Mutagenetix > Incidental Mutation

Incidental Mutation 'R1163:Kdm1b'

100680

Institutional Source

Beutler Lab

Gene Symbol

Kdm1b

Ensembl Gene

ENSMUSG00000038080

Gene Name

lysine (K)-specific demethylase 1B

Synonyms

Aof1, 4632428N09Rik

MMRRC Submission

039236-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.504) question?

Stock #

R1163 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

47196849-47238085 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 47225398 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 527 (V527A)

Ref Sequence

ENSEMBL: ENSMUSP00000038373 (fasta)

Gene Model

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

AlphaFold

Q8CIG3

Predicted Effect

probably benign
Transcript: ENSMUST00000037025
AA Change: V527A

PolyPhen 2 Score 0.021 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: V527A

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

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.3%
20x: 92.7%

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: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700113H08Rik	T	A	10: 86,957,284 (GRCm39)	Y7N	probably damaging	Het
4930579F01Rik	T	G	3: 137,882,271 (GRCm39)	D18A	probably damaging	Het
Abca8a	T	C	11: 109,962,356 (GRCm39)	D499G	probably benign	Het
Adamts1	G	C	16: 85,599,525 (GRCm39)	A25G	probably benign	Het
Adamts2	A	T	11: 50,670,541 (GRCm39)	I552F	probably damaging	Het
Akap3	A	G	6: 126,841,750 (GRCm39)	D123G	probably damaging	Het
Ankar	C	T	1: 72,727,864 (GRCm39)	V350I	possibly damaging	Het
Apob	A	G	12: 8,061,654 (GRCm39)	T3379A	probably damaging	Het
Ash1l	G	T	3: 88,942,570 (GRCm39)		probably null	Het
Atp2b1	T	C	10: 98,815,713 (GRCm39)	I119T	possibly damaging	Het
B3gnt2	A	T	11: 22,786,558 (GRCm39)	M210K	probably benign	Het
Bcl11a	A	G	11: 24,115,143 (GRCm39)	N829D	probably benign	Het
Btnl4	T	C	17: 34,689,049 (GRCm39)	E337G	possibly damaging	Het
Casr	A	T	16: 36,315,169 (GRCm39)	V967D	probably damaging	Het
Cd200	A	T	16: 45,212,715 (GRCm39)	V244D	probably damaging	Het
Cd200r4	A	G	16: 44,658,383 (GRCm39)	N256D	probably benign	Het
Cep68	A	G	11: 20,190,539 (GRCm39)	S158P	probably damaging	Het
Chst10	A	T	1: 38,910,783 (GRCm39)	V123D	probably damaging	Het
Cobll1	T	C	2: 64,928,623 (GRCm39)	H938R	probably damaging	Het
Creld2	G	A	15: 88,704,834 (GRCm39)	W103*	probably null	Het
Dmkn	T	G	7: 30,464,476 (GRCm39)	C205G	probably damaging	Het
Dock8	A	G	19: 25,028,867 (GRCm39)	I24V	probably benign	Het
Dpp3	C	T	19: 4,964,951 (GRCm39)	W488*	probably null	Het
Dpp9	C	A	17: 56,506,426 (GRCm39)	A365S	possibly damaging	Het
Egfr	A	T	11: 16,833,546 (GRCm39)	T605S	probably benign	Het
Eme2	G	A	17: 25,111,892 (GRCm39)	S263F	probably damaging	Het
Fam83g	T	C	11: 61,594,262 (GRCm39)	S599P	probably damaging	Het
Fscn1	G	T	5: 142,946,598 (GRCm39)	W132L	probably damaging	Het
Gbp2b	A	G	3: 142,304,857 (GRCm39)	T98A	probably damaging	Het
Gm4922	C	T	10: 18,659,469 (GRCm39)	A418T	possibly damaging	Het
Golgb1	G	T	16: 36,736,488 (GRCm39)	V1912L	possibly damaging	Het
Gon4l	T	C	3: 88,799,842 (GRCm39)	L829P	probably damaging	Het
Grm3	T	A	5: 9,620,738 (GRCm39)	I169L	probably benign	Het
Gsdma2	A	G	11: 98,541,684 (GRCm39)	D137G	probably damaging	Het
Hhip	T	C	8: 80,719,105 (GRCm39)	Y474C	probably damaging	Het
Hsph1	A	T	5: 149,554,266 (GRCm39)	V163E	probably damaging	Het
Ifi203	T	C	1: 173,751,703 (GRCm39)	K373E	probably damaging	Het
Itsn2	A	G	12: 4,762,009 (GRCm39)	T1540A	probably benign	Het
Kdm5d	G	A	Y: 898,029 (GRCm39)	A22T	probably benign	Het
Khdrbs1	A	T	4: 129,619,379 (GRCm39)	F254Y	possibly damaging	Het
Kif26a	T	C	12: 112,146,379 (GRCm39)	F1822L	probably benign	Het
Krt1	C	A	15: 101,756,600 (GRCm39)	E308*	probably null	Het
Lrrc47	T	A	4: 154,096,274 (GRCm39)	M1K	probably null	Het
Mrgpra4	A	T	7: 47,631,224 (GRCm39)	W126R	probably damaging	Het
Nlrp4e	G	A	7: 23,020,397 (GRCm39)	V295I	probably benign	Het
Or1l4b	A	T	2: 37,037,039 (GRCm39)	T272S	probably damaging	Het
Or2f1	G	A	6: 42,721,057 (GRCm39)	V29I	probably benign	Het
Or4c10	G	T	2: 89,760,449 (GRCm39)	V99F	possibly damaging	Het
Or5ac19	A	G	16: 59,089,518 (GRCm39)	S171P	probably benign	Het
Or5ac24	A	T	16: 59,165,425 (GRCm39)	I213N	probably damaging	Het
Or5b96	T	A	19: 12,867,513 (GRCm39)	T143S	probably benign	Het
Or6c66	A	G	10: 129,461,516 (GRCm39)	V138A	possibly damaging	Het
Or8h10	A	G	2: 86,809,020 (GRCm39)	L40P	probably damaging	Het
Or8k41	A	T	2: 86,313,582 (GRCm39)	F168Y	probably damaging	Het
Plec	G	T	15: 76,068,038 (GRCm39)	N1190K	possibly damaging	Het
Plin1	T	C	7: 79,379,719 (GRCm39)	T44A	probably damaging	Het
Pou3f2	TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG	TTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG	4: 22,487,697 (GRCm39)		probably benign	Het
Pramel22	A	G	4: 143,383,204 (GRCm39)	L5P	probably damaging	Het
Psg27	A	G	7: 18,299,234 (GRCm39)	L29P	probably damaging	Het
Psmd13	C	A	7: 140,477,367 (GRCm39)	T292N	probably damaging	Het
Rab1b	A	T	19: 5,154,684 (GRCm39)	Y88*	probably null	Het
Reln	T	A	5: 22,104,027 (GRCm39)	I3315L	probably benign	Het
Rmdn2	A	T	17: 79,966,880 (GRCm39)	M257L	probably benign	Het
Rnd1	A	T	15: 98,574,435 (GRCm39)	F47L	probably damaging	Het
Rnf41	G	A	10: 128,274,076 (GRCm39)	V243I	probably benign	Het
Rnf43	C	G	11: 87,620,339 (GRCm39)	S226R	probably damaging	Het
Scn5a	A	T	9: 119,362,993 (GRCm39)	D542E	probably damaging	Het
Sema5b	A	T	16: 35,448,466 (GRCm39)	I81F	probably benign	Het
Serinc5	G	A	13: 92,819,285 (GRCm39)	C73Y	probably damaging	Het
Serpina3g	A	T	12: 104,205,551 (GRCm39)	N97Y	possibly damaging	Het
Shq1	A	G	6: 100,614,033 (GRCm39)	S262P	probably damaging	Het
Smad4	A	T	18: 73,781,978 (GRCm39)	I428N	probably damaging	Het
Snip1	G	T	4: 124,966,613 (GRCm39)	G348W	probably damaging	Het
Spg11	A	G	2: 121,901,422 (GRCm39)	L1506P	probably damaging	Het
Stard9	G	A	2: 120,526,694 (GRCm39)	V984I	possibly damaging	Het
Svopl	A	T	6: 38,006,635 (GRCm39)	F121I	possibly damaging	Het
Tjp1	A	T	7: 64,972,802 (GRCm39)	V546E	probably damaging	Het
Tmem116	T	A	5: 121,631,819 (GRCm39)	F110L	probably damaging	Het
Ttyh2	C	T	11: 114,601,714 (GRCm39)	T446M	probably benign	Het
Tubb1	A	T	2: 174,299,532 (GRCm39)	I405L	probably benign	Het
Uba5	A	T	9: 103,933,025 (GRCm39)	F155L	possibly damaging	Het
Ubd	C	T	17: 37,506,212 (GRCm39)	H33Y	probably damaging	Het
Ube3d	A	T	9: 86,322,648 (GRCm39)	D175E	probably benign	Het
Usp24	A	G	4: 106,278,157 (GRCm39)	Q2293R	probably benign	Het
Vmn1r175	T	A	7: 23,507,937 (GRCm39)	H230L	probably benign	Het
Vmn1r88	A	G	7: 12,912,060 (GRCm39)	I139V	probably benign	Het
Vmn2r1	T	C	3: 63,994,046 (GRCm39)	F131L	probably benign	Het
Yipf3	T	C	17: 46,562,155 (GRCm39)		probably null	Het
Zdhhc19	A	G	16: 32,325,258 (GRCm39)	K192R	probably benign	Het
Zfy1	G	A	Y: 725,611 (GRCm39)	T718I	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
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
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

Posted On

2014-01-15