Mutagenetix > Incidental Mutation

Incidental Mutation 'R3980:Kdm5b'

311226

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

040843-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.269) question?

Stock #

R3980 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

134560171-134635285 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 134619670 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 1019 (D1019G)

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: D1019G

PolyPhen 2 Score 0.112 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000038138
Gene: ENSMUSG00000042207
AA Change: D1019G

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: D1019G

PolyPhen 2 Score 0.112 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000107817
Gene: ENSMUSG00000042207
AA Change: D1019G

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

1x: 99.1%
3x: 98.5%
10x: 97.2%
20x: 94.8%

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrb1	G	A	15: 74,582,943	G268R	probably damaging	Het
Amacr	T	A	15: 10,988,929	Y240*	probably null	Het
Ankhd1	A	T	18: 36,647,613	H1906L	probably damaging	Het
Arhgef25	C	A	10: 127,187,220	C106F	probably damaging	Het
Bean1	A	T	8: 104,211,098	Q103L	possibly damaging	Het
Ccr9	A	T	9: 123,779,376	N41I	probably benign	Het
Ceacam16	A	G	7: 19,858,633	F117L	probably benign	Het
Col4a1	T	C	8: 11,239,155		probably benign	Het
Csk	A	G	9: 57,630,780	Y48H	probably damaging	Het
Csmd1	T	A	8: 15,906,056	K3384*	probably null	Het
Ctnnd2	T	A	15: 30,669,443	H399Q	probably benign	Het
Cutal	T	C	2: 34,882,313	Y30H	possibly damaging	Het
Cybb	T	C	X: 9,444,588	Y425C	probably damaging	Het
Dab2	A	G	15: 6,435,163		probably null	Het
Defb30	C	A	14: 63,035,972	C64F	probably damaging	Het
Eif2a	T	C	3: 58,539,539	I45T	probably benign	Het
Esyt1	T	A	10: 128,511,524	D1044V	probably damaging	Het
Fam196b	G	A	11: 34,402,678	C240Y	probably benign	Het
Gabpb2	A	T	3: 95,188,770	V382E	probably damaging	Het
Glb1	T	A	9: 114,417,064	I61K	probably damaging	Het
Kcnt1	T	C	2: 25,893,214	V263A	possibly damaging	Het
Klhl2	A	T	8: 64,743,075	L545M	probably damaging	Het
Klhl2	C	A	8: 64,743,081	G543C	probably damaging	Het
Krt31	G	T	11: 100,048,204	Q264K	probably damaging	Het
Lmnb1	A	G	18: 56,731,019	D232G	probably damaging	Het
Loxhd1	T	C	18: 77,414,159	F859L	probably damaging	Het
Map7	C	A	10: 20,267,353	T416K	unknown	Het
Med18	T	A	4: 132,462,940	I45F	probably benign	Het
Mn1	A	T	5: 111,421,770	H1202L	possibly damaging	Het
Mpp7	T	C	18: 7,444,062	D120G	probably benign	Het
Nlrp1b	A	T	11: 71,181,611	F469I	possibly damaging	Het
Nos3	T	A	5: 24,377,931	D685E	probably damaging	Het
Nrap	G	A	19: 56,381,552	A206V	probably benign	Het
Nuggc	T	C	14: 65,619,093		probably null	Het
Oasl1	C	T	5: 114,932,898	T274I	probably damaging	Het
Olfr1335	T	A	4: 118,809,303	Y187F	probably benign	Het
Olfr559	T	C	7: 102,723,752	N246S	probably damaging	Het
Parp3	T	C	9: 106,474,068	D278G	probably damaging	Het
Phc3	T	A	3: 30,936,931	Q346L	probably damaging	Het
Pigo	A	G	4: 43,019,231	L1029P	probably damaging	Het
Plcb3	A	G	19: 6,966,435	I66T	probably damaging	Het
Plch2	T	C	4: 154,984,798	S1019G	probably benign	Het
Plekhg6	C	A	6: 125,373,183	C264F	probably damaging	Het
Plxna2	C	T	1: 194,749,317	S538F	probably damaging	Het
Pou4f2	G	T	8: 78,435,438	H179N	possibly damaging	Het
Prpf39	T	C	12: 65,061,457		probably benign	Het
Rapgef1	G	A	2: 29,719,650	V700I	probably benign	Het
Rdh14	A	G	12: 10,394,703	I185V	probably benign	Het
Rnf111	A	T	9: 70,442,325	H785Q	probably damaging	Het
Rttn	C	T	18: 89,017,275	R758W	probably benign	Het
Sik3	G	A	9: 46,202,063	V601M	probably damaging	Het
Slc22a14	T	C	9: 119,178,486	T286A	probably benign	Het
Slc36a3	G	A	11: 55,135,383	T203I	probably benign	Het
Spata31	A	T	13: 64,922,654	Q872L	probably benign	Het
Spata31d1c	A	G	13: 65,035,160	D172G	possibly damaging	Het
Sphkap	A	T	1: 83,267,494		probably null	Het
Stat6	T	C	10: 127,655,379	V463A	probably damaging	Het
Stx7	T	C	10: 24,185,049	S225P	probably damaging	Het
Sult2a7	A	T	7: 14,473,409		probably benign	Het
Tada2a	A	T	11: 84,103,120	F179L	probably benign	Het
Tas2r103	A	G	6: 133,036,317	L262P	probably benign	Het
Tfap2d	A	G	1: 19,165,963	I382V	possibly damaging	Het
Tshr	C	A	12: 91,537,743	A485D	probably damaging	Het
Vmn1r32	T	A	6: 66,553,714	Y26F	probably damaging	Het
Vmn1r5	A	G	6: 56,985,651	T104A	probably damaging	Het
Wbp1l	T	A	19: 46,653,957		probably null	Het

Other mutations in Kdm5b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00230:Kdm5b	APN	1	134620955	missense	probably damaging	1.00
IGL01458:Kdm5b	APN	1	134621986	missense	possibly damaging	0.53
IGL01567:Kdm5b	APN	1	134602540	missense	probably damaging	1.00
IGL01625:Kdm5b	APN	1	134617968	missense	possibly damaging	0.74
IGL01970:Kdm5b	APN	1	134600727	missense	probably damaging	1.00
IGL02183:Kdm5b	APN	1	134624931	missense	probably benign	0.09
IGL02592:Kdm5b	APN	1	134624853	missense	probably damaging	0.99
IGL02695:Kdm5b	APN	1	134604485	missense	possibly damaging	0.94
IGL02697:Kdm5b	APN	1	134588773	splice site	probably benign
IGL03036:Kdm5b	APN	1	134608937	missense	probably damaging	1.00
IGL03056:Kdm5b	APN	1	134587979	missense	probably damaging	0.99
IGL03206:Kdm5b	APN	1	134627317	missense	probably benign
IGL03342:Kdm5b	APN	1	134602576	missense	probably benign	0.00
IGL03388:Kdm5b	APN	1	134627322	missense	probably benign
amaryllis	UTSW	1	134609061	critical splice donor site	probably null
PIT4486001:Kdm5b	UTSW	1	134628685	missense	probably damaging	1.00
R0233:Kdm5b	UTSW	1	134604634	splice site	probably benign
R0334:Kdm5b	UTSW	1	134604522	missense	probably damaging	0.99
R0504:Kdm5b	UTSW	1	134621023	critical splice donor site	probably null
R0505:Kdm5b	UTSW	1	134602571	missense	probably damaging	0.96
R0521:Kdm5b	UTSW	1	134618033	missense	possibly damaging	0.65
R1004:Kdm5b	UTSW	1	134588904	missense	possibly damaging	0.71
R1087:Kdm5b	UTSW	1	134600637	missense	probably damaging	1.00
R1126:Kdm5b	UTSW	1	134613991	missense	possibly damaging	0.90
R1221:Kdm5b	UTSW	1	134599091	missense	probably damaging	0.98
R1230:Kdm5b	UTSW	1	134613254	missense	probably damaging	1.00
R1345:Kdm5b	UTSW	1	134630550	missense	possibly damaging	0.94
R1482:Kdm5b	UTSW	1	134624897	missense	probably damaging	1.00
R1582:Kdm5b	UTSW	1	134624853	missense	probably damaging	0.99
R1653:Kdm5b	UTSW	1	134602481	missense	probably damaging	1.00
R1693:Kdm5b	UTSW	1	134597576	splice site	probably benign
R1721:Kdm5b	UTSW	1	134613181	splice site	probably benign
R1741:Kdm5b	UTSW	1	134618017	missense	possibly damaging	0.82
R1762:Kdm5b	UTSW	1	134604467	nonsense	probably null
R1820:Kdm5b	UTSW	1	134597670	missense	possibly damaging	0.87
R1872:Kdm5b	UTSW	1	134624994	missense	probably damaging	1.00
R1966:Kdm5b	UTSW	1	134613873	splice site	probably null
R2056:Kdm5b	UTSW	1	134613214	missense	probably benign	0.05
R2059:Kdm5b	UTSW	1	134613214	missense	probably benign	0.05
R2405:Kdm5b	UTSW	1	134609016	missense	probably damaging	0.97
R3417:Kdm5b	UTSW	1	134587977	missense	probably damaging	1.00
R3771:Kdm5b	UTSW	1	134613345	missense	probably damaging	1.00
R3783:Kdm5b	UTSW	1	134630542	missense	probably benign
R3803:Kdm5b	UTSW	1	134615941	missense	probably benign	0.07
R3983:Kdm5b	UTSW	1	134631304	missense	possibly damaging	0.91
R4013:Kdm5b	UTSW	1	134627329	missense	possibly damaging	0.86
R4162:Kdm5b	UTSW	1	134625161	missense	probably benign	0.01
R4701:Kdm5b	UTSW	1	134606012	intron	probably benign
R4791:Kdm5b	UTSW	1	134630800	missense	possibly damaging	0.82
R4836:Kdm5b	UTSW	1	134593315	splice site	probably null
R4924:Kdm5b	UTSW	1	134631351	missense	probably benign	0.00
R5135:Kdm5b	UTSW	1	134588746	intron	probably benign
R5248:Kdm5b	UTSW	1	134620997	missense	probably benign	0.11
R5290:Kdm5b	UTSW	1	134622099	splice site	probably null
R5358:Kdm5b	UTSW	1	134607694	nonsense	probably null
R5388:Kdm5b	UTSW	1	134608897	nonsense	probably null
R5396:Kdm5b	UTSW	1	134622098	splice site	probably null
R5397:Kdm5b	UTSW	1	134622098	splice site	probably null
R5398:Kdm5b	UTSW	1	134622098	splice site	probably null
R5399:Kdm5b	UTSW	1	134622098	splice site	probably null
R5529:Kdm5b	UTSW	1	134588003	missense	probably damaging	1.00
R5540:Kdm5b	UTSW	1	134631241	missense	probably damaging	0.98
R5661:Kdm5b	UTSW	1	134599073	missense	probably benign	0.01
R5663:Kdm5b	UTSW	1	134630635	missense	probably benign
R5822:Kdm5b	UTSW	1	134588773	splice site	probably benign
R6226:Kdm5b	UTSW	1	134608878	missense	probably damaging	0.99
R6368:Kdm5b	UTSW	1	134599207	missense	probably damaging	1.00
R6681:Kdm5b	UTSW	1	134613269	missense	possibly damaging	0.90
R6715:Kdm5b	UTSW	1	134609061	critical splice donor site	probably null
R7132:Kdm5b	UTSW	1	134599106	missense	probably damaging	1.00
R7202:Kdm5b	UTSW	1	134624759	missense	probably benign
R7258:Kdm5b	UTSW	1	134621021	missense	probably damaging	1.00
R7335:Kdm5b	UTSW	1	134560439	missense	probably damaging	1.00
R7420:Kdm5b	UTSW	1	134604497	missense	probably benign	0.14
R7426:Kdm5b	UTSW	1	134595833	missense	probably benign	0.02
R7452:Kdm5b	UTSW	1	134624948	missense	probably damaging	1.00
R7595:Kdm5b	UTSW	1	134608966	missense	probably benign	0.00
R7612:Kdm5b	UTSW	1	134624918	nonsense	probably null
R7704:Kdm5b	UTSW	1	134587931	missense	probably damaging	1.00
R7846:Kdm5b	UTSW	1	134617840	missense	probably damaging	1.00
R8115:Kdm5b	UTSW	1	134619673	missense	possibly damaging	0.83
R8146:Kdm5b	UTSW	1	134625126	missense	probably benign	0.05
R8160:Kdm5b	UTSW	1	134613919	missense	probably damaging	1.00
R8527:Kdm5b	UTSW	1	134605774	missense	possibly damaging	0.78
R8542:Kdm5b	UTSW	1	134605774	missense	possibly damaging	0.78
R8930:Kdm5b	UTSW	1	134616272	missense	probably damaging	1.00
R8932:Kdm5b	UTSW	1	134616272	missense	probably damaging	1.00
R8950:Kdm5b	UTSW	1	134613926	missense	possibly damaging	0.84
R9089:Kdm5b	UTSW	1	134607768	missense	probably damaging	0.98
R9109:Kdm5b	UTSW	1	134600755	critical splice donor site	probably null
R9133:Kdm5b	UTSW	1	134602585	missense	probably benign
R9298:Kdm5b	UTSW	1	134600755	critical splice donor site	probably null
R9423:Kdm5b	UTSW	1	134587967	missense	possibly damaging	0.85
R9630:Kdm5b	UTSW	1	134585233	critical splice donor site	probably null
R9670:Kdm5b	UTSW	1	134630502	nonsense	probably null
X0063:Kdm5b	UTSW	1	134588876	missense	probably benign	0.07
Z1176:Kdm5b	UTSW	1	134625035	missense	probably damaging	1.00
Z1177:Kdm5b	UTSW	1	134595798	frame shift	probably null

Predicted Primers

PCR Primer
(F):5'- GAAATGATCTTCCTAGTCTTTTGGC -3'
(R):5'- TTTAGCATCAAGGGCCACAG -3'

Sequencing Primer
(F):5'- GTCTGTAACTCCAAGGGATCCATG -3'
(R):5'- TTGGGAGGACTACAGCCTC -3'

Posted On

2015-04-29