Mutagenetix > Incidental Mutation

Incidental Mutation 'R5541:Kdm1b'

435985

Institutional Source

Beutler Lab

Gene Symbol

Kdm1b

Ensembl Gene

ENSMUSG00000038080

Gene Name

lysine (K)-specific demethylase 1B

Synonyms

4632428N09Rik, Aof1

MMRRC Submission

043099-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.557) question?

Stock #

R5541 (G1)

Quality Score

149

Status

Validated

Chromosome

Chromosomal Location

47043499-47085279 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 47079196 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Threonine at position 714 (M714T)

Ref Sequence

ENSEMBL: ENSMUSP00000038373 (fasta)

Gene Model

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

AlphaFold

Q8CIG3

Predicted Effect

probably damaging
Transcript: ENSMUST00000037025
AA Change: M714T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: M714T

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

unknown
Transcript: ENSMUST00000143518
AA Change: M330T

SMART Domains

Protein: ENSMUSP00000114999
Gene: ENSMUSG00000038080
AA Change: M330T

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

0.4718

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.4%
20x: 95.2%

Validation Efficiency

100% (63/63)

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: 58 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610009B22Rik	T	C	11: 51,685,969	H34R	probably benign	Het
1700113H08Rik	A	G	10: 87,225,946	K86R	probably benign	Het
Abca13	T	C	11: 9,291,545	V1136A	probably benign	Het
Als2cr12	A	G	1: 58,658,429	M384T	probably benign	Het
Arfgap2	G	A	2: 91,275,769	R530H	probably benign	Het
Arhgap30	T	C	1: 171,404,139		probably null	Het
Asb7	T	C	7: 66,679,269	R8G	probably benign	Het
Bod1l	T	C	5: 41,791,933	N2949D	probably benign	Het
Ccdc86	T	C	19: 10,948,554	E227G	probably damaging	Het
Cercam	A	G	2: 29,875,629	D261G	probably benign	Het
Chd9	A	T	8: 91,051,504	E2714D	probably benign	Het
Dcp1a	T	A	14: 30,502,839	S126R	probably damaging	Het
Defa17	T	A	8: 21,656,549	C64S	probably damaging	Het
Depdc5	A	T	5: 32,864,629		probably benign	Het
Dhx29	A	G	13: 112,940,374	N259S	possibly damaging	Het
Dnah6	A	T	6: 73,192,988	L323Q	possibly damaging	Het
Dnah9	T	C	11: 66,145,336	Y416C	probably damaging	Het
Faap100	T	A	11: 120,377,632	E105V	possibly damaging	Het
Fbxw15	T	G	9: 109,565,430	I106L	probably benign	Het
Gm10610	A	G	7: 83,549,406		noncoding transcript	Het
Gpr22	A	G	12: 31,709,349	F258S	probably damaging	Het
Grip1	A	T	10: 120,072,718	I618F	probably damaging	Het
H2afy2	T	C	10: 61,747,717	I215V	probably benign	Het
Hspg2	C	A	4: 137,542,825	Q2365K	probably benign	Het
Hspg2	C	T	4: 137,520,551	T1233I	probably damaging	Het
Intu	A	G	3: 40,692,587		probably null	Het
Kif21a	A	G	15: 90,968,113	M924T	probably damaging	Het
Klb	A	T	5: 65,379,234	M636L	probably benign	Het
Klrb1a	G	A	6: 128,609,736	H219Y	probably benign	Het
March10	C	T	11: 105,390,131	D443N	probably damaging	Het
Nos1	A	G	5: 117,905,394	E578G	probably damaging	Het
Olfr1502	T	C	19: 13,861,964	I57T	probably benign	Het
Olfr887	T	C	9: 38,085,123	C96R	probably damaging	Het
Pard3b	A	G	1: 61,639,343	Y34C	probably damaging	Het
Pcdh17	T	A	14: 84,447,416	V441E	probably damaging	Het
Pde6g	A	T	11: 120,448,172	I64N	probably damaging	Het
Pdia4	C	T	6: 47,796,637	V593M	probably damaging	Het
Pnn	T	G	12: 59,071,930	V433G	possibly damaging	Het
Rbak	G	A	5: 143,173,990	S436F	probably damaging	Het
Rpl11	A	G	4: 136,052,732		probably benign	Het
Ryr1	G	T	7: 29,086,185	Q1701K	probably damaging	Het
Scn1a	T	A	2: 66,324,633	T661S	probably benign	Het
Smg1	T	A	7: 118,157,163		probably benign	Het
St8sia2	T	C	7: 73,966,900	D109G	probably benign	Het
Stk-ps1	T	A	17: 36,398,213		noncoding transcript	Het
Stxbp3-ps	C	T	19: 9,557,970		noncoding transcript	Het
Taf1d	T	A	9: 15,308,850	F132I	probably damaging	Het
Tfap2b	A	G	1: 19,214,026	S35G	possibly damaging	Het
Tnk2	C	T	16: 32,669,523	T198I	probably benign	Het
Ube2q2	T	A	9: 55,191,879	V168E	possibly damaging	Het
Ucma	A	G	2: 4,981,330	R105G	probably benign	Het
Vmn2r97	C	T	17: 18,928,355	Q171*	probably null	Het
Wapl	T	C	14: 34,730,662		probably null	Het
Zfand4	T	A	6: 116,314,295	C397S	possibly damaging	Het
Zfhx3	A	G	8: 108,948,951	N2211S	probably damaging	Het
Zfp143	G	T	7: 110,070,480	G39C	probably benign	Het
Zfp568	T	A	7: 30,022,876	D414E	possibly damaging	Het
Zfp574	C	T	7: 25,081,950	A799V	probably damaging	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
R4548: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
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'- TAGTGTGCATGCGGAGAAC -3'
(R):5'- GAACTAAGTCTCAGCACCTGTG -3'

Sequencing Primer
(F):5'- TGTGCATGCGGAGAACTGATG -3'
(R):5'- GCTGTGGCCTGATACTAAGG -3'

Posted On

2016-10-24