Mutagenetix > Incidental Mutation

Incidental Mutation 'R1669:Kdm1b'

187481

Institutional Source

Beutler Lab

Gene Symbol

Kdm1b

Ensembl Gene

ENSMUSG00000038080

Gene Name

lysine (K)-specific demethylase 1B

Synonyms

4632428N09Rik, Aof1

MMRRC Submission

039705-MU

Accession Numbers

Is this an essential gene?

Possibly essential (E-score: 0.536) question?

Stock #

R1669 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

47043499-47085279 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 47068548 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Cysteine at position 488 (R488C)

Ref Sequence

ENSEMBL: ENSMUSP00000038373 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000037025]

AlphaFold

Q8CIG3

Predicted Effect

probably damaging
Transcript: ENSMUST00000037025
AA Change: R488C

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: R488C

Domain	Start	End	E-Value	Type
Pfam:zf-CW	138	191	2.6e-13	PFAM
low complexity region	235	253	N/A	INTRINSIC
Pfam:SWIRM	286	369	6e-12	PFAM
Pfam:Pyr_redox_2	368	490	3.1e-8	PFAM
Pfam:Thi4	375	446	2.2e-10	PFAM
Pfam:FAD_binding_3	388	423	4.1e-7	PFAM
Pfam:HI0933_like	389	428	1.6e-7	PFAM
Pfam:FAD_binding_2	390	428	1.6e-6	PFAM
Pfam:Pyr_redox	390	438	8e-8	PFAM
Pfam:NAD_binding_8	393	460	1.6e-13	PFAM
Pfam:Amino_oxidase	398	824	3.7e-86	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128977

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131120

Predicted Effect

probably benign
Transcript: ENSMUST00000143518

SMART Domains

Protein: ENSMUSP00000114999
Gene: ENSMUSG00000038080

Domain	Start	End	E-Value	Type
Pfam:SWIRM	3	86	1.1e-12	PFAM
Pfam:Thi4	91	163	3.5e-10	PFAM
Pfam:FAD_binding_3	105	140	3.5e-7	PFAM
Pfam:HI0933_like	106	145	1.7e-7	PFAM
Pfam:Pyr_redox_2	106	251	1.5e-10	PFAM
Pfam:FAD_binding_2	107	150	5.7e-7	PFAM
Pfam:Pyr_redox	107	158	6.4e-8	PFAM
Pfam:Pyr_redox_3	109	288	1.2e-13	PFAM
Pfam:NAD_binding_8	110	177	2.3e-13	PFAM
Pfam:Amino_oxidase	115	181	8.6e-19	PFAM
Pfam:Amino_oxidase	178	441	4.5e-63	PFAM

Meta Mutation Damage Score

0.2633

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.5%
20x: 93.3%

Validation Efficiency

99% (85/86)

MGI Phenotype

PHENOTYPE: Homozygous null mice of both sexes are viable, grossly normal and male mice are fertile; however, heterozygous progeny of homozygous null mothers display severe placental defects, embryonic growth impairment, neural tube defects and pericardial edema, and do not survive past E10.5. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ano10	A	C	9: 122,257,183	L258R	possibly damaging	Het
Ap3d1	A	G	10: 80,710,836		probably benign	Het
Aplp2	G	T	9: 31,167,733		probably benign	Het
Arhgap11a	T	C	2: 113,841,912	D237G	possibly damaging	Het
Arhgef4	A	T	1: 34,732,158	H1182L	possibly damaging	Het
Ash1l	G	A	3: 89,067,242		probably null	Het
Bicdl1	C	A	5: 115,656,016	V224L	possibly damaging	Het
Cacna1h	C	A	17: 25,383,471	V1422L	probably damaging	Het
Card10	T	C	15: 78,793,953	E365G	probably benign	Het
Cd180	C	T	13: 102,705,490	T348I	probably damaging	Het
Cds2	T	A	2: 132,295,519		probably null	Het
Chaf1a	C	A	17: 56,063,339	D601E	probably benign	Het
Coprs	C	T	8: 13,885,704	W12*	probably null	Het
Cpsf3	T	A	12: 21,305,331	M424K	probably damaging	Het
Cxcl13	T	A	5: 95,958,741	N57K	probably damaging	Het
Dact1	C	T	12: 71,318,773	T776M	probably damaging	Het
Depdc1a	A	G	3: 159,522,924	K438E	probably benign	Het
Dopey2	T	A	16: 93,769,660	S992T	probably damaging	Het
Dusp11	A	T	6: 85,950,026	H202Q	probably benign	Het
Ezr	T	C	17: 6,739,313	E584G	probably damaging	Het
F830104G03Rik	A	G	3: 56,890,577	V6A	unknown	Het
Fam227a	G	A	15: 79,620,677		probably null	Het
Gapvd1	T	G	2: 34,730,682		probably null	Het
Gm10267	T	C	18: 44,157,300	R47G	probably damaging	Het
Gm13088	T	G	4: 143,654,346	E369A	possibly damaging	Het
Gm6614	T	A	6: 141,987,689	I457F	probably benign	Het
Hectd3	T	A	4: 116,999,643	D462E	probably damaging	Het
Hfe	A	T	13: 23,706,127	L133*	probably null	Het
Hpcal4	T	C	4: 123,189,076	F72L	probably damaging	Het
Itgb4	G	A	11: 115,991,330	R825H	probably benign	Het
Kcnh8	T	A	17: 52,893,968	Y477N	probably damaging	Het
Kctd1	T	C	18: 15,062,460	N369D	possibly damaging	Het
Kif1c	C	T	11: 70,728,397	L953F	probably damaging	Het
Klra8	A	T	6: 130,115,629	C236*	probably null	Het
Lca5l	T	C	16: 96,159,808	R485G	possibly damaging	Het
Lrrc2	A	G	9: 110,981,650	T363A	probably damaging	Het
Lsmem1	GTACATACATACATACATACATACATACA	GTACATACATACATACATACATACATACATACA	12: 40,185,261		probably null	Het
Lyst	G	A	13: 13,644,087	G1314D	possibly damaging	Het
Mmp10	A	T	9: 7,505,525		probably null	Het
Mmp13	A	G	9: 7,277,926	D273G	probably benign	Het
Morc2a	G	A	11: 3,675,885	V162M	probably benign	Het
Msh4	C	T	3: 153,876,720	R417Q	possibly damaging	Het
Nedd9	A	T	13: 41,311,794	V790E	probably damaging	Het
Nlgn1	C	A	3: 25,436,134	L476F	probably damaging	Het
Nox4	C	A	7: 87,295,889	Q118K	probably benign	Het
Nxf1	A	G	19: 8,772,131	T131A	possibly damaging	Het
Olfr1261	T	A	2: 89,993,800		probably null	Het
Olfr13	T	A	6: 43,174,821	S278R	probably damaging	Het
Olfr1361	A	T	13: 21,659,286	S12R	possibly damaging	Het
Olfr1447	A	T	19: 12,901,288	I164K	possibly damaging	Het
Olfr518	T	A	7: 108,880,713	T298S	probably benign	Het
Olfr643	A	T	7: 104,059,309	S98T	probably benign	Het
Oog3	C	A	4: 144,158,438	R309S	probably benign	Het
Oosp3	C	T	19: 11,701,014		probably benign	Het
P2ry6	A	G	7: 100,938,423	V243A	probably damaging	Het
Pgc	C	A	17: 47,733,790	P321T	probably damaging	Het
Prkd1	G	A	12: 50,394,926	H277Y	probably damaging	Het
Prkdc	T	A	16: 15,734,058	S2043T	probably damaging	Het
Rasal3	T	C	17: 32,403,098	N96D	possibly damaging	Het
Rnf4	T	C	5: 34,351,280	F162S	probably damaging	Het
Ros1	A	T	10: 52,161,811	N421K	probably damaging	Het
Rtn4rl1	A	G	11: 75,265,927	D395G	probably benign	Het
Scn8a	T	G	15: 101,011,120	V823G	probably damaging	Het
Sema3d	T	A	5: 12,508,084		probably benign	Het
Slc12a2	T	C	18: 57,904,235	I501T	probably damaging	Het
Slc12a7	C	T	13: 73,795,113	T382I	probably benign	Het
Slc16a12	T	A	19: 34,680,381	I41L	probably benign	Het
Slc1a1	C	A	19: 28,911,794	T489K	probably benign	Het
Slc24a3	C	T	2: 145,613,592	P467L	probably damaging	Het
Snai2	A	T	16: 14,707,044	Y138F	possibly damaging	Het
Sorcs1	A	C	19: 50,475,422	Y197D	probably damaging	Het
Sppl2a	T	A	2: 126,917,794		probably benign	Het
Srgap3	G	A	6: 112,722,904	P1038S	probably benign	Het
Ttn	T	C	2: 76,724,463	E30699G	probably damaging	Het
Vmn2r124	T	A	17: 18,062,944	M300K	possibly damaging	Het
Vwf	T	C	6: 125,647,906	S1873P	possibly damaging	Het
Wrap73	A	G	4: 154,156,131	D360G	probably damaging	Het
Zfp366	T	C	13: 99,229,561	M410T	probably damaging	Het
Zfp608	C	T	18: 54,987,739	V259I	probably benign	Het
Zfp69	C	T	4: 120,947,498		probably benign	Het
Zfp995	T	C	17: 21,879,964	T430A	probably benign	Het

Other mutations in Kdm1b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00587:Kdm1b	APN	13	47068540	missense	probably benign	0.01
IGL00924:Kdm1b	APN	13	47068480	missense	probably benign
IGL01553:Kdm1b	APN	13	47080548	missense	probably damaging	0.96
IGL01663:Kdm1b	APN	13	47073737	missense	probably damaging	0.99
IGL02385:Kdm1b	APN	13	47068506	missense	possibly damaging	0.49
IGL02505:Kdm1b	APN	13	47060855	missense	probably damaging	1.00
IGL02826:Kdm1b	APN	13	47080467	missense	probably damaging	1.00
IGL03257:Kdm1b	APN	13	47049266	missense	probably damaging	1.00
R0052:Kdm1b	UTSW	13	47064117	missense	probably damaging	1.00
R0319:Kdm1b	UTSW	13	47053719	missense	probably benign
R0426:Kdm1b	UTSW	13	47064244	splice site	probably benign
R0599:Kdm1b	UTSW	13	47058810	missense	possibly damaging	0.47
R0764:Kdm1b	UTSW	13	47068603	missense	possibly damaging	0.70
R1163:Kdm1b	UTSW	13	47071922	missense	probably benign	0.02
R1543:Kdm1b	UTSW	13	47068521	missense	probably damaging	0.99
R1584:Kdm1b	UTSW	13	47064054	missense	probably damaging	1.00
R1627:Kdm1b	UTSW	13	47064231	critical splice donor site	probably null
R1758:Kdm1b	UTSW	13	47060768	missense	probably benign	0.00
R1860:Kdm1b	UTSW	13	47049190	missense	probably benign	0.03
R1907:Kdm1b	UTSW	13	47064120	missense	probably benign	0.00
R2225:Kdm1b	UTSW	13	47064088	frame shift	probably null
R2239:Kdm1b	UTSW	13	47073755	missense	probably damaging	1.00
R2271:Kdm1b	UTSW	13	47064088	frame shift	probably null
R2302:Kdm1b	UTSW	13	47064088	frame shift	probably null
R2303:Kdm1b	UTSW	13	47064088	frame shift	probably null
R2380:Kdm1b	UTSW	13	47073755	missense	probably damaging	1.00
R2442:Kdm1b	UTSW	13	47062975	missense	probably benign	0.32
R3022:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R3054:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R3545:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R3546:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R3548:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4094:Kdm1b	UTSW	13	47063020	missense	probably damaging	1.00
R4419:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4420:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4502:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4547:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4548:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4785:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4793:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4804:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4882:Kdm1b	UTSW	13	47060893	missense	probably benign
R4906:Kdm1b	UTSW	13	47063144	critical splice donor site	probably null
R4965:Kdm1b	UTSW	13	47074367	missense	probably damaging	0.98
R5039:Kdm1b	UTSW	13	47077486	missense	probably damaging	1.00
R5098:Kdm1b	UTSW	13	47062991	missense	probably damaging	1.00
R5265:Kdm1b	UTSW	13	47062969	missense	probably benign	0.35
R5541:Kdm1b	UTSW	13	47079196	missense	probably damaging	1.00
R5814:Kdm1b	UTSW	13	47063146	splice site	probably null
R6046:Kdm1b	UTSW	13	47079253	missense	possibly damaging	0.92
R6798:Kdm1b	UTSW	13	47068536	missense	probably benign	0.00
R6903:Kdm1b	UTSW	13	47074404	missense	probably benign	0.00
R7831:Kdm1b	UTSW	13	47050622	missense	probably benign	0.17
R7973:Kdm1b	UTSW	13	47077446	missense	probably benign	0.00
R8181:Kdm1b	UTSW	13	47051901	critical splice donor site	probably null
R8248:Kdm1b	UTSW	13	47071878	intron	probably benign
R8821:Kdm1b	UTSW	13	47064141	missense	possibly damaging	0.94
R8831:Kdm1b	UTSW	13	47064141	missense	possibly damaging	0.94
R8842:Kdm1b	UTSW	13	47078356	missense	probably damaging	1.00
R8861:Kdm1b	UTSW	13	47064106	missense	probably benign	0.02
R8885:Kdm1b	UTSW	13	47053708	nonsense	probably null
R9038:Kdm1b	UTSW	13	47049294	missense	probably benign	0.07
R9132:Kdm1b	UTSW	13	47071982	missense	probably benign	0.05
R9268:Kdm1b	UTSW	13	47064229	missense	probably benign	0.00
R9616:Kdm1b	UTSW	13	47080554	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGAAGCTGTTGTCGCCTTATCTCC -3'
(R):5'- CCTGCCCACCTCTGAGAAAATCTG -3'

Sequencing Primer
(F):5'- TATTAGCGTCATCATGAGAGCG -3'
(R):5'- TGCAGAGTTCAGCCAAAGG -3'

Posted On

2014-05-09