Mutagenetix > Incidental Mutation

Incidental Mutation 'R1758:Kdm1b'

195119

Institutional Source

Beutler Lab

Gene Symbol

Kdm1b

Ensembl Gene

ENSMUSG00000038080

Gene Name

lysine (K)-specific demethylase 1B

Synonyms

Aof1, 4632428N09Rik

MMRRC Submission

039790-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.504) question?

Stock #

R1758 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

47196849-47238085 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 47214244 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 197 (S197T)

Ref Sequence

ENSEMBL: ENSMUSP00000038373 (fasta)

Gene Model

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

AlphaFold

Q8CIG3

Predicted Effect

probably benign
Transcript: ENSMUST00000037025
AA Change: S197T

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: S197T

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: 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

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.6%
20x: 93.2%

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: 95 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700029H14Rik	T	C	8: 13,612,237 (GRCm39)	R38G	possibly damaging	Het
4930590J08Rik	T	C	6: 91,892,203 (GRCm39)	V155A	possibly damaging	Het
Adgb	A	G	10: 10,302,349 (GRCm39)	S406P	probably damaging	Het
Adgrb2	C	A	4: 129,905,668 (GRCm39)	T893N	probably damaging	Het
Adgrf5	T	C	17: 43,735,484 (GRCm39)		probably null	Het
Alms1	T	A	6: 85,605,487 (GRCm39)	I2379N	probably damaging	Het
Arap3	C	T	18: 38,122,965 (GRCm39)	V512I	probably benign	Het
Atf4	C	T	15: 80,141,414 (GRCm39)	T268I	probably benign	Het
Cblif	G	A	19: 11,735,179 (GRCm39)	M266I	probably damaging	Het
Ccdc154	T	C	17: 25,382,156 (GRCm39)	L25P	probably damaging	Het
Ccdc9	G	A	7: 16,010,161 (GRCm39)	S381F	probably damaging	Het
Cdk17	C	T	10: 93,044,112 (GRCm39)	T17M	probably damaging	Het
Cep128	T	C	12: 91,314,352 (GRCm39)	N142S	probably benign	Het
Cep78	A	G	19: 15,936,900 (GRCm39)	I602T	probably damaging	Het
Clasp1	C	T	1: 118,475,755 (GRCm39)	T935I	probably damaging	Het
Cnr1	T	C	4: 33,945,000 (GRCm39)	S463P	probably damaging	Het
Cntnap1	T	A	11: 101,075,449 (GRCm39)	W876R	probably damaging	Het
Cntnap5c	A	G	17: 58,349,545 (GRCm39)	D286G	probably damaging	Het
Copa	C	T	1: 171,931,711 (GRCm39)	R321C	probably damaging	Het
Cspg4b	A	G	13: 113,505,266 (GRCm39)	T2132A	possibly damaging	Het
Ctla2a	T	G	13: 61,083,256 (GRCm39)	E98A	probably damaging	Het
Cux1	A	T	5: 136,421,176 (GRCm39)	D183E	probably damaging	Het
Cxcl15	A	C	5: 90,949,323 (GRCm39)	T163P	unknown	Het
Ddias	T	C	7: 92,508,571 (GRCm39)	N448S	probably benign	Het
Dhx8	T	C	11: 101,657,564 (GRCm39)	F1152S	probably damaging	Het
Dnah12	C	A	14: 26,488,071 (GRCm39)	Q992K	probably benign	Het
Eno3	G	T	11: 70,552,251 (GRCm39)	W301L	possibly damaging	Het
Faap100	A	T	11: 120,268,059 (GRCm39)	V238E	probably damaging	Het
Fgf4	A	G	7: 144,416,049 (GRCm39)	S137G	probably benign	Het
Fhod3	A	C	18: 25,253,367 (GRCm39)	D1439A	possibly damaging	Het
Frem2	A	G	3: 53,560,778 (GRCm39)	L1243P	probably damaging	Het
Gkn3	T	G	6: 87,365,817 (GRCm39)	M1L	probably benign	Het
Gm10250	T	C	15: 5,150,509 (GRCm39)		probably benign	Het
Gm12185	T	C	11: 48,798,859 (GRCm39)	T545A	possibly damaging	Het
Gm14226	T	A	2: 154,867,378 (GRCm39)	L445H	probably damaging	Het
Gm3404	A	T	5: 146,463,036 (GRCm39)	M73L	probably benign	Het
Gm973	G	T	1: 59,673,169 (GRCm39)	R976S	unknown	Het
Gpr146	A	T	5: 139,379,137 (GRCm39)	H313L	probably benign	Het
Gys2	T	A	6: 142,418,432 (GRCm39)	E32D	probably damaging	Het
Igsf10	G	A	3: 59,236,617 (GRCm39)	T1188I	probably benign	Het
Igsf9b	A	T	9: 27,245,548 (GRCm39)	T1172S	possibly damaging	Het
Itga8	T	A	2: 12,270,144 (GRCm39)	N114I	possibly damaging	Het
Itsn2	T	A	12: 4,708,160 (GRCm39)	V795E	possibly damaging	Het
Kif5c	G	A	2: 49,613,145 (GRCm39)	R161Q	probably benign	Het
Krt33b	T	C	11: 99,916,361 (GRCm39)	Y232C	probably damaging	Het
Lonrf2	G	A	1: 38,852,357 (GRCm39)	P165S	probably benign	Het
Lrp1	A	T	10: 127,424,453 (GRCm39)	N744K	possibly damaging	Het
Mcm10	C	A	2: 5,008,861 (GRCm39)	L369F	probably damaging	Het
Muc5ac	T	A	7: 141,355,268 (GRCm39)	I1018N	possibly damaging	Het
Myom2	T	C	8: 15,115,795 (GRCm39)	L70P	probably benign	Het
Myt1l	T	A	12: 29,877,241 (GRCm39)	N297K	unknown	Het
Ncr1	C	T	7: 4,343,807 (GRCm39)	T98I	probably benign	Het
Nek3	T	C	8: 22,650,278 (GRCm39)	E78G	probably damaging	Het
Nfatc3	T	A	8: 106,825,768 (GRCm39)	N606K	probably damaging	Het
Nup107	T	G	10: 117,597,248 (GRCm39)	D669A	probably damaging	Het
Or10ag52	A	T	2: 87,043,758 (GRCm39)	Q174L	probably benign	Het
Or10c1	A	T	17: 37,522,204 (GRCm39)	I180N	possibly damaging	Het
Or4c3	T	C	2: 89,851,673 (GRCm39)	T246A	probably benign	Het
Or8b55	A	T	9: 38,726,871 (GRCm39)	H24L	probably benign	Het
Pcnx1	T	C	12: 82,030,258 (GRCm39)	V1711A	probably benign	Het
Pik3c3	A	G	18: 30,410,063 (GRCm39)	D99G	probably damaging	Het
Pinx1	C	A	14: 64,157,024 (GRCm39)	T317K	probably benign	Het
Ppargc1b	G	T	18: 61,431,857 (GRCm39)		probably null	Het
Pradc1	T	A	6: 85,424,203 (GRCm39)	I119F	possibly damaging	Het
Psat1	G	T	19: 15,892,243 (GRCm39)	T242K	probably damaging	Het
Psma6	G	A	12: 55,454,317 (GRCm39)	C28Y	probably damaging	Het
Pyurf	A	T	6: 57,668,817 (GRCm39)	C58*	probably null	Het
Rab3gap2	C	A	1: 185,016,081 (GRCm39)	A1331E	probably benign	Het
Rnase4	T	C	14: 51,342,722 (GRCm39)	*149Q	probably null	Het
Ruvbl2	T	C	7: 45,074,586 (GRCm39)	K184R	probably benign	Het
Scn7a	T	G	2: 66,510,527 (GRCm39)	M1292L	probably benign	Het
Scn7a	A	T	2: 66,531,231 (GRCm39)	Y549N	probably damaging	Het
Selp	A	G	1: 163,959,854 (GRCm39)	D370G	possibly damaging	Het
Slc22a15	G	A	3: 101,767,769 (GRCm39)	Q386*	probably null	Het
Slc22a29	A	G	19: 8,195,126 (GRCm39)		probably null	Het
Slc26a7	A	C	4: 14,548,491 (GRCm39)	I266S	possibly damaging	Het
Smpd4	T	C	16: 17,443,872 (GRCm39)	S112P	probably damaging	Het
Smpd4	T	A	16: 17,458,744 (GRCm39)	L165Q	probably damaging	Het
Snx33	A	G	9: 56,833,982 (GRCm39)	I29T	probably benign	Het
Spen	G	A	4: 141,203,686 (GRCm39)	P1647L	unknown	Het
Strip2	T	C	6: 29,941,940 (GRCm39)		probably null	Het
Swsap1	C	T	9: 21,867,280 (GRCm39)	R75*	probably null	Het
Tesl1	A	G	X: 23,772,990 (GRCm39)	I164V	probably benign	Het
Tmem210	C	T	2: 25,178,435 (GRCm39)	T32I	probably damaging	Het
Tnn	C	T	1: 159,975,154 (GRCm39)	R91H	possibly damaging	Het
Tnni1	G	A	1: 135,736,420 (GRCm39)	R94H	probably damaging	Het
Tnrc6c	T	A	11: 117,651,556 (GRCm39)	V1693D	probably benign	Het
Trip4	G	A	9: 65,782,259 (GRCm39)	Q158*	probably null	Het
Ttc39b	T	C	4: 83,155,586 (GRCm39)	E474G	probably damaging	Het
Usp50	C	A	2: 126,617,782 (GRCm39)	C221F	probably damaging	Het
Vmn1r171	T	C	7: 23,331,781 (GRCm39)	I2T	probably benign	Het
Wdr62	T	A	7: 29,967,328 (GRCm39)	I309F	probably damaging	Het
Xdh	A	T	17: 74,217,204 (GRCm39)	V688E	probably damaging	Het
Zfyve26	A	G	12: 79,285,718 (GRCm39)	L2353P	probably damaging	Het
Zgpat	C	A	2: 181,020,633 (GRCm39)	R269S	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
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
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'- TTTCCAGGTTGCCGAAGGTTGC -3'
(R):5'- GAAGGCCAACTGCATAGCCAAATG -3'

Sequencing Primer
(F):5'- GCCGAAGGTTGCCATTTC -3'
(R):5'- GCAACCGTGAGTGCTTTATAC -3'

Posted On

2014-05-23