Mutagenetix > Incidental Mutation

Incidental Mutation 'R4906:Kdm1b'

378227

Institutional Source

Beutler Lab

Gene Symbol

Kdm1b

Ensembl Gene

ENSMUSG00000038080

Gene Name

lysine (K)-specific demethylase 1B

Synonyms

Aof1, 4632428N09Rik

MMRRC Submission

042508-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.406) question?

Stock #

R4906 (G1)

Quality Score

169

Status

Not validated

Chromosome

Chromosomal Location

47196849-47238085 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

T to C at 47216620 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Gene Model

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

AlphaFold

Q8CIG3

Predicted Effect

probably null
Transcript: ENSMUST00000037025

SMART Domains

Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080

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 null
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

Coding Region Coverage

1x: 98.9%
3x: 98.1%
10x: 95.7%
20x: 90.5%

Validation Efficiency

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: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5330417H12Rik	T	C	7: 107,223,897 (GRCm39)		probably benign	Het
Ablim2	C	T	5: 35,959,766 (GRCm39)	R73C	possibly damaging	Het
Adgrf2	T	C	17: 43,022,084 (GRCm39)	I247V	probably benign	Het
Adgrv1	A	G	13: 81,418,857 (GRCm39)		probably null	Het
Ankrd22	T	A	19: 34,126,752 (GRCm39)	K26I	possibly damaging	Het
Arhgap32	T	A	9: 32,156,552 (GRCm39)		probably null	Het
Armc10	A	G	5: 21,866,522 (GRCm39)	Y262C	probably damaging	Het
Arrb2	A	G	11: 70,330,725 (GRCm39)	D374G	probably benign	Het
Ascc3	C	T	10: 50,625,227 (GRCm39)	R1675C	probably damaging	Het
Atg5	T	C	10: 44,239,046 (GRCm39)	*276R	probably null	Het
Bcl11b	G	A	12: 107,882,968 (GRCm39)	T377M	probably damaging	Het
C1s2	C	A	6: 124,612,073 (GRCm39)	E104*	probably null	Het
Carf	A	T	1: 60,180,526 (GRCm39)	H316L	probably damaging	Het
Ccdc77	A	T	6: 120,311,796 (GRCm39)	I234N	probably damaging	Het
Cd300c2	A	T	11: 114,887,826 (GRCm39)	V192E	possibly damaging	Het
Cep72	G	A	13: 74,207,584 (GRCm39)	R62C	probably damaging	Het
Clasp1	T	A	1: 118,436,640 (GRCm39)	L308*	probably null	Het
Clec2g	A	G	6: 128,956,411 (GRCm39)	S25G	probably benign	Het
Cngb1	T	C	8: 95,978,601 (GRCm39)	M1046V	probably damaging	Het
Cobll1	A	T	2: 64,928,037 (GRCm39)	D1095E	probably benign	Het
Cpeb2	A	G	5: 43,402,005 (GRCm39)	H662R	possibly damaging	Het
Cps1	A	T	1: 67,178,922 (GRCm39)	T45S	probably benign	Het
Cspp1	A	G	1: 10,152,553 (GRCm39)	Q368R	possibly damaging	Het
Dcaf6	C	A	1: 165,239,032 (GRCm39)		probably null	Het
Dcst1	T	C	3: 89,257,814 (GRCm39)	Y652C	possibly damaging	Het
Elf5	T	G	2: 103,279,918 (GRCm39)	Y225*	probably null	Het
Ermap	A	C	4: 119,046,015 (GRCm39)		probably benign	Het
Fam186b	A	T	15: 99,169,202 (GRCm39)	V915D	probably damaging	Het
Fbxo34	C	A	14: 47,766,911 (GRCm39)	N90K	probably benign	Het
Flnc	A	G	6: 29,447,524 (GRCm39)	E1109G	probably damaging	Het
Flt1	C	A	5: 147,620,749 (GRCm39)	A132S	probably benign	Het
Gabpb2	A	G	3: 95,097,947 (GRCm39)	V242A	probably benign	Het
Gas2l3	CACTCGTCATACT	CACT	10: 89,266,820 (GRCm39)		probably benign	Het
Gm21798	A	T	15: 64,689,732 (GRCm39)		probably benign	Het
Gpr179	A	T	11: 97,237,487 (GRCm39)	S345T	possibly damaging	Het
Gusb	A	T	5: 130,026,959 (GRCm39)	F377L	probably damaging	Het
Hnrnpu	T	C	1: 178,156,938 (GRCm39)		probably benign	Het
Htr3b	C	T	9: 48,848,348 (GRCm39)		probably null	Het
Iqub	A	T	6: 24,501,368 (GRCm39)	V194D	probably damaging	Het
Itga2b	A	G	11: 102,351,985 (GRCm39)	V504A	probably benign	Het
Itga4	T	A	2: 79,118,592 (GRCm39)	F430L	probably damaging	Het
Jcad	C	A	18: 4,673,762 (GRCm39)	P508H	probably damaging	Het
Jph1	T	C	1: 17,161,835 (GRCm39)	T276A	probably damaging	Het
Kansl2	A	G	15: 98,429,771 (GRCm39)	F87S	possibly damaging	Het
Kif5b	C	T	18: 6,220,930 (GRCm39)	D393N	probably benign	Het
Kmt2d	A	T	15: 98,747,420 (GRCm39)		probably benign	Het
Krt75	A	G	15: 101,478,674 (GRCm39)	I320T	probably damaging	Het
Lhfpl7	T	A	5: 113,386,036 (GRCm39)	M161K	probably benign	Het
Lipo5	T	C	19: 33,443,348 (GRCm39)	N156S	unknown	Het
Mblac2	A	C	13: 81,859,706 (GRCm39)	Q19P	probably null	Het
Mdfic2	A	T	6: 98,215,080 (GRCm39)	M181K	probably damaging	Het
Mfsd4b3-ps	T	C	10: 39,824,056 (GRCm39)	H68R	probably damaging	Het
Mzb1	A	T	18: 35,781,006 (GRCm39)		probably null	Het
Nup210l	T	A	3: 90,077,337 (GRCm39)	I891N	probably benign	Het
Nwd1	G	A	8: 73,398,841 (GRCm39)	R667Q	probably damaging	Het
Oas1h	C	T	5: 121,005,172 (GRCm39)	Q207*	probably null	Het
Or13c7d	A	T	4: 43,770,476 (GRCm39)	F178L	possibly damaging	Het
Pcdh15	C	T	10: 74,340,625 (GRCm39)	R1120*	probably null	Het
Pfkl	A	G	10: 77,824,144 (GRCm39)	L748P	probably damaging	Het
Phldb2	T	A	16: 45,571,758 (GRCm39)	K473N	probably damaging	Het
Rapgef6	G	A	11: 54,443,662 (GRCm39)	V82I	probably damaging	Het
Rfc3	A	T	5: 151,570,960 (GRCm39)	L112Q	probably damaging	Het
Rsph6a	T	A	7: 18,801,997 (GRCm39)	C349S	possibly damaging	Het
Sec16a	A	T	2: 26,331,979 (GRCm39)		probably benign	Het
Septin14	T	A	5: 129,770,030 (GRCm39)	Y222F	probably benign	Het
Skor2	T	C	18: 76,947,990 (GRCm39)	S571P	possibly damaging	Het
Slc13a5	T	A	11: 72,148,244 (GRCm39)	M264L	probably damaging	Het
Slc45a3	T	A	1: 131,909,315 (GRCm39)	V504E	probably damaging	Het
Smg1	C	T	7: 117,751,631 (GRCm39)		probably benign	Het
Smim20	A	G	5: 53,434,503 (GRCm39)	N45S	probably null	Het
Spp2	A	T	1: 88,339,991 (GRCm39)	S111C	probably damaging	Het
Sspo	A	G	6: 48,442,664 (GRCm39)		probably null	Het
Sycp2	C	T	2: 178,045,450 (GRCm39)		probably null	Het
Tas2r113	A	G	6: 132,870,521 (GRCm39)	N183S	possibly damaging	Het
Tcaf2	A	T	6: 42,606,679 (GRCm39)	M425K	probably benign	Het
Tdrp	A	G	8: 14,003,845 (GRCm39)	V164A	possibly damaging	Het
Tmbim1	A	G	1: 74,328,568 (GRCm39)	F298S	probably damaging	Het
Tmem89	A	G	9: 108,743,829 (GRCm39)		probably benign	Het
Trpm2	G	T	10: 77,768,023 (GRCm39)	C825*	probably null	Het
Tsc1	A	G	2: 28,565,201 (GRCm39)	E421G	possibly damaging	Het
Usp24	T	C	4: 106,245,834 (GRCm39)	I1364T	probably benign	Het
Vmn1r52	G	A	6: 90,155,930 (GRCm39)	G78E	possibly damaging	Het
Vmn2r73	T	G	7: 85,506,829 (GRCm39)	I828L	probably damaging	Het
Vwa5b1	A	T	4: 138,338,058 (GRCm39)	D87E	probably benign	Het
Zfp1010	T	C	2: 176,957,223 (GRCm39)	T92A	possibly damaging	Het
Zfp451	A	T	1: 33,844,465 (GRCm39)	D47E	probably damaging	Het
Zfp821	A	G	8: 110,450,841 (GRCm39)	E278G	probably damaging	Het
Zfp930	A	T	8: 69,681,597 (GRCm39)	T430S	probably benign	Het
Zfp994	G	T	17: 22,419,448 (GRCm39)	Y500*	probably null	Het
Zmat3	A	T	3: 32,397,836 (GRCm39)	I142N	probably damaging	Het
Zzef1	T	A	11: 72,792,214 (GRCm39)	I2266N	probably damaging	Het

Other mutations in Kdm1b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00587:Kdm1b	APN	13	47,222,016 (GRCm39)	missense	probably benign	0.01
IGL00924:Kdm1b	APN	13	47,221,956 (GRCm39)	missense	probably benign
IGL01553:Kdm1b	APN	13	47,234,024 (GRCm39)	missense	probably damaging	0.96
IGL01663:Kdm1b	APN	13	47,227,213 (GRCm39)	missense	probably damaging	0.99
IGL02385:Kdm1b	APN	13	47,221,982 (GRCm39)	missense	possibly damaging	0.49
IGL02505:Kdm1b	APN	13	47,214,331 (GRCm39)	missense	probably damaging	1.00
IGL02826:Kdm1b	APN	13	47,233,943 (GRCm39)	missense	probably damaging	1.00
IGL03257:Kdm1b	APN	13	47,202,742 (GRCm39)	missense	probably damaging	1.00
R0052:Kdm1b	UTSW	13	47,217,593 (GRCm39)	missense	probably damaging	1.00
R0319:Kdm1b	UTSW	13	47,207,195 (GRCm39)	missense	probably benign
R0426:Kdm1b	UTSW	13	47,217,720 (GRCm39)	splice site	probably benign
R0599:Kdm1b	UTSW	13	47,212,286 (GRCm39)	missense	possibly damaging	0.47
R0764:Kdm1b	UTSW	13	47,222,079 (GRCm39)	missense	possibly damaging	0.70
R1163:Kdm1b	UTSW	13	47,225,398 (GRCm39)	missense	probably benign	0.02
R1543:Kdm1b	UTSW	13	47,221,997 (GRCm39)	missense	probably damaging	0.99
R1584:Kdm1b	UTSW	13	47,217,530 (GRCm39)	missense	probably damaging	1.00
R1627:Kdm1b	UTSW	13	47,217,707 (GRCm39)	critical splice donor site	probably null
R1669:Kdm1b	UTSW	13	47,222,024 (GRCm39)	missense	probably damaging	1.00
R1758:Kdm1b	UTSW	13	47,214,244 (GRCm39)	missense	probably benign	0.00
R1860:Kdm1b	UTSW	13	47,202,666 (GRCm39)	missense	probably benign	0.03
R1907:Kdm1b	UTSW	13	47,217,596 (GRCm39)	missense	probably benign	0.00
R2225:Kdm1b	UTSW	13	47,217,564 (GRCm39)	frame shift	probably null
R2239:Kdm1b	UTSW	13	47,227,231 (GRCm39)	missense	probably damaging	1.00
R2271:Kdm1b	UTSW	13	47,217,564 (GRCm39)	frame shift	probably null
R2302:Kdm1b	UTSW	13	47,217,564 (GRCm39)	frame shift	probably null
R2303:Kdm1b	UTSW	13	47,217,564 (GRCm39)	frame shift	probably null
R2380:Kdm1b	UTSW	13	47,227,231 (GRCm39)	missense	probably damaging	1.00
R2442:Kdm1b	UTSW	13	47,216,451 (GRCm39)	missense	probably benign	0.32
R3022:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R3054:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R3545:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R3546:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R3548:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4094:Kdm1b	UTSW	13	47,216,496 (GRCm39)	missense	probably damaging	1.00
R4419:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4420:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4502:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4547:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4548:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4785:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4793:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4804:Kdm1b	UTSW	13	47,216,553 (GRCm39)	missense	probably damaging	1.00
R4882:Kdm1b	UTSW	13	47,214,369 (GRCm39)	missense	probably benign
R4965:Kdm1b	UTSW	13	47,227,843 (GRCm39)	missense	probably damaging	0.98
R5039:Kdm1b	UTSW	13	47,230,962 (GRCm39)	missense	probably damaging	1.00
R5098:Kdm1b	UTSW	13	47,216,467 (GRCm39)	missense	probably damaging	1.00
R5265:Kdm1b	UTSW	13	47,216,445 (GRCm39)	missense	probably benign	0.35
R5541:Kdm1b	UTSW	13	47,232,672 (GRCm39)	missense	probably damaging	1.00
R5814:Kdm1b	UTSW	13	47,216,622 (GRCm39)	splice site	probably null
R6046:Kdm1b	UTSW	13	47,232,729 (GRCm39)	missense	possibly damaging	0.92
R6798:Kdm1b	UTSW	13	47,222,012 (GRCm39)	missense	probably benign	0.00
R6903:Kdm1b	UTSW	13	47,227,880 (GRCm39)	missense	probably benign	0.00
R7831:Kdm1b	UTSW	13	47,204,098 (GRCm39)	missense	probably benign	0.17
R7973:Kdm1b	UTSW	13	47,230,922 (GRCm39)	missense	probably benign	0.00
R8181:Kdm1b	UTSW	13	47,205,377 (GRCm39)	critical splice donor site	probably null
R8248:Kdm1b	UTSW	13	47,225,354 (GRCm39)	intron	probably benign
R8821:Kdm1b	UTSW	13	47,217,617 (GRCm39)	missense	possibly damaging	0.94
R8831:Kdm1b	UTSW	13	47,217,617 (GRCm39)	missense	possibly damaging	0.94
R8842:Kdm1b	UTSW	13	47,231,832 (GRCm39)	missense	probably damaging	1.00
R8861:Kdm1b	UTSW	13	47,217,582 (GRCm39)	missense	probably benign	0.02
R8885:Kdm1b	UTSW	13	47,207,184 (GRCm39)	nonsense	probably null
R9038:Kdm1b	UTSW	13	47,202,770 (GRCm39)	missense	probably benign	0.07
R9132:Kdm1b	UTSW	13	47,225,458 (GRCm39)	missense	probably benign	0.05
R9268:Kdm1b	UTSW	13	47,217,705 (GRCm39)	missense	probably benign	0.00
R9616:Kdm1b	UTSW	13	47,234,030 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGTACTTCCAGCCGTTCTAC -3'
(R):5'- CTGCTAGTTAGTCACCGTGG -3'

Sequencing Primer
(F):5'- TTCTACCAGCCCAACGAGTGTG -3'
(R):5'- GACGACTCTGCTAGTTAGTCACTATG -3'

Posted On

2016-04-15