Mutagenetix > Incidental Mutation

Incidental Mutation 'R4548:Kdm1b'

333877

Institutional Source

Beutler Lab

Gene Symbol

Kdm1b

Ensembl Gene

ENSMUSG00000038080

Gene Name

lysine (K)-specific demethylase 1B

Synonyms

4632428N09Rik, Aof1

MMRRC Submission

041594-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.467) question?

Stock #

R4548 (G1)

Quality Score

217

Status

Not validated

Chromosome

Chromosomal Location

47043499-47085279 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 47063077 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Tryptophan at position 308 (R308W)

Ref Sequence

ENSEMBL: ENSMUSP00000038373 (fasta)

Gene Model

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

AlphaFold

Q8CIG3

Predicted Effect

probably damaging
Transcript: ENSMUST00000037025
AA Change: R308W

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: R308W

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

unknown
Transcript: ENSMUST00000143518
AA Change: R24W

SMART Domains

Protein: ENSMUSP00000114999
Gene: ENSMUSG00000038080
AA Change: R24W

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

0.6467

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.4%

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: 37 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca17	A	T	17: 24,334,271	F155L	possibly damaging	Het
Adcy6	A	G	15: 98,598,659	I545T	probably damaging	Het
Akip1	C	A	7: 109,704,986	S90*	probably null	Het
Anln	T	C	9: 22,362,888	D551G	possibly damaging	Het
Arhgef17	T	C	7: 100,931,129	Q204R	possibly damaging	Het
Arl6ip1	AAAATAAATAAATAAATAAATAAATA	AAAATAAATAAATAAATAAATAAATAAATA	7: 118,121,899		probably benign	Het
Bcl2l11	A	G	2: 128,129,646	E75G	probably benign	Het
Cfap45	A	G	1: 172,545,108	I457V	probably benign	Het
Cfap65	G	A	1: 74,907,612	T1313I	probably damaging	Het
Cntln	C	A	4: 85,096,842	H1123Q	probably benign	Het
Cops3	C	T	11: 59,827,845		probably null	Het
Dis3l2	A	T	1: 87,049,671	T861S	probably benign	Het
Dnajc11	A	G	4: 151,973,617	N281S	possibly damaging	Het
Fabp3	C	T	4: 130,312,452		probably null	Het
Fras1	A	G	5: 96,709,895	D2016G	probably benign	Het
Gpr39	G	A	1: 125,677,991	V219I	probably benign	Het
Greb1	T	C	12: 16,699,675	D1050G	probably damaging	Het
Kcnh6	T	C	11: 106,009,049	F48S	probably damaging	Het
Mrm2	T	C	5: 140,328,496	T195A	probably benign	Het
Myzap	T	C	9: 71,550,246	E289G	possibly damaging	Het
Nemp1	A	G	10: 127,696,344	E373G	probably benign	Het
Olfr1100	T	C	2: 86,978,670	N42S	probably damaging	Het
Olfr155	T	A	4: 43,854,834	I175N	probably damaging	Het
Polr1c	A	T	17: 46,247,809		probably null	Het
Rev1	A	G	1: 38,059,194	M756T	possibly damaging	Het
Sacs	A	G	14: 61,191,938	D482G	probably damaging	Het
Sfrp4	A	G	13: 19,623,766	M112V	possibly damaging	Het
Slc7a4	T	C	16: 17,575,345	T197A	probably benign	Het
Snx27	C	T	3: 94,526,439		probably benign	Het
Spata5	T	A	3: 37,432,027	N299K	probably benign	Het
Speer2	T	C	16: 69,858,849	K30E	probably damaging	Het
Ssh2	G	A	11: 77,450,184	A721T	probably benign	Het
Trappc3	A	G	4: 126,272,751	D39G	possibly damaging	Het
Ttc28	G	A	5: 111,271,224	S1362N	possibly damaging	Het
Ugt2b35	A	T	5: 87,008,275	K409*	probably null	Het
Vmn2r92	A	T	17: 18,171,316	M527L	probably benign	Het
Zbed5	T	A	5: 129,902,851	L547*	probably null	Het

Other mutations in Kdm1b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00587:Kdm1b	APN	13	47068540	missense	probably benign	0.01
IGL00924:Kdm1b	APN	13	47068480	missense	probably benign
IGL01553:Kdm1b	APN	13	47080548	missense	probably damaging	0.96
IGL01663:Kdm1b	APN	13	47073737	missense	probably damaging	0.99
IGL02385:Kdm1b	APN	13	47068506	missense	possibly damaging	0.49
IGL02505:Kdm1b	APN	13	47060855	missense	probably damaging	1.00
IGL02826:Kdm1b	APN	13	47080467	missense	probably damaging	1.00
IGL03257:Kdm1b	APN	13	47049266	missense	probably damaging	1.00
R0052:Kdm1b	UTSW	13	47064117	missense	probably damaging	1.00
R0319:Kdm1b	UTSW	13	47053719	missense	probably benign
R0426:Kdm1b	UTSW	13	47064244	splice site	probably benign
R0599:Kdm1b	UTSW	13	47058810	missense	possibly damaging	0.47
R0764:Kdm1b	UTSW	13	47068603	missense	possibly damaging	0.70
R1163:Kdm1b	UTSW	13	47071922	missense	probably benign	0.02
R1543:Kdm1b	UTSW	13	47068521	missense	probably damaging	0.99
R1584:Kdm1b	UTSW	13	47064054	missense	probably damaging	1.00
R1627:Kdm1b	UTSW	13	47064231	critical splice donor site	probably null
R1669:Kdm1b	UTSW	13	47068548	missense	probably damaging	1.00
R1758:Kdm1b	UTSW	13	47060768	missense	probably benign	0.00
R1860:Kdm1b	UTSW	13	47049190	missense	probably benign	0.03
R1907:Kdm1b	UTSW	13	47064120	missense	probably benign	0.00
R2225:Kdm1b	UTSW	13	47064088	frame shift	probably null
R2239:Kdm1b	UTSW	13	47073755	missense	probably damaging	1.00
R2271:Kdm1b	UTSW	13	47064088	frame shift	probably null
R2302:Kdm1b	UTSW	13	47064088	frame shift	probably null
R2303:Kdm1b	UTSW	13	47064088	frame shift	probably null
R2380:Kdm1b	UTSW	13	47073755	missense	probably damaging	1.00
R2442:Kdm1b	UTSW	13	47062975	missense	probably benign	0.32
R3022:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R3054:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R3545:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R3546:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R3548:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4094:Kdm1b	UTSW	13	47063020	missense	probably damaging	1.00
R4419:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4420:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4502:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4547:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4785:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4793:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4804:Kdm1b	UTSW	13	47063077	missense	probably damaging	1.00
R4882:Kdm1b	UTSW	13	47060893	missense	probably benign
R4906:Kdm1b	UTSW	13	47063144	critical splice donor site	probably null
R4965:Kdm1b	UTSW	13	47074367	missense	probably damaging	0.98
R5039:Kdm1b	UTSW	13	47077486	missense	probably damaging	1.00
R5098:Kdm1b	UTSW	13	47062991	missense	probably damaging	1.00
R5265:Kdm1b	UTSW	13	47062969	missense	probably benign	0.35
R5541:Kdm1b	UTSW	13	47079196	missense	probably damaging	1.00
R5814:Kdm1b	UTSW	13	47063146	splice site	probably null
R6046:Kdm1b	UTSW	13	47079253	missense	possibly damaging	0.92
R6798:Kdm1b	UTSW	13	47068536	missense	probably benign	0.00
R6903:Kdm1b	UTSW	13	47074404	missense	probably benign	0.00
R7831:Kdm1b	UTSW	13	47050622	missense	probably benign	0.17
R7973:Kdm1b	UTSW	13	47077446	missense	probably benign	0.00
R8181:Kdm1b	UTSW	13	47051901	critical splice donor site	probably null
R8248:Kdm1b	UTSW	13	47071878	intron	probably benign
R8821:Kdm1b	UTSW	13	47064141	missense	possibly damaging	0.94
R8831:Kdm1b	UTSW	13	47064141	missense	possibly damaging	0.94
R8842:Kdm1b	UTSW	13	47078356	missense	probably damaging	1.00
R8861:Kdm1b	UTSW	13	47064106	missense	probably benign	0.02
R8885:Kdm1b	UTSW	13	47053708	nonsense	probably null
R9038:Kdm1b	UTSW	13	47049294	missense	probably benign	0.07
R9132:Kdm1b	UTSW	13	47071982	missense	probably benign	0.05
R9268:Kdm1b	UTSW	13	47064229	missense	probably benign	0.00
R9616:Kdm1b	UTSW	13	47080554	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TCTGGCTGTTTTGCAAGTCC -3'
(R):5'- ATGGCTGACGACTCTGCTAG -3'

Sequencing Primer
(F):5'- CAAGTCCCAGCTTGCAGAG -3'
(R):5'- AGTTAGTCACCATGGCTGAC -3'

Posted On

2015-08-18