Mutagenetix > Incidental Mutation

Incidental Mutation 'R1860:Kdm1b'

203835

Institutional Source

Beutler Lab

Gene Symbol

Kdm1b

Ensembl Gene

ENSMUSG00000038080

Gene Name

lysine (K)-specific demethylase 1B

Synonyms

4632428N09Rik, Aof1

MMRRC Submission

039883-MU

Accession Numbers

Is this an essential gene?

Possibly essential (E-score: 0.536) question?

Stock #

R1860 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

47043499-47085279 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 47049190 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 34 (A34T)

Ref Sequence

ENSEMBL: ENSMUSP00000117793 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000037025] [ENSMUST00000143868] [ENSMUST00000154802]

AlphaFold

Q8CIG3

Predicted Effect

probably benign
Transcript: ENSMUST00000037025
AA Change: A34T

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)

SMART Domains

Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: A34T

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 benign
Transcript: ENSMUST00000143868
AA Change: A34T

PolyPhen 2 Score 0.032 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000117793
Gene: ENSMUSG00000038080
AA Change: A34T

Domain	Start	End	E-Value	Type
Pfam:zf-CW	137	175	3.6e-13	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000154802

SMART Domains

Protein: ENSMUSP00000121827
Gene: ENSMUSG00000021376

Domain	Start	End	E-Value	Type
Pfam:TPMT	19	182	2.9e-62	PFAM

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.1%
20x: 91.7%

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930522L14Rik	A	G	5: 109,736,232	C587R	probably damaging	Het
Abca16	T	A	7: 120,534,763	S1320T	probably benign	Het
Abra	C	A	15: 41,869,034	R212L	probably damaging	Het
Acadsb	T	A	7: 131,444,229		probably null	Het
Adam26a	A	G	8: 43,569,541	V304A	possibly damaging	Het
Adgre1	T	C	17: 57,441,363	V521A	probably benign	Het
Adh5	G	A	3: 138,453,778	V288I	probably benign	Het
Astn1	A	C	1: 158,601,945	N753T	probably damaging	Het
Atad2	A	T	15: 58,096,718		probably null	Het
Best3	A	G	10: 116,993,273	T153A	probably damaging	Het
Ccdc122	G	A	14: 77,111,407	V226I	probably damaging	Het
Ccdc175	T	C	12: 72,105,926	Q735R	probably benign	Het
Cd19	T	A	7: 126,409,641	I499F	probably damaging	Het
Cftr	T	A	6: 18,268,289	L749H	probably benign	Het
Clec2h	G	T	6: 128,675,827	G186W	probably damaging	Het
Cpsf3	T	A	12: 21,296,732	I202N	probably damaging	Het
Crebbp	G	T	16: 4,087,736	T1669N	possibly damaging	Het
Csmd3	A	T	15: 47,659,192	C2694S	probably damaging	Het
Cul4a	G	A	8: 13,123,565	R204Q	probably damaging	Het
D230025D16Rik	A	G	8: 105,240,071	E150G	probably null	Het
Derl2	A	G	11: 71,018,343	F43S	probably damaging	Het
Dnah14	T	A	1: 181,763,960	N3348K	probably damaging	Het
Dnhd1	T	C	7: 105,704,205	V2855A	probably benign	Het
Dpysl4	G	T	7: 139,090,299	C27F	probably benign	Het
Fam228b	G	A	12: 4,748,314	A163V	probably damaging	Het
Fscn1	T	C	5: 142,970,063		probably null	Het
Fzd5	C	A	1: 64,734,994	R536L	probably damaging	Het
Gm8180	T	A	14: 43,783,739	H4L	probably benign	Het
Gpr176	T	A	2: 118,373,178	N4Y	probably damaging	Het
Grin3a	T	C	4: 49,665,309	I1109V	possibly damaging	Het
H2afy	A	G	13: 56,083,204	L287P	probably damaging	Het
Hcar1	T	A	5: 123,879,029	I200F	probably damaging	Het
Heatr4	G	A	12: 83,979,728	Q252*	probably null	Het
Hps1	G	A	19: 42,762,449	H371Y	probably damaging	Het
Ikzf2	T	C	1: 69,570,502	T195A	probably damaging	Het
Lef1	A	G	3: 131,111,641	N57S	probably damaging	Het
Ltn1	A	T	16: 87,416,343	D443E	probably benign	Het
Mamdc2	T	C	19: 23,359,153	T331A	probably damaging	Het
March10	A	T	11: 105,397,078	S133T	probably damaging	Het
Mb	A	G	15: 77,017,584	Y104H	probably damaging	Het
Mrc1	C	A	2: 14,328,579	P1357Q	probably benign	Het
Nfib	C	T	4: 82,323,680	V425M	probably damaging	Het
Olfr1197	T	G	2: 88,729,330	I90L	probably damaging	Het
Olfr1262	G	A	2: 90,003,146	V247I	probably benign	Het
Olfr1272	C	A	2: 90,282,158	C139F	probably damaging	Het
Olfr1467	T	A	19: 13,365,341	S238T	possibly damaging	Het
Olfr473	A	G	7: 107,934,390	Y290C	probably damaging	Het
Olfr527	G	A	7: 140,336,219	R119H	possibly damaging	Het
Olfr654	T	C	7: 104,587,905	S34P	probably damaging	Het
Olfr732	A	T	14: 50,281,391	Y287*	probably null	Het
Olfr784	T	C	10: 129,388,086	F151S	probably damaging	Het
Olfr916	A	T	9: 38,658,365	V9E	probably damaging	Het
Piezo1	T	C	8: 122,495,750	N919S	possibly damaging	Het
Prkaca	T	C	8: 83,981,223	S46P	probably benign	Het
Prkcb	T	G	7: 122,568,201	V378G	probably damaging	Het
Ptprf	A	T	4: 118,223,932	L576Q	probably damaging	Het
Rapgef4	T	C	2: 72,234,720	V687A	probably benign	Het
Rsad2	C	T	12: 26,450,617	V224I	probably damaging	Het
Ryr1	A	T	7: 29,009,552	D4796E	unknown	Het
Scn1a	C	T	2: 66,317,982	S1073N	probably damaging	Het
Slc26a3	A	G	12: 31,465,846	M582V	probably benign	Het
Tbc1d32	A	T	10: 56,123,537	Y846*	probably null	Het
Tbk1	A	T	10: 121,547,171	M719K	probably benign	Het
Timeless	A	G	10: 128,246,114	K536R	probably benign	Het
Tle6	G	T	10: 81,594,329	Q330K	probably damaging	Het
Tmem208	A	G	8: 105,334,806	K155E	possibly damaging	Het
Toe1	T	C	4: 116,805,229	Y273C	probably damaging	Het
Tppp2	A	C	14: 51,920,605	N169T	probably benign	Het
Ttll6	T	A	11: 96,138,874	Y204*	probably null	Het
Ubxn11	G	A	4: 134,124,838	S32N	probably damaging	Het
Usp8	G	A	2: 126,756,040	C961Y	probably damaging	Het
Vdac3	A	T	8: 22,580,499	I132K	possibly damaging	Het
Vmn2r124	G	T	17: 18,049,497	W5L	probably benign	Het
Vmn2r71	A	T	7: 85,615,574	D38V	probably damaging	Het
Vmn2r87	C	T	10: 130,479,886	V104I	probably benign	Het
Vmn2r97	C	T	17: 18,947,386	T634I	probably benign	Het
Vps50	T	C	6: 3,520,279		probably null	Het
Wwc2	T	C	8: 47,990,102	N32S	possibly damaging	Het
Ythdc2	T	A	18: 44,872,956	I1172K	possibly damaging	Het
Zfp14	C	T	7: 30,038,691	V290M	probably damaging	Het
Zfp317	G	A	9: 19,641,984	A18T	possibly damaging	Het
Zfp354b	A	T	11: 50,923,542	N185K	probably benign	Het
Zscan21	T	A	5: 138,126,630	D269E	probably benign	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
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
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'- TAGTCTGTTGCCAGGATGCAG -3'
(R):5'- AGCAGTCAGGATTAGCAGGC -3'

Sequencing Primer
(F):5'- ATGCAGCCTCTGGAGCTGTG -3'
(R):5'- CCTGCATTTGGTTTTAGAAGAGTAAC -3'

Posted On

2014-06-23