Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL03206:Kdm5b'

413131

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Kdm5b

Ensembl Gene

ENSMUSG00000042207

Gene Name

lysine demethylase 5B

Synonyms

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

Accession Numbers

Essential gene?

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

Stock #

IGL03206

Quality Score

Status

Chromosome

Chromosomal Location

134487916-134560621 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 134555055 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 1321 (N1321S)

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 benign
Transcript: ENSMUST00000047714
AA Change: N1321S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207
AA Change: N1321S

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 benign
Transcript: ENSMUST00000112198
AA Change: N1321S

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000107817
Gene: ENSMUSG00000042207
AA Change: N1321S

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

Coding Region Coverage

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: 45 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2ml1	T	A	6: 128,530,239 (GRCm39)	E939D	possibly damaging	Het
Aloxe3	C	A	11: 69,020,472 (GRCm39)	A172D	possibly damaging	Het
Bscl2	G	A	19: 8,820,453 (GRCm39)	R158Q	probably damaging	Het
Cdon	A	G	9: 35,414,602 (GRCm39)	D1159G	probably benign	Het
Cep164	A	G	9: 45,714,023 (GRCm39)	V203A	probably benign	Het
Chml	T	C	1: 175,515,303 (GRCm39)	D206G	probably benign	Het
E2f6	T	C	12: 16,872,090 (GRCm39)		probably benign	Het
Emilin3	T	A	2: 160,752,719 (GRCm39)	Y77F	probably damaging	Het
Fbxw15	A	T	9: 109,394,430 (GRCm39)	N128K	possibly damaging	Het
Gjd2	A	G	2: 113,842,204 (GRCm39)	L91P	probably damaging	Het
Gm12830	T	A	4: 114,702,314 (GRCm39)		probably benign	Het
Gpr161	T	A	1: 165,149,218 (GRCm39)	L529Q	probably damaging	Het
Hoxd10	T	A	2: 74,522,776 (GRCm39)	Y151*	probably null	Het
Iars1	A	G	13: 49,846,546 (GRCm39)	D215G	possibly damaging	Het
Ift140	T	C	17: 25,311,800 (GRCm39)	V1241A	probably damaging	Het
Lrat	T	A	3: 82,810,656 (GRCm39)	I122F	probably damaging	Het
Myl10	C	T	5: 136,726,796 (GRCm39)	Q106*	probably null	Het
Ncapd2	A	T	6: 125,148,660 (GRCm39)	Y1018N	possibly damaging	Het
Ndrg1	C	T	15: 66,814,936 (GRCm39)	W172*	probably null	Het
Nphs2	T	C	1: 156,153,701 (GRCm39)	M264T	probably damaging	Het
Nrxn3	A	T	12: 89,227,278 (GRCm39)	R677S	possibly damaging	Het
Nudt12	T	C	17: 59,314,667 (GRCm39)	T306A	probably benign	Het
Numb	A	G	12: 83,872,070 (GRCm39)		probably benign	Het
Or10h28	T	A	17: 33,487,725 (GRCm39)	I9K	possibly damaging	Het
Or2y1	A	T	11: 49,385,536 (GRCm39)	M59L	probably benign	Het
Or5p58	C	T	7: 107,694,261 (GRCm39)	C172Y	probably damaging	Het
Pbld2	T	A	10: 62,883,261 (GRCm39)	D94E	probably benign	Het
Pkd1l3	C	A	8: 110,350,345 (GRCm39)	Q397K	probably benign	Het
Ppp4r3a	A	T	12: 101,024,878 (GRCm39)	L207H	probably damaging	Het
Ranbp2	T	A	10: 58,301,369 (GRCm39)	I674N	probably damaging	Het
Retnlg	G	T	16: 48,694,655 (GRCm39)	C101F	probably damaging	Het
Rif1	T	A	2: 51,993,634 (GRCm39)	I849N	probably damaging	Het
Serpinb9d	T	C	13: 33,382,014 (GRCm39)	I161T	possibly damaging	Het
Slc17a6	T	C	7: 51,315,771 (GRCm39)		probably benign	Het
Smg8	A	C	11: 86,976,814 (GRCm39)		probably null	Het
Spata31d1c	C	A	13: 65,183,407 (GRCm39)	N316K	probably benign	Het
Tlr1	A	G	5: 65,082,400 (GRCm39)	S726P	probably damaging	Het
Trim69	A	C	2: 122,003,636 (GRCm39)	D195A	probably benign	Het
Ttc16	T	G	2: 32,661,897 (GRCm39)		probably null	Het
Usp53	T	A	3: 122,746,832 (GRCm39)	M405L	probably benign	Het
Ywhag	G	A	5: 135,939,914 (GRCm39)	R227*	probably null	Het
Zfp335	G	T	2: 164,734,601 (GRCm39)		probably benign	Het
Zfp607a	T	C	7: 27,577,248 (GRCm39)	I106T	possibly damaging	Het
Zfp959	T	C	17: 56,204,613 (GRCm39)	S214P	possibly damaging	Het
Zfyve9	T	C	4: 108,546,406 (GRCm39)	M868V	possibly damaging	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
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
R9109:Kdm5b	UTSW	1	134,528,493 (GRCm39)	critical splice donor site	probably null
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

Posted On

2016-08-02