Mutagenetix > Incidental Mutation

Incidental Mutation 'R9616:Kdm1b'

724611

Institutional Source

Beutler Lab

Gene Symbol

Kdm1b

Ensembl Gene

ENSMUSG00000038080

Gene Name

lysine (K)-specific demethylase 1B

Synonyms

4632428N09Rik, Aof1

MMRRC Submission

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.406) question?

Stock #

R9616 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

47043499-47085279 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 47080554 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 788 (E788G)

Ref Sequence

ENSEMBL: ENSMUSP00000038373 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000021807] [ENSMUST00000037025]

AlphaFold

Q8CIG3

Predicted Effect

probably benign
Transcript: ENSMUST00000021807

SMART Domains

Protein: ENSMUSP00000021807
Gene: ENSMUSG00000021377

Domain	Start	End	E-Value	Type
low complexity region	3	18	N/A	INTRINSIC
low complexity region	31	55	N/A	INTRINSIC
low complexity region	58	69	N/A	INTRINSIC
SAP	153	187	2.97e-8	SMART
low complexity region	190	210	N/A	INTRINSIC
low complexity region	231	315	N/A	INTRINSIC
Pfam:DEK_C	327	379	3.4e-19	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000037025
AA Change: E788G

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

SMART Domains

Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: E788G

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

SMART Domains

Protein: ENSMUSP00000114999
Gene: ENSMUSG00000038080
AA Change: E404G

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: 100.0%
3x: 99.9%
10x: 99.6%
20x: 99.0%

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: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3110040M04Rik	T	A	1: 151,204,729 (GRCm38)	D189E	probably benign	Het
Abca13	A	T	11: 9,290,501 (GRCm38)	H788L	probably benign	Het
Abcb1b	A	G	5: 8,812,779 (GRCm38)	I154V	probably benign	Het
Acsm4	A	G	7: 119,694,649 (GRCm38)	N81S	probably benign	Het
Adamts5	G	A	16: 85,862,786 (GRCm38)	H873Y	probably benign	Het
Aox4	C	T	1: 58,228,861 (GRCm38)	T200I	possibly damaging	Het
Arhgap33	A	G	7: 30,529,942 (GRCm38)	V336A	probably damaging	Het
Brca1	C	T	11: 101,525,857 (GRCm38)	E484K	probably damaging	Het
Capn13	T	A	17: 73,365,969 (GRCm38)	D113V	probably benign	Het
Catsper2	TAGGATGGCTTTTCTCAGGATAGCTTTTCTCAGGATGGCTTTTCTCAGGATAGCTTTTCTCAGGATGGCTTTTCTCAGGATAGCTTTTCT	TAGGATGGCTTTTCTCAGGATAGCTTTTCTCAGGATGGCTTTTCTCAGGATAGCTTTTCT	2: 121,397,572 (GRCm38)		probably benign	Het
Ceacam3	G	A	7: 17,158,153 (GRCm38)	E274K		Het
Cfh	A	T	1: 140,102,516 (GRCm38)	I891K	probably damaging	Het
Cgn	A	G	3: 94,763,025 (GRCm38)	S1041P	probably damaging	Het
Cldn18	T	C	9: 99,698,862 (GRCm38)	D111G	probably benign	Het
Cnp	G	A	11: 100,576,435 (GRCm38)	R68Q	probably benign	Het
Cntn4	T	A	6: 106,697,564 (GRCm38)	C1008*	probably null	Het
Cntnap5a	T	C	1: 116,101,593 (GRCm38)	I259T	probably benign	Het
Cubn	A	G	2: 13,314,718 (GRCm38)	I2897T	probably benign	Het
Cyp2c39	T	A	19: 39,513,204 (GRCm38)	L67Q	probably damaging	Het
Dclk1	G	A	3: 55,480,433 (GRCm38)	C100Y	probably damaging	Het
Ddc	C	T	11: 11,822,288 (GRCm38)	W349*	probably null	Het
Dennd3	A	G	15: 73,568,714 (GRCm38)	E1198G	probably benign	Het
Dnah1	T	C	14: 31,304,443 (GRCm38)	D826G	probably null	Het
Dpp4	T	C	2: 62,387,085 (GRCm38)	Y56C	probably damaging	Het
Etv6	A	G	6: 134,266,332 (GRCm38)	D350G	possibly damaging	Het
Fat1	C	A	8: 44,953,038 (GRCm38)	P942Q	probably damaging	Het
Fbxl5	A	G	5: 43,758,817 (GRCm38)	F418L	probably benign	Het
Fbxo11	T	A	17: 88,008,670 (GRCm38)	H368L		Het
Fhl2	G	T	1: 43,128,386 (GRCm38)	H182Q	probably damaging	Het
Gabpa	T	A	16: 84,852,573 (GRCm38)	C223S	probably damaging	Het
Gigyf2	T	C	1: 87,428,604 (GRCm38)	I803T	unknown	Het
Greb1	A	T	12: 16,740,037 (GRCm38)	N3K	probably damaging	Het
Hmcn1	T	G	1: 150,808,722 (GRCm38)	S366R	probably benign	Het
Il17b	A	G	18: 61,692,292 (GRCm38)	Q133R	probably benign	Het
Inha	T	A	1: 75,509,567 (GRCm38)	S169T	probably benign	Het
Itsn1	G	A	16: 91,853,167 (GRCm38)	R243H	probably benign	Het
Kcnu1	G	GA	8: 25,913,647 (GRCm38)		probably null	Het
Kdm2a	A	T	19: 4,320,280 (GRCm38)	I1059N	probably damaging	Het
Klk1b9	G	T	7: 43,979,371 (GRCm38)	G100C	probably benign	Het
Knl1	A	T	2: 119,076,944 (GRCm38)	N1650Y	probably damaging	Het
Knl1	T	C	2: 119,069,513 (GRCm38)	V565A	probably benign	Het
Lpp	T	C	16: 24,761,969 (GRCm38)	V270A	probably benign	Het
Lrrc15	A	G	16: 30,273,699 (GRCm38)	L274P	probably damaging	Het
Mertk	C	T	2: 128,801,335 (GRCm38)	L885F	probably benign	Het
Mpst	T	A	15: 78,410,161 (GRCm38)	L31*	probably null	Het
Ms4a10	T	C	19: 10,967,076 (GRCm38)	T115A	possibly damaging	Het
Myof	A	G	19: 37,934,815 (GRCm38)	I1330T	possibly damaging	Het
Ncam2	T	C	16: 81,443,254 (GRCm38)	I201T	probably damaging	Het
Nefh	T	A	11: 4,939,443 (GRCm38)	K1059*	probably null	Het
Nek1	T	C	8: 61,020,073 (GRCm38)	Y168H	probably damaging	Het
Nek11	T	A	9: 105,204,812 (GRCm38)	T531S	probably damaging	Het
Nelfa	G	A	5: 33,901,783 (GRCm38)	P243S	possibly damaging	Het
Niban1	T	C	1: 151,636,442 (GRCm38)	Y32H	probably damaging	Het
Notum	G	T	11: 120,660,148 (GRCm38)	T64K		Het
Or13c7d	T	A	4: 43,770,193 (GRCm38)	K273*	probably null	Het
Or52b2	A	C	7: 105,337,313 (GRCm38)	Y134*	probably null	Het
Or9i16	A	G	19: 13,887,497 (GRCm38)	S238P	probably damaging	Het
Otof	A	G	5: 30,382,364 (GRCm38)	I1035T	possibly damaging	Het
Otud3	A	G	4: 138,897,614 (GRCm38)	Y259H	probably benign	Het
Per1	G	T	11: 69,102,728 (GRCm38)	C368F	probably damaging	Het
Pitrm1	G	T	13: 6,555,566 (GRCm38)	R183L	probably damaging	Het
Prl3a1	C	T	13: 27,275,135 (GRCm38)	A119V		Het
Pycard	C	T	7: 127,993,604 (GRCm38)	G17E	probably benign	Het
Rnf13	A	G	3: 57,833,009 (GRCm38)	D249G	possibly damaging	Het
Sdhaf2	T	C	19: 10,517,325 (GRCm38)	Y33C	probably damaging	Het
Sdk2	A	G	11: 113,800,235 (GRCm38)	V1838A	probably benign	Het
Sgo2b	C	T	8: 63,927,240 (GRCm38)	V853I	probably benign	Het
Slc1a4	T	C	11: 20,332,403 (GRCm38)	T24A	probably benign	Het
Slc8a1	T	C	17: 81,647,978 (GRCm38)	T544A	probably benign	Het
Sntg2	T	C	12: 30,276,733 (GRCm38)	N143S	probably benign	Het
Sphkap	T	C	1: 83,277,268 (GRCm38)	E920G	probably damaging	Het
Srgap2	T	A	1: 131,325,090 (GRCm38)	H132L		Het
Srgap3	A	T	6: 112,771,563 (GRCm38)	V376D	probably damaging	Het
Stxbp5l	T	C	16: 37,215,952 (GRCm38)	K434E	probably damaging	Het
Tab2	A	T	10: 7,919,241 (GRCm38)	N492K	possibly damaging	Het
Tbc1d32	T	C	10: 56,161,150 (GRCm38)	Q666R	possibly damaging	Het
Tekt4	T	C	17: 25,473,808 (GRCm38)		probably null	Het
Tnni3k	G	A	3: 154,962,087 (GRCm38)	Q230*	probably null	Het
Trp53bp1	A	C	2: 121,236,176 (GRCm38)	S690A	probably benign	Het
Trpa1	C	A	1: 14,918,853 (GRCm38)		probably benign	Het
Trpm1	T	G	7: 64,208,384 (GRCm38)	V324G	probably damaging	Het
Usp29	A	G	7: 6,963,180 (GRCm38)	E674G	possibly damaging	Het
Vmn2r59	T	C	7: 42,011,875 (GRCm38)	R839G	probably damaging	Het
Vmn2r6	A	G	3: 64,538,303 (GRCm38)	L667P	probably damaging	Het
Vmn2r91	T	A	17: 18,136,043 (GRCm38)	F657L	possibly damaging	Het
Vps13d	A	G	4: 145,098,131 (GRCm38)	V2923A		Het
Xylb	T	A	9: 119,371,956 (GRCm38)	L220Q	probably damaging	Het
Zbtb10	C	T	3: 9,251,413 (GRCm38)	T95M	probably benign	Het
Zfp263	C	T	16: 3,749,618 (GRCm38)	P599L	probably damaging	Het
Zfp532	A	G	18: 65,656,568 (GRCm38)	E1026G	probably benign	Het
Zfp78	A	G	7: 6,379,079 (GRCm38)	N376S	probably benign	Het

Other mutations in Kdm1b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00587:Kdm1b	APN	13	47,068,540 (GRCm38)	missense	probably benign	0.01
IGL00924:Kdm1b	APN	13	47,068,480 (GRCm38)	missense	probably benign
IGL01553:Kdm1b	APN	13	47,080,548 (GRCm38)	missense	probably damaging	0.96
IGL01663:Kdm1b	APN	13	47,073,737 (GRCm38)	missense	probably damaging	0.99
IGL02385:Kdm1b	APN	13	47,068,506 (GRCm38)	missense	possibly damaging	0.49
IGL02505:Kdm1b	APN	13	47,060,855 (GRCm38)	missense	probably damaging	1.00
IGL02826:Kdm1b	APN	13	47,080,467 (GRCm38)	missense	probably damaging	1.00
IGL03257:Kdm1b	APN	13	47,049,266 (GRCm38)	missense	probably damaging	1.00
R0052:Kdm1b	UTSW	13	47,064,117 (GRCm38)	missense	probably damaging	1.00
R0319:Kdm1b	UTSW	13	47,053,719 (GRCm38)	missense	probably benign
R0426:Kdm1b	UTSW	13	47,064,244 (GRCm38)	splice site	probably benign
R0599:Kdm1b	UTSW	13	47,058,810 (GRCm38)	missense	possibly damaging	0.47
R0764:Kdm1b	UTSW	13	47,068,603 (GRCm38)	missense	possibly damaging	0.70
R1163:Kdm1b	UTSW	13	47,071,922 (GRCm38)	missense	probably benign	0.02
R1543:Kdm1b	UTSW	13	47,068,521 (GRCm38)	missense	probably damaging	0.99
R1584:Kdm1b	UTSW	13	47,064,054 (GRCm38)	missense	probably damaging	1.00
R1627:Kdm1b	UTSW	13	47,064,231 (GRCm38)	critical splice donor site	probably null
R1669:Kdm1b	UTSW	13	47,068,548 (GRCm38)	missense	probably damaging	1.00
R1758:Kdm1b	UTSW	13	47,060,768 (GRCm38)	missense	probably benign	0.00
R1860:Kdm1b	UTSW	13	47,049,190 (GRCm38)	missense	probably benign	0.03
R1907:Kdm1b	UTSW	13	47,064,120 (GRCm38)	missense	probably benign	0.00
R2225:Kdm1b	UTSW	13	47,064,088 (GRCm38)	frame shift	probably null
R2239:Kdm1b	UTSW	13	47,073,755 (GRCm38)	missense	probably damaging	1.00
R2271:Kdm1b	UTSW	13	47,064,088 (GRCm38)	frame shift	probably null
R2302:Kdm1b	UTSW	13	47,064,088 (GRCm38)	frame shift	probably null
R2303:Kdm1b	UTSW	13	47,064,088 (GRCm38)	frame shift	probably null
R2380:Kdm1b	UTSW	13	47,073,755 (GRCm38)	missense	probably damaging	1.00
R2442:Kdm1b	UTSW	13	47,062,975 (GRCm38)	missense	probably benign	0.32
R3022:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R3054:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R3545:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R3546:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R3548:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4094:Kdm1b	UTSW	13	47,063,020 (GRCm38)	missense	probably damaging	1.00
R4419:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4420:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4502:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4547:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4548:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4785:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4793:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4804:Kdm1b	UTSW	13	47,063,077 (GRCm38)	missense	probably damaging	1.00
R4882:Kdm1b	UTSW	13	47,060,893 (GRCm38)	missense	probably benign
R4906:Kdm1b	UTSW	13	47,063,144 (GRCm38)	critical splice donor site	probably null
R4965:Kdm1b	UTSW	13	47,074,367 (GRCm38)	missense	probably damaging	0.98
R5039:Kdm1b	UTSW	13	47,077,486 (GRCm38)	missense	probably damaging	1.00
R5098:Kdm1b	UTSW	13	47,062,991 (GRCm38)	missense	probably damaging	1.00
R5265:Kdm1b	UTSW	13	47,062,969 (GRCm38)	missense	probably benign	0.35
R5541:Kdm1b	UTSW	13	47,079,196 (GRCm38)	missense	probably damaging	1.00
R5814:Kdm1b	UTSW	13	47,063,146 (GRCm38)	splice site	probably null
R6046:Kdm1b	UTSW	13	47,079,253 (GRCm38)	missense	possibly damaging	0.92
R6798:Kdm1b	UTSW	13	47,068,536 (GRCm38)	missense	probably benign	0.00
R6903:Kdm1b	UTSW	13	47,074,404 (GRCm38)	missense	probably benign	0.00
R7831:Kdm1b	UTSW	13	47,050,622 (GRCm38)	missense	probably benign	0.17
R7973:Kdm1b	UTSW	13	47,077,446 (GRCm38)	missense	probably benign	0.00
R8181:Kdm1b	UTSW	13	47,051,901 (GRCm38)	critical splice donor site	probably null
R8248:Kdm1b	UTSW	13	47,071,878 (GRCm38)	intron	probably benign
R8821:Kdm1b	UTSW	13	47,064,141 (GRCm38)	missense	possibly damaging	0.94
R8831:Kdm1b	UTSW	13	47,064,141 (GRCm38)	missense	possibly damaging	0.94
R8842:Kdm1b	UTSW	13	47,078,356 (GRCm38)	missense	probably damaging	1.00
R8861:Kdm1b	UTSW	13	47,064,106 (GRCm38)	missense	probably benign	0.02
R8885:Kdm1b	UTSW	13	47,053,708 (GRCm38)	nonsense	probably null
R9038:Kdm1b	UTSW	13	47,049,294 (GRCm38)	missense	probably benign	0.07
R9132:Kdm1b	UTSW	13	47,071,982 (GRCm38)	missense	probably benign	0.05
R9268:Kdm1b	UTSW	13	47,064,229 (GRCm38)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- TCAGGAACCTAACAGTGAGCAG -3'
(R):5'- GTGCTAGCTTTCAGAATGGAGAG -3'

Sequencing Primer
(F):5'- CCTACGAGGGCAAGATGCTTG -3'
(R):5'- AGCTTTCAGAATGGAGAGGGCTTC -3'

Posted On

2022-09-12