Mutagenetix > Incidental Mutation

Incidental Mutation 'R4420:Kdm1b'

327063

Institutional Source

Beutler Lab

Gene Symbol

Kdm1b

Ensembl Gene

ENSMUSG00000038080

Gene Name

lysine (K)-specific demethylase 1B

Synonyms

4632428N09Rik, Aof1

MMRRC Submission

041141-MU

Accession Numbers

Is this an essential gene?

Possibly essential (E-score: 0.536) question?

Stock #

R4420 (G1)

Quality Score

225

Status

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: 95.3%

Validation Efficiency

96% (53/55)

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: 48 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Arhgef17	G	A	7: 100,882,308		probably benign	Het
Atp1b1	T	C	1: 164,453,558	T53A	probably damaging	Het
Carmil3	A	G	14: 55,493,588	Q104R	probably damaging	Het
Casz1	T	G	4: 148,948,918	N1382K	possibly damaging	Het
Chfr	T	A	5: 110,170,880	C585*	probably null	Het
Chp2	T	C	7: 122,221,938	F174S	probably damaging	Het
Dclre1c	A	T	2: 3,433,745		probably null	Het
Dnah6	A	G	6: 73,191,479	V487A	probably benign	Het
Dnah9	T	C	11: 66,118,749	R771G	probably benign	Het
Duox1	G	A	2: 122,327,126	A578T	probably benign	Het
Elp3	G	A	14: 65,580,791	A140V	probably damaging	Het
Fbrsl1	T	C	5: 110,378,986	H387R	possibly damaging	Het
Gnat3	T	C	5: 17,999,801	S151P	probably damaging	Het
Gucy1a2	T	A	9: 3,634,640	L228H	probably damaging	Het
Gzmn	A	T	14: 56,166,006	H215Q	probably benign	Het
Heg1	A	T	16: 33,727,435	E864V	probably benign	Het
Hoxb9	T	C	11: 96,271,981	V147A	probably benign	Het
Hsf5	T	G	11: 87,657,304	H604Q	probably benign	Het
Hus1	T	C	11: 9,000,133	E196G	probably damaging	Het
Il12rb2	G	T	6: 67,316,410		probably null	Het
Irs1	T	C	1: 82,288,450	S682G	possibly damaging	Het
Jcad	T	C	18: 4,676,032	S1265P	probably benign	Het
Matk	A	G	10: 81,262,457	S361G	possibly damaging	Het
Mroh5	TGGAG	TG	15: 73,783,074		probably benign	Het
Nceh1	A	G	3: 27,241,649	D353G	probably damaging	Het
Nqo1	C	T	8: 107,392,117		probably null	Het
Olfr1086	A	G	2: 86,676,919	V138A	possibly damaging	Het
Pcdh7	T	C	5: 58,129,170	I1196T	probably benign	Het
Pla2g4d	A	G	2: 120,284,163	V29A	probably benign	Het
Ppfibp1	T	A	6: 147,026,238	Y794*	probably null	Het
Prdx5	C	A	19: 6,907,964		probably null	Het
Psme4	C	T	11: 30,812,028	T456I	possibly damaging	Het
Ptprd	A	T	4: 76,039,377	S923R	possibly damaging	Het
Samd12	G	A	15: 53,860,259	R13W	probably damaging	Het
Slc35f4	A	T	14: 49,313,577		probably benign	Het
Smc1b	A	G	15: 85,112,830	Y530H	probably damaging	Het
Spata2l	T	C	8: 123,234,029	T174A	possibly damaging	Het
Sugct	C	T	13: 17,452,545	C241Y	probably damaging	Het
Tarbp1	G	T	8: 126,447,080	A965D	possibly damaging	Het
Tas1r3	A	G	4: 155,862,332	V272A	probably damaging	Het
Tas2r117	T	A	6: 132,803,349	L150*	probably null	Het
Trip10	C	T	17: 57,255,448	P322L	probably benign	Het
Wdfy3	A	C	5: 101,910,984	H1487Q	probably damaging	Het
Wdr95	G	A	5: 149,532,666	V8M	probably damaging	Het
Zc3h15	C	A	2: 83,658,012	A98E	probably damaging	Het
Zfp763	T	G	17: 33,018,481	K563N	probably benign	Het
Zmym2	G	A	14: 56,956,878	D1198N	probably damaging	Het
Zp1	C	T	19: 10,914,760		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
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
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'- TGTTTTGCAAGTCCCAGCTTG -3'
(R):5'- TAGTCACCATGGCTGACGACTC -3'

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

Posted On

2015-07-07