Mutagenetix > Incidental Mutation

Incidental Mutation 'R8831:Kdm1b'

673855

Institutional Source

Beutler Lab

Gene Symbol

Kdm1b

Ensembl Gene

ENSMUSG00000038080

Gene Name

lysine (K)-specific demethylase 1B

Synonyms

4632428N09Rik, Aof1

MMRRC Submission

068659-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.557) question?

Stock #

R8831 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

47043499-47085279 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 47064141 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Isoleucine at position 359 (L359I)

Ref Sequence

ENSEMBL: ENSMUSP00000038373 (fasta)

Gene Model

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

AlphaFold

Q8CIG3

Predicted Effect

possibly damaging
Transcript: ENSMUST00000037025
AA Change: L359I

PolyPhen 2 Score 0.944 (Sensitivity: 0.80; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: L359I

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

probably damaging
Transcript: ENSMUST00000143518
AA Change: L75I

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000114999
Gene: ENSMUSG00000038080
AA Change: L75I

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: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

Validation Efficiency

99% (81/82)

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: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A230072I06Rik	A	T	8: 12,279,688 (GRCm38)	I48L	unknown	Het
Abcc3	A	C	11: 94,350,961 (GRCm38)	C1415G	probably damaging	Het
Abcf3	C	T	16: 20,550,464 (GRCm38)	R205C	probably damaging	Het
Abcg5	G	T	17: 84,668,995 (GRCm38)	H471Q	probably damaging	Het
Actl6b	G	A	5: 137,567,043 (GRCm38)	R363Q	probably damaging	Het
Adcy1	T	A	11: 7,161,362 (GRCm38)	D884E	probably benign	Het
Aldh3a1	A	G	11: 61,216,316 (GRCm38)	Y282C	probably damaging	Het
Amdhd2	A	G	17: 24,157,738 (GRCm38)		probably null	Het
Arfgef3	A	G	10: 18,652,743 (GRCm38)	S299P	possibly damaging	Het
Asic2	A	T	11: 81,967,900 (GRCm38)	N95K	probably damaging	Het
Atp2c2	A	G	8: 119,749,294 (GRCm38)		probably null	Het
Atrn	T	C	2: 130,906,601 (GRCm38)	L14P	probably benign	Het
C8b	A	G	4: 104,790,677 (GRCm38)	Y355C	probably damaging	Het
Carm1	A	G	9: 21,580,367 (GRCm38)	E244G	probably damaging	Het
Cd300c2	A	T	11: 115,001,018 (GRCm38)	C39*	probably null	Het
Cish	T	A	9: 107,300,472 (GRCm38)	F116I	probably damaging	Het
Clstn1	G	A	4: 149,646,323 (GRCm38)	R837Q	probably benign	Het
Cox10	A	G	11: 63,964,480 (GRCm38)	F325S	probably damaging	Het
Cplane1	T	C	15: 8,182,136 (GRCm38)	I320T	probably benign	Het
Ctps1	A	T	4: 120,567,310 (GRCm38)	S36T	possibly damaging	Het
Dchs2	T	C	3: 83,285,363 (GRCm38)	L1705P	probably benign	Het
Defb25	C	A	2: 152,622,979 (GRCm38)	V17L	probably benign	Het
Dhx16	A	G	17: 35,888,108 (GRCm38)	D782G	probably damaging	Het
Dhx30	A	G	9: 110,088,251 (GRCm38)	S399P	probably benign	Het
Dhx58	T	A	11: 100,703,980 (GRCm38)	K30M	probably damaging	Het
Drc7	G	A	8: 95,062,217 (GRCm38)	R301Q	probably damaging	Het
Dsg1a	T	C	18: 20,320,308 (GRCm38)	V21A	probably damaging	Het
Ercc6	T	A	14: 32,560,827 (GRCm38)		probably null	Het
Fam193a	A	G	5: 34,459,030 (GRCm38)	T850A	probably benign	Het
Fgf10	A	G	13: 118,789,135 (GRCm38)	D150G	probably damaging	Het
Flii	A	T	11: 60,725,248 (GRCm38)	N28K	probably benign	Het
Gfi1	G	A	5: 107,720,272 (GRCm38)	R377C	probably damaging	Het
Gfra2	A	T	14: 70,967,063 (GRCm38)	N324I	probably benign	Het
Gm10308	A	G	17: 91,089,003 (GRCm38)	R118G	unknown	Het
Gm10801	T	A	2: 98,663,989 (GRCm38)	V137E	probably damaging	Het
Hmmr	G	A	11: 40,721,672 (GRCm38)	S206F	probably damaging	Het
Hsd3b9	A	T	3: 98,446,731 (GRCm38)	W151R	probably benign	Het
Ift80	G	A	3: 68,962,250 (GRCm38)	A236V	probably damaging	Het
Il1rn	A	T	2: 24,349,493 (GRCm38)	T134S	possibly damaging	Het
Il6st	G	T	13: 112,504,380 (GRCm38)	D897Y	probably damaging	Het
Imp4	T	C	1: 34,444,364 (GRCm38)	M257T	probably benign	Het
Impdh2	T	C	9: 108,564,758 (GRCm38)	L377S	probably damaging	Het
Kidins220	A	T	12: 25,036,455 (GRCm38)	I963L	possibly damaging	Het
Mdm4	T	C	1: 133,003,863 (GRCm38)	R148G	probably benign	Het
Myl10	G	C	5: 136,697,971 (GRCm38)	V70L	probably benign	Het
Ncor1	A	T	11: 62,369,408 (GRCm38)	D505E	probably benign	Het
Necab3	A	T	2: 154,554,687 (GRCm38)	L107Q	probably damaging	Het
Nkx2-4	G	A	2: 147,085,194 (GRCm38)	P51L	probably benign	Het
Nol11	T	C	11: 107,176,836 (GRCm38)	T388A	probably benign	Het
Npc1	T	A	18: 12,200,820 (GRCm38)	M735L	probably benign	Het
Nr1h3	C	A	2: 91,190,746 (GRCm38)	R232L	probably benign	Het
Nrcam	T	A	12: 44,544,897 (GRCm38)		probably null	Het
Or1j13	G	A	2: 36,479,782 (GRCm38)	T116I	possibly damaging	Het
Or52s1b	T	A	7: 103,172,996 (GRCm38)	I214L	probably benign	Het
Pabpn1	T	C	14: 54,894,457 (GRCm38)	V101A	probably damaging	Het
Pcare	A	T	17: 71,752,310 (GRCm38)	V124E	probably benign	Het
Pcbp2	A	G	15: 102,486,018 (GRCm38)	D217G	probably benign	Het
Pcdhb12	A	G	18: 37,437,333 (GRCm38)	M511V	probably benign	Het
Phf3	T	A	1: 30,821,266 (GRCm38)	K828*	probably null	Het
Plcg1	G	C	2: 160,747,812 (GRCm38)	K85N	probably benign	Het
Prag1	A	T	8: 36,146,737 (GRCm38)	T1148S	probably benign	Het
Prmt3	A	G	7: 49,828,981 (GRCm38)	E430G	probably null	Het
Prx	G	T	7: 27,518,113 (GRCm38)	V819F	probably damaging	Het
Ptpn18	A	T	1: 34,472,190 (GRCm38)	R338W	probably null	Het
Rab6a	T	C	7: 100,634,724 (GRCm38)	Y128H	probably benign	Het
Rgs2	T	C	1: 144,001,759 (GRCm38)	Y186C	probably damaging	Het
Rhbdl1	C	T	17: 25,834,883 (GRCm38)	V342M	probably damaging	Het
Rpn1	A	G	6: 88,084,793 (GRCm38)	Q88R	probably benign	Het
Slc19a2	C	T	1: 164,256,874 (GRCm38)	T111M	probably damaging	Het
Slc35e4	G	A	11: 3,913,087 (GRCm38)	P34L	possibly damaging	Het
Slc7a6os	A	T	8: 106,210,557 (GRCm38)	D90E	probably benign	Het
Ssh3	A	G	19: 4,269,025 (GRCm38)	V19A	possibly damaging	Het
Susd1	C	T	4: 59,379,594 (GRCm38)		probably benign	Het
Tcf19	A	T	17: 35,514,897 (GRCm38)	M121K	possibly damaging	Het
Tcp11	G	A	17: 28,080,219 (GRCm38)	R21C	probably damaging	Het
Tcp11l2	A	G	10: 84,613,658 (GRCm38)	I496V	probably damaging	Het
Tenm3	C	T	8: 48,276,382 (GRCm38)	A1530T		Het
Tmem127	T	A	2: 127,257,059 (GRCm38)	V171D	probably damaging	Het
Tyrp1	G	A	4: 80,835,162 (GRCm38)	C30Y	probably damaging	Het
Usp48	A	T	4: 137,613,769 (GRCm38)	D360V	probably damaging	Het
Vamp4	T	A	1: 162,574,383 (GRCm38)	D11E	possibly damaging	Het
Vmn1r14	T	C	6: 57,233,520 (GRCm38)	F28L	probably benign	Het
Vmn2r69	G	T	7: 85,409,810 (GRCm38)	C514*	probably null	Het
Vmn2r84	G	A	10: 130,391,099 (GRCm38)	A290V	probably benign	Het
Zfp1007	A	T	5: 109,676,308 (GRCm38)	S425R	probably benign	Het
Zhx3	T	A	2: 160,780,771 (GRCm38)	Y492F	probably benign	Het

Other mutations in Kdm1b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00587:Kdm1b	APN	13	47,068,540 (GRCm38)	missense	probably benign	0.01
IGL00924:Kdm1b	APN	13	47,068,480 (GRCm38)	missense	probably benign
IGL01553:Kdm1b	APN	13	47,080,548 (GRCm38)	missense	probably damaging	0.96
IGL01663:Kdm1b	APN	13	47,073,737 (GRCm38)	missense	probably damaging	0.99
IGL02385:Kdm1b	APN	13	47,068,506 (GRCm38)	missense	possibly damaging	0.49
IGL02505:Kdm1b	APN	13	47,060,855 (GRCm38)	missense	probably damaging	1.00
IGL02826:Kdm1b	APN	13	47,080,467 (GRCm38)	missense	probably damaging	1.00
IGL03257:Kdm1b	APN	13	47,049,266 (GRCm38)	missense	probably damaging	1.00
R0052:Kdm1b	UTSW	13	47,064,117 (GRCm38)	missense	probably damaging	1.00
R0319:Kdm1b	UTSW	13	47,053,719 (GRCm38)	missense	probably benign
R0426:Kdm1b	UTSW	13	47,064,244 (GRCm38)	splice site	probably benign
R0599:Kdm1b	UTSW	13	47,058,810 (GRCm38)	missense	possibly damaging	0.47
R0764:Kdm1b	UTSW	13	47,068,603 (GRCm38)	missense	possibly damaging	0.70
R1163:Kdm1b	UTSW	13	47,071,922 (GRCm38)	missense	probably benign	0.02
R1543:Kdm1b	UTSW	13	47,068,521 (GRCm38)	missense	probably damaging	0.99
R1584:Kdm1b	UTSW	13	47,064,054 (GRCm38)	missense	probably damaging	1.00
R1627:Kdm1b	UTSW	13	47,064,231 (GRCm38)	critical splice donor site	probably null
R1669:Kdm1b	UTSW	13	47,068,548 (GRCm38)	missense	probably damaging	1.00
R1758:Kdm1b	UTSW	13	47,060,768 (GRCm38)	missense	probably benign	0.00
R1860:Kdm1b	UTSW	13	47,049,190 (GRCm38)	missense	probably benign	0.03
R1907:Kdm1b	UTSW	13	47,064,120 (GRCm38)	missense	probably benign	0.00
R2225:Kdm1b	UTSW	13	47,064,088 (GRCm38)	frame shift	probably null
R2239:Kdm1b	UTSW	13	47,073,755 (GRCm38)	missense	probably damaging	1.00
R2271:Kdm1b	UTSW	13	47,064,088 (GRCm38)	frame shift	probably null
R2302:Kdm1b	UTSW	13	47,064,088 (GRCm38)	frame shift	probably null
R2303:Kdm1b	UTSW	13	47,064,088 (GRCm38)	frame shift	probably null
R2380:Kdm1b	UTSW	13	47,073,755 (GRCm38)	missense	probably damaging	1.00
R2442:Kdm1b	UTSW	13	47,062,975 (GRCm38)	missense	probably benign	0.32
R3022:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R3054:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R3545:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R3546:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R3548:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4094:Kdm1b	UTSW	13	47,063,020 (GRCm38)	missense	probably damaging	1.00
R4419:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4420:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4502:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4547:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4548:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4785:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4793:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4804:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4882:Kdm1b	UTSW	13	47,060,893 (GRCm38)	missense	probably benign
R4906:Kdm1b	UTSW	13	47,063,144 (GRCm38)	critical splice donor site	probably null
R4965:Kdm1b	UTSW	13	47,074,367 (GRCm38)	missense	probably damaging	0.98
R5039:Kdm1b	UTSW	13	47,077,486 (GRCm38)	missense	probably damaging	1.00
R5098:Kdm1b	UTSW	13	47,062,991 (GRCm38)	missense	probably damaging	1.00
R5265:Kdm1b	UTSW	13	47,062,969 (GRCm38)	missense	probably benign	0.35
R5541:Kdm1b	UTSW	13	47,079,196 (GRCm38)	missense	probably damaging	1.00
R5814:Kdm1b	UTSW	13	47,063,146 (GRCm38)	splice site	probably null
R6046:Kdm1b	UTSW	13	47,079,253 (GRCm38)	missense	possibly damaging	0.92
R6798:Kdm1b	UTSW	13	47,068,536 (GRCm38)	missense	probably benign	0.00
R6903:Kdm1b	UTSW	13	47,074,404 (GRCm38)	missense	probably benign	0.00
R7831:Kdm1b	UTSW	13	47,050,622 (GRCm38)	missense	probably benign	0.17
R7973:Kdm1b	UTSW	13	47,077,446 (GRCm38)	missense	probably benign	0.00
R8181:Kdm1b	UTSW	13	47,051,901 (GRCm38)	critical splice donor site	probably null
R8248:Kdm1b	UTSW	13	47,071,878 (GRCm38)	intron	probably benign
R8821:Kdm1b	UTSW	13	47,064,141 (GRCm38)	missense	possibly damaging	0.94
R8842:Kdm1b	UTSW	13	47,078,356 (GRCm38)	missense	probably damaging	1.00
R8861:Kdm1b	UTSW	13	47,064,106 (GRCm38)	missense	probably benign	0.02
R8885:Kdm1b	UTSW	13	47,053,708 (GRCm38)	nonsense	probably null
R9038:Kdm1b	UTSW	13	47,049,294 (GRCm38)	missense	probably benign	0.07
R9132:Kdm1b	UTSW	13	47,071,982 (GRCm38)	missense	probably benign	0.05
R9268:Kdm1b	UTSW	13	47,064,229 (GRCm38)	missense	probably benign	0.00
R9616:Kdm1b	UTSW	13	47,080,554 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GACTAACTAGTTTGAGTGCTGGG -3'
(R):5'- CTGCAGTATCTGGTACCAGTATAG -3'

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

Posted On

2021-07-15