39)		probably null	Het
Svop	G	A	5: 114,168,231 (GRCm39)	T456M	probably benign	Het
Synrg	A	G	11: 83,900,278 (GRCm39)	D750G	probably damaging	Het
Syt14	C	A	1: 192,612,944 (GRCm39)	E336*	probably null	Het
Tcp10c	A	T	17: 13,576,650 (GRCm39)	Q76H	probably damaging	Het
Tcp11l1	C	T	2: 104,528,897 (GRCm39)	V134I	possibly damaging	Het
Tex51	T	C	18: 32,594,029 (GRCm39)	R110G	possibly damaging	Het
Tle3	T	A	9: 61,319,562 (GRCm39)	H443Q	possibly damaging	Het
Unc13a	C	T	8: 72,108,335 (GRCm39)	R506Q	possibly damaging	Het
Vmn2r27	T	C	6: 124,174,224 (GRCm39)	Y542C	possibly damaging	Het
Vmn2r5	T	G	3: 64,411,411 (GRCm39)	N386H	possibly damaging	Het
Vmn2r91	A	G	17: 18,327,905 (GRCm39)	I500V	probably damaging	Het
Wdfy4	A	T	14: 32,760,704 (GRCm39)		probably null	Het
Zfp709	A	T	8: 72,644,648 (GRCm39)	E692D	possibly damaging	Het
Zglp1	A	T	9: 20,977,482 (GRCm39)	L111Q	probably benign	Het

Other mutations in Kdm5b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00230:Kdm5b	APN	1	134,548,693 (GRCm39)	missense	probably damaging	1.00
IGL01458:Kdm5b	APN	1	134,549,724 (GRCm39)	missense	possibly damaging	0.53
IGL01567:Kdm5b	APN	1	134,530,278 (GRCm39)	missense	probably damaging	1.00
IGL01625:Kdm5b	APN	1	134,545,706 (GRCm39)	missense	possibly damaging	0.74
IGL01970:Kdm5b	APN	1	134,528,465 (GRCm39)	missense	probably damaging	1.00
IGL02183:Kdm5b	APN	1	134,552,669 (GRCm39)	missense	probably benign	0.09
IGL02592:Kdm5b	APN	1	134,552,591 (GRCm39)	missense	probably damaging	0.99
IGL02695:Kdm5b	APN	1	134,532,223 (GRCm39)	missense	possibly damaging	0.94
IGL02697:Kdm5b	APN	1	134,516,511 (GRCm39)	splice site	probably benign
IGL03036:Kdm5b	APN	1	134,536,675 (GRCm39)	missense	probably damaging	1.00
IGL03056:Kdm5b	APN	1	134,515,717 (GRCm39)	missense	probably damaging	0.99
IGL03206:Kdm5b	APN	1	134,555,055 (GRCm39)	missense	probably benign
IGL03342:Kdm5b	APN	1	134,530,314 (GRCm39)	missense	probably benign	0.00
IGL03388:Kdm5b	APN	1	134,555,060 (GRCm39)	missense	probably benign
amaryllis	UTSW	1	134,536,799 (GRCm39)	critical splice donor site	probably null
PIT4486001:Kdm5b	UTSW	1	134,556,423 (GRCm39)	missense	probably damaging	1.00
R0233:Kdm5b	UTSW	1	134,532,372 (GRCm39)	splice site	probably benign
R0334:Kdm5b	UTSW	1	134,532,260 (GRCm39)	missense	probably damaging	0.99
R0504:Kdm5b	UTSW	1	134,548,761 (GRCm39)	critical splice donor site	probably null
R0505:Kdm5b	UTSW	1	134,530,309 (GRCm39)	missense	probably damaging	0.96
R0521:Kdm5b	UTSW	1	134,545,771 (GRCm39)	missense	possibly damaging	0.65
R1004:Kdm5b	UTSW	1	134,516,642 (GRCm39)	missense	possibly damaging	0.71
R1087:Kdm5b	UTSW	1	134,528,375 (GRCm39)	missense	probably damaging	1.00
R1126:Kdm5b	UTSW	1	134,541,729 (GRCm39)	missense	possibly damaging	0.90
R1221:Kdm5b	UTSW	1	134,526,829 (GRCm39)	missense	probably damaging	0.98
R1230:Kdm5b	UTSW	1	134,540,992 (GRCm39)	missense	probably damaging	1.00
R1345:Kdm5b	UTSW	1	134,558,288 (GRCm39)	missense	possibly damaging	0.94
R1482:Kdm5b	UTSW	1	134,552,635 (GRCm39)	missense	probably damaging	1.00
R1582:Kdm5b	UTSW	1	134,552,591 (GRCm39)	missense	probably damaging	0.99
R1653:Kdm5b	UTSW	1	134,530,219 (GRCm39)	missense	probably damaging	1.00
R1693:Kdm5b	UTSW	1	134,525,314 (GRCm39)	splice site	probably benign
R1721:Kdm5b	UTSW	1	134,540,919 (GRCm39)	splice site	probably benign
R1741:Kdm5b	UTSW	1	134,545,755 (GRCm39)	missense	possibly damaging	0.82
R1762:Kdm5b	UTSW	1	134,532,205 (GRCm39)	nonsense	probably null
R1820:Kdm5b	UTSW	1	134,525,408 (GRCm39)	missense	possibly damaging	0.87
R1872:Kdm5b	UTSW	1	134,552,732 (GRCm39)	missense	probably damaging	1.00
R1966:Kdm5b	UTSW	1	134,541,611 (GRCm39)	splice site	probably null
R2056:Kdm5b	UTSW	1	134,540,952 (GRCm39)	missense	probably benign	0.05
R2059:Kdm5b	UTSW	1	134,540,952 (GRCm39)	missense	probably benign	0.05
R2405:Kdm5b	UTSW	1	134,536,754 (GRCm39)	missense	probably damaging	0.97
R3417:Kdm5b	UTSW	1	134,515,715 (GRCm39)	missense	probably damaging	1.00
R3771:Kdm5b	UTSW	1	134,541,083 (GRCm39)	missense	probably damaging	1.00
R3783:Kdm5b	UTSW	1	134,558,280 (GRCm39)	missense	probably benign
R3803:Kdm5b	UTSW	1	134,543,679 (GRCm39)	missense	probably benign	0.07
R3980:Kdm5b	UTSW	1	134,547,408 (GRCm39)	missense	probably benign	0.11
R3983:Kdm5b	UTSW	1	134,559,042 (GRCm39)	missense	possibly damaging	0.91
R4013:Kdm5b	UTSW	1	134,555,067 (GRCm39)	missense	possibly damaging	0.86
R4162:Kdm5b	UTSW	1	134,552,899 (GRCm39)	missense	probably benign	0.01
R4701:Kdm5b	UTSW	1	134,533,750 (GRCm39)	intron	probably benign
R4791:Kdm5b	UTSW	1	134,558,538 (GRCm39)	missense	possibly damaging	0.82
R4836:Kdm5b	UTSW	1	134,521,053 (GRCm39)	splice site	probably null
R4924:Kdm5b	UTSW	1	134,559,089 (GRCm39)	missense	probably benign	0.00
R5135:Kdm5b	UTSW	1	134,516,484 (GRCm39)	intron	probably benign
R5248:Kdm5b	UTSW	1	134,548,735 (GRCm39)	missense	probably benign	0.11
R5290:Kdm5b	UTSW	1	134,549,837 (GRCm39)	splice site	probably null
R5358:Kdm5b	UTSW	1	134,535,432 (GRCm39)	nonsense	probably null
R5388:Kdm5b	UTSW	1	134,536,635 (GRCm39)	nonsense	probably null
R5396:Kdm5b	UTSW	1	134,549,836 (GRCm39)	splice site	probably null
R5397:Kdm5b	UTSW	1	134,549,836 (GRCm39)	splice site	probably null
R5398:Kdm5b	UTSW	1	134,549,836 (GRCm39)	splice site	probably null
R5399:Kdm5b	UTSW	1	134,549,836 (GRCm39)	splice site	probably null
R5529:Kdm5b	UTSW	1	134,515,741 (GRCm39)	missense	probably damaging	1.00
R5540:Kdm5b	UTSW	1	134,558,979 (GRCm39)	missense	probably damaging	0.98
R5661:Kdm5b	UTSW	1	134,526,811 (GRCm39)	missense	probably benign	0.01
R5663:Kdm5b	UTSW	1	134,558,373 (GRCm39)	missense	probably benign
R5822:Kdm5b	UTSW	1	134,516,511 (GRCm39)	splice site	probably benign
R6226:Kdm5b	UTSW	1	134,536,616 (GRCm39)	missense	probably damaging	0.99
R6368:Kdm5b	UTSW	1	134,526,945 (GRCm39)	missense	probably damaging	1.00
R6681:Kdm5b	UTSW	1	134,541,007 (GRCm39)	missense	possibly damaging	0.90
R6715:Kdm5b	UTSW	1	134,536,799 (GRCm39)	critical splice donor site	probably null
R7132:Kdm5b	UTSW	1	134,526,844 (GRCm39)	missense	probably damaging	1.00
R7202:Kdm5b	UTSW	1	134,552,497 (GRCm39)	missense	probably benign
R7258:Kdm5b	UTSW	1	134,548,759 (GRCm39)	missense	probably damaging	1.00
R7335:Kdm5b	UTSW	1	134,488,177 (GRCm39)	missense	probably damaging	1.00
R7420:Kdm5b	UTSW	1	134,532,235 (GRCm39)	missense	probably benign	0.14
R7426:Kdm5b	UTSW	1	134,523,571 (GRCm39)	missense	probably benign	0.02
R7452:Kdm5b	UTSW	1	134,552,686 (GRCm39)	missense	probably damaging	1.00
R7595:Kdm5b	UTSW	1	134,536,704 (GRCm39)	missense	probably benign	0.00
R7612:Kdm5b	UTSW	1	134,552,656 (GRCm39)	nonsense	probably null
R7704:Kdm5b	UTSW	1	134,515,669 (GRCm39)	missense	probably damaging	1.00
R7846:Kdm5b	UTSW	1	134,545,578 (GRCm39)	missense	probably damaging	1.00
R8115:Kdm5b	UTSW	1	134,547,411 (GRCm39)	missense	possibly damaging	0.83
R8146:Kdm5b	UTSW	1	134,552,864 (GRCm39)	missense	probably benign	0.05
R8160:Kdm5b	UTSW	1	134,541,657 (GRCm39)	missense	probably damaging	1.00
R8527:Kdm5b	UTSW	1	134,533,512 (GRCm39)	missense	possibly damaging	0.78
R8542:Kdm5b	UTSW	1	134,533,512 (GRCm39)	missense	possibly damaging	0.78
R8930:Kdm5b	UTSW	1	134,544,010 (GRCm39)	missense	probably damaging	1.00
R8932:Kdm5b	UTSW	1	134,544,010 (GRCm39)	missense	probably damaging	1.00
R8950:Kdm5b	UTSW	1	134,541,664 (GRCm39)	missense	possibly damaging	0.84
R9089:Kdm5b	UTSW	1	134,535,506 (GRCm39)	missense	probably damaging	0.98
R9133:Kdm5b	UTSW	1	134,530,323 (GRCm39)	missense	probably benign
R9298:Kdm5b	UTSW	1	134,528,493 (GRCm39)	critical splice donor site	probably null
R9423:Kdm5b	UTSW	1	134,515,705 (GRCm39)	missense	possibly damaging	0.85
R9630:Kdm5b	UTSW	1	134,512,971 (GRCm39)	critical splice donor site	probably null
R9670:Kdm5b	UTSW	1	134,558,240 (GRCm39)	nonsense	probably null
X0063:Kdm5b	UTSW	1	134,516,614 (GRCm39)	missense	probably benign	0.07
Z1176:Kdm5b	UTSW	1	134,552,773 (GRCm39)	missense	probably damaging	1.00
Z1177:Kdm5b	UTSW	1	134,523,536 (GRCm39)	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- GTCATTTGAAAGTGTCACCTGG -3'
(R):5'- AGTCCATGTGTGCTAGTGGC -3'

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

Posted On

2021-12-30