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 (K)-specific demethylase 5B

Synonyms

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

Accession Numbers

Essential gene?

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

Stock #

IGL03206

Quality Score

Status

Chromosome

Chromosomal Location

134560171-134635285 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 134627317 bp (GRCm38)

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: 128,553,276 (GRCm38)	E939D	possibly damaging	Het
Aloxe3	C	A	11: 69,129,646 (GRCm38)	A172D	possibly damaging	Het
Bscl2	G	A	19: 8,843,089 (GRCm38)	R158Q	probably damaging	Het
Cdon	A	G	9: 35,503,306 (GRCm38)	D1159G	probably benign	Het
Cep164	A	G	9: 45,802,725 (GRCm38)	V203A	probably benign	Het
Chml	T	C	1: 175,687,737 (GRCm38)	D206G	probably benign	Het
E2f6	T	C	12: 16,822,089 (GRCm38)		probably benign	Het
Emilin3	T	A	2: 160,910,799 (GRCm38)	Y77F	probably damaging	Het
Fbxw15	A	T	9: 109,565,362 (GRCm38)	N128K	possibly damaging	Het
Gjd2	A	G	2: 114,011,723 (GRCm38)	L91P	probably damaging	Het
Gm12830	T	A	4: 114,845,117 (GRCm38)		probably benign	Het
Gpr161	T	A	1: 165,321,649 (GRCm38)	L529Q	probably damaging	Het
Hoxd10	T	A	2: 74,692,432 (GRCm38)	Y151*	probably null	Het
Iars	A	G	13: 49,693,070 (GRCm38)	D215G	possibly damaging	Het
Ift140	T	C	17: 25,092,826 (GRCm38)	V1241A	probably damaging	Het
Lrat	T	A	3: 82,903,349 (GRCm38)	I122F	probably damaging	Het
Myl10	C	T	5: 136,697,942 (GRCm38)	Q106*	probably null	Het
Ncapd2	A	T	6: 125,171,697 (GRCm38)	Y1018N	possibly damaging	Het
Ndrg1	C	T	15: 66,943,087 (GRCm38)	W172*	probably null	Het
Nphs2	T	C	1: 156,326,131 (GRCm38)	M264T	probably damaging	Het
Nrxn3	A	T	12: 89,260,508 (GRCm38)	R677S	possibly damaging	Het
Nudt12	T	C	17: 59,007,672 (GRCm38)	T306A	probably benign	Het
Numb	A	G	12: 83,825,296 (GRCm38)		probably benign	Het
Olfr1385	A	T	11: 49,494,709 (GRCm38)	M59L	probably benign	Het
Olfr482	C	T	7: 108,095,054 (GRCm38)	C172Y	probably damaging	Het
Olfr63	T	A	17: 33,268,751 (GRCm38)	I9K	possibly damaging	Het
Pbld2	T	A	10: 63,047,482 (GRCm38)	D94E	probably benign	Het
Pkd1l3	C	A	8: 109,623,713 (GRCm38)	Q397K	probably benign	Het
Ppp4r3a	A	T	12: 101,058,619 (GRCm38)	L207H	probably damaging	Het
Ranbp2	T	A	10: 58,465,547 (GRCm38)	I674N	probably damaging	Het
Retnlg	G	T	16: 48,874,292 (GRCm38)	C101F	probably damaging	Het
Rif1	T	A	2: 52,103,622 (GRCm38)	I849N	probably damaging	Het
Serpinb9d	T	C	13: 33,198,031 (GRCm38)	I161T	possibly damaging	Het
Slc17a6	T	C	7: 51,666,023 (GRCm38)		probably benign	Het
Smg8	A	C	11: 87,085,988 (GRCm38)		probably null	Het
Spata31d1c	C	A	13: 65,035,593 (GRCm38)	N316K	probably benign	Het
Tlr1	A	G	5: 64,925,057 (GRCm38)	S726P	probably damaging	Het
Trim69	A	C	2: 122,173,155 (GRCm38)	D195A	probably benign	Het
Ttc16	T	G	2: 32,771,885 (GRCm38)		probably null	Het
Usp53	T	A	3: 122,953,183 (GRCm38)	M405L	probably benign	Het
Ywhag	G	A	5: 135,911,060 (GRCm38)	R227*	probably null	Het
Zfp335	G	T	2: 164,892,681 (GRCm38)		probably benign	Het
Zfp607a	T	C	7: 27,877,823 (GRCm38)	I106T	possibly damaging	Het
Zfp959	T	C	17: 55,897,613 (GRCm38)	S214P	possibly damaging	Het
Zfyve9	T	C	4: 108,689,209 (GRCm38)	M868V	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
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
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

Posted On

2016-08-02