Mutagenetix > Incidental Mutation

Incidental Mutation 'R2303:Kdm1b'

244503

Institutional Source

Beutler Lab

Gene Symbol

Kdm1b

Ensembl Gene

ENSMUSG00000038080

Gene Name

lysine (K)-specific demethylase 1B

Synonyms

Aof1, 4632428N09Rik

MMRRC Submission

040302-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.504) question?

Stock #

R2303 (G1)

Quality Score

150

Status

Validated

Chromosome

Chromosomal Location

47196849-47238085 bp(+) (GRCm39)

Type of Mutation

frame shift

DNA Base Change (assembly)

TCATTGTCC to TCATTGTCCATTGTCC at 47217564 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

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 94.9%

Validation Efficiency

100% (40/40)

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: 36 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930583I09Rik	T	G	17: 65,141,561 (GRCm39)	D14A	unknown	Het
Aars1	C	A	8: 111,779,134 (GRCm39)	T756K	possibly damaging	Het
Abca9	A	T	11: 110,049,052 (GRCm39)	M252K	probably benign	Het
Acan	A	G	7: 78,749,705 (GRCm39)	E1492G	probably benign	Het
Arid1a	C	A	4: 133,414,562 (GRCm39)	R1223L	unknown	Het
Ash1l	T	C	3: 88,933,733 (GRCm39)	L2003S	probably damaging	Het
Cct8	A	T	16: 87,287,220 (GRCm39)		probably null	Het
Dagla	T	C	19: 10,229,467 (GRCm39)	T598A	probably damaging	Het
Ercc3	A	G	18: 32,378,600 (GRCm39)	I194V	probably benign	Het
Fbxo46	A	G	7: 18,870,541 (GRCm39)	N387D	possibly damaging	Het
Fn1	C	T	1: 71,653,195 (GRCm39)		probably null	Het
Gkn3	C	T	6: 87,360,507 (GRCm39)	A163T	probably damaging	Het
Gnrhr	C	T	5: 86,345,608 (GRCm39)	G26D	probably benign	Het
Hmcn1	A	T	1: 150,579,977 (GRCm39)	L1920Q	probably damaging	Het
Kank2	T	A	9: 21,681,061 (GRCm39)	I823F	probably benign	Het
Kcnh8	GAGACCAACGAGCAGCTGATGCTTCAGA	GAGA	17: 53,032,934 (GRCm39)	74	probably benign	Het
Mfsd6	T	A	1: 52,715,672 (GRCm39)	N535I	probably damaging	Het
Mgat5	T	C	1: 127,374,036 (GRCm39)	Y479H	probably benign	Het
Ncoa7	G	A	10: 30,530,431 (GRCm39)	T701I	probably damaging	Het
Or6c2	T	C	10: 129,362,918 (GRCm39)	V274A	probably benign	Het
Pcdh18	T	C	3: 49,709,723 (GRCm39)	R531G	probably damaging	Het
Pcdhb6	A	G	18: 37,469,284 (GRCm39)	H51R	probably damaging	Het
Pdik1l	G	A	4: 134,011,559 (GRCm39)	Q95*	probably null	Het
Ppp4r3b	A	T	11: 29,150,741 (GRCm39)	H469L	possibly damaging	Het
Prnp	A	G	2: 131,779,046 (GRCm39)	T233A	probably benign	Het
Rcan1	T	C	16: 92,190,484 (GRCm39)	T152A	possibly damaging	Het
Sema3g	T	C	14: 30,944,572 (GRCm39)	F329L	probably damaging	Het
Setd1a	G	A	7: 127,398,327 (GRCm39)		probably benign	Het
Slc40a1	G	A	1: 45,950,044 (GRCm39)		probably benign	Het
Slco5a1	C	T	1: 12,949,486 (GRCm39)	G635S	probably damaging	Het
Spg11	C	T	2: 121,899,318 (GRCm39)	C1589Y	probably damaging	Het
Stab1	T	C	14: 30,868,027 (GRCm39)	T1616A	probably damaging	Het
Trappc11	A	G	8: 47,956,451 (GRCm39)	Y842H	probably damaging	Het
Vwde	T	A	6: 13,215,806 (GRCm39)		probably benign	Het
Zcchc8	A	G	5: 123,838,660 (GRCm39)	L626P	probably benign	Het
Zfhx4	A	G	3: 5,462,120 (GRCm39)	H1240R	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
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
R4906:Kdm1b	UTSW	13	47,216,620 (GRCm39)	critical splice donor site	probably null
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'- CCATGGTGACTAACTAGTTTGAGTG -3'
(R):5'- GAGCCTACCGCACATCCAG -3'

Sequencing Primer
(F):5'- TCCAGCCACATATGTAGCAGAGG -3'
(R):5'- CATCCAGCTGCTTACATTGTGGTAG -3'

Posted On

2014-10-30