Mutagenetix > Incidental Mutation

Incidental Mutation 'R8885:Kdm1b'

677271

Institutional Source

Beutler Lab

Gene Symbol

Kdm1b

Ensembl Gene

ENSMUSG00000038080

Gene Name

lysine (K)-specific demethylase 1B

Synonyms

4632428N09Rik, Aof1

MMRRC Submission

068751-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.557) question?

Stock #

R8885 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

47043499-47085279 bp(+) (GRCm38)

Type of Mutation

nonsense

DNA Base Change (assembly)

T to A at 47053708 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Stop codon at position 169 (C169*)

Ref Sequence

ENSEMBL: ENSMUSP00000038373 (fasta)

Gene Model

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

AlphaFold

Q8CIG3

Predicted Effect

probably null
Transcript: ENSMUST00000037025
AA Change: C169*

SMART Domains

Protein: ENSMUSP00000038373
Gene: ENSMUSG00000038080
AA Change: C169*

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 null
Transcript: ENSMUST00000143868
AA Change: C169*

SMART Domains

Protein: ENSMUSP00000117793
Gene: ENSMUSG00000038080
AA Change: C169*

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

Meta Mutation Damage Score

0.9756

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (104/104)

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: 106 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210408I21Rik	A	T	13: 77,323,406 (GRCm38)	S977C	possibly damaging	Het
4921507P07Rik	A	T	6: 50,574,048 (GRCm38)	Y474N	possibly damaging	Het
Abca8a	T	A	11: 110,069,479 (GRCm38)	D646V	probably damaging	Het
Adss	T	A	1: 177,769,960 (GRCm38)	Y378F	probably damaging	Het
Akap6	C	T	12: 53,141,536 (GRCm38)	A1911V	probably benign	Het
Alg2	T	C	4: 47,474,159 (GRCm38)	Y43C	probably benign	Het
Alk	A	C	17: 71,895,763 (GRCm38)	V1159G	probably damaging	Het
Alx3	A	T	3: 107,600,694 (GRCm38)	Q173L	probably damaging	Het
Aqp9	A	G	9: 71,162,311 (GRCm38)		probably benign	Het
Atf7ip	C	A	6: 136,587,143 (GRCm38)	L787I	probably benign	Het
Bbs9	A	T	9: 22,678,938 (GRCm38)	E657D	possibly damaging	Het
Bean1	G	A	8: 104,182,120 (GRCm38)		probably null	Het
Cactin	G	T	10: 81,321,248 (GRCm38)	R13L	unknown	Het
Ccdc178	T	C	18: 22,067,664 (GRCm38)	E412G	probably damaging	Het
Ccdc30	A	G	4: 119,324,562 (GRCm38)	I583T	probably damaging	Het
Ccl8	T	C	11: 82,116,107 (GRCm38)	Y49H	probably damaging	Het
Clptm1	T	A	7: 19,639,007 (GRCm38)	K199N	probably damaging	Het
Cnbp	G	A	6: 87,845,664 (GRCm38)	S39L	probably benign	Het
Cnih3	T	A	1: 181,409,872 (GRCm38)		probably benign	Het
Cnksr3	A	T	10: 7,140,201 (GRCm38)		probably benign	Het
Cntn1	A	G	15: 92,261,499 (GRCm38)	I512V	probably benign	Het
Col20a1	A	G	2: 180,998,503 (GRCm38)		probably benign	Het
Col28a1	A	T	6: 8,127,360 (GRCm38)		probably benign	Het
Col6a2	A	T	10: 76,614,907 (GRCm38)	Y63*	probably null	Het
Copa	T	G	1: 172,097,745 (GRCm38)	F190V	probably damaging	Het
Crisp4	A	C	1: 18,136,924 (GRCm38)		probably benign	Het
Cxcl2	C	T	5: 90,904,226 (GRCm38)	Q64*	probably null	Het
Cxcr5	T	C	9: 44,514,252 (GRCm38)	D36G	probably benign	Het
Cyp20a1	T	A	1: 60,372,606 (GRCm38)	V271E	possibly damaging	Het
D430041D05Rik	T	C	2: 104,241,193 (GRCm38)	Y570C	probably damaging	Het
Ddi1	T	G	9: 6,266,198 (GRCm38)	D57A	probably benign	Het
Ddx11	T	A	17: 66,143,465 (GRCm38)	S492T	probably benign	Het
Dhx34	C	T	7: 16,216,451 (GRCm38)	R264H	probably damaging	Het
Dnah3	T	A	7: 119,962,152 (GRCm38)	I328F		Het
Dnah5	C	T	15: 28,327,740 (GRCm38)	R2087C	probably damaging	Het
Dnah8	C	G	17: 30,708,312 (GRCm38)	S1314W	possibly damaging	Het
Dock2	T	C	11: 34,310,396 (GRCm38)	N982D	probably benign	Het
Dync1h1	A	G	12: 110,616,738 (GRCm38)	D423G	probably damaging	Het
Ect2l	A	C	10: 18,172,835 (GRCm38)	L213V	probably damaging	Het
Fam210a	T	C	18: 68,276,144 (GRCm38)	I32V	probably benign	Het
Fancg	A	G	4: 43,007,266 (GRCm38)		probably null	Het
Fastkd5	T	C	2: 130,615,191 (GRCm38)	E493G	probably benign	Het
Fbxo38	T	C	18: 62,526,201 (GRCm38)	M342V	probably damaging	Het
Flnc	A	C	6: 29,455,411 (GRCm38)	K2020Q	probably damaging	Het
Flt4	A	G	11: 49,636,333 (GRCm38)		probably benign	Het
Frmd4b	G	T	6: 97,412,519 (GRCm38)	P129T	probably benign	Het
Galnt13	C	A	2: 54,880,126 (GRCm38)	A310E	probably benign	Het
Gm4884	T	A	7: 41,044,684 (GRCm38)	Y692*	probably null	Het
Gm6309	T	A	5: 146,168,293 (GRCm38)	D270V	probably damaging	Het
Grip1	G	T	10: 119,454,287 (GRCm38)		probably benign	Het
Itpr3	G	A	17: 27,118,677 (GRCm38)		probably benign	Het
Kdf1	G	T	4: 133,528,194 (GRCm38)	C74F	probably damaging	Het
Kmt2c	G	T	5: 25,315,079 (GRCm38)	T2011K	probably benign	Het
Lama1	G	A	17: 67,773,784 (GRCm38)	G1269E		Het
Lamb3	C	T	1: 193,334,874 (GRCm38)	A791V	probably benign	Het
Leng9	G	T	7: 4,148,775 (GRCm38)	R301S	possibly damaging	Het
Lgr6	C	A	1: 134,987,604 (GRCm38)	V746L	probably benign	Het
Lrp5	T	A	19: 3,652,170 (GRCm38)	S216C	probably damaging	Het
Ltn1	T	C	16: 87,381,545 (GRCm38)	T1599A	probably damaging	Het
Map2k1	G	T	9: 64,187,324 (GRCm38)	N345K	probably damaging	Het
Map4k1	T	A	7: 28,989,437 (GRCm38)	D304E	probably benign	Het
Mcpt1	C	T	14: 56,019,065 (GRCm38)	T86I	probably damaging	Het
Mcpt9	T	C	14: 56,027,696 (GRCm38)	K116R	probably benign	Het
Morc2a	G	T	11: 3,678,584 (GRCm38)	A346S	probably damaging	Het
Mybpc3	A	T	2: 91,123,892 (GRCm38)	Q370L	probably benign	Het
Nars2	T	C	7: 97,002,888 (GRCm38)	S229P	probably damaging	Het
Ndufa10	A	T	1: 92,469,971 (GRCm38)	Y118N	probably damaging	Het
Nek11	A	T	9: 105,295,372 (GRCm38)		probably null	Het
Notch4	T	C	17: 34,584,496 (GRCm38)	V1463A	possibly damaging	Het
Nrcam	T	C	12: 44,564,125 (GRCm38)	I536T	probably benign	Het
Olfr771	T	C	10: 129,160,465 (GRCm38)	Y173C	probably benign	Het
Pbld1	A	T	10: 63,076,447 (GRCm38)	T285S	probably benign	Het
Pcdhgb8	A	T	18: 37,763,124 (GRCm38)	T416S	possibly damaging	Het
Plekhg6	T	C	6: 125,374,560 (GRCm38)	D242G	probably damaging	Het
Pnmt	T	A	11: 98,387,754 (GRCm38)	V182D	probably benign	Het
Ppp1r13b	G	T	12: 111,833,437 (GRCm38)	N758K	probably damaging	Het
Prex2	A	G	1: 11,170,575 (GRCm38)		probably benign	Het
Prss3	A	T	6: 41,377,578 (GRCm38)	L7Q	probably damaging	Het
Prss43	T	A	9: 110,830,978 (GRCm38)	L370Q	probably damaging	Het
Rac1	A	T	5: 143,508,130 (GRCm38)	V104E	probably damaging	Het
Rgs9	T	C	11: 109,275,623 (GRCm38)	Y107C	probably damaging	Het
Rnase13	C	T	14: 51,922,483 (GRCm38)	W66*	probably null	Het
Rrp1b	G	A	17: 32,051,714 (GRCm38)	V216I	possibly damaging	Het
Serinc1	A	G	10: 57,519,768 (GRCm38)	S309P	probably benign	Het
Serpine3	T	A	14: 62,665,138 (GRCm38)	L66Q	probably damaging	Het
Smc5	C	T	19: 23,213,870 (GRCm38)	V924M	probably damaging	Het
Srgap1	A	T	10: 121,925,640 (GRCm38)		probably benign	Het
Stab1	T	C	14: 31,161,814 (GRCm38)	E262G	possibly damaging	Het
Ston2	A	G	12: 91,639,724 (GRCm38)	*896R	probably null	Het
Syt6	A	G	3: 103,625,625 (GRCm38)	M442V	probably benign	Het
Tap1	T	C	17: 34,189,562 (GRCm38)		probably null	Het
Tbx3	A	C	5: 119,680,559 (GRCm38)	S420R	probably benign	Het
Tespa1	A	T	10: 130,362,447 (GRCm38)	Q446L	probably benign	Het
Tifab	T	C	13: 56,176,295 (GRCm38)	M112V	probably benign	Het
Trpv5	A	T	6: 41,653,258 (GRCm38)	S633T	possibly damaging	Het
Ttn	A	T	2: 76,914,466 (GRCm38)	V5413E	probably damaging	Het
Ttn	T	C	2: 76,853,892 (GRCm38)	K838R	unknown	Het
Tub	C	A	7: 109,029,586 (GRCm38)	N415K		Het
Vmn2r3	T	C	3: 64,274,962 (GRCm38)	M439V	probably benign	Het
Vps13c	A	G	9: 67,943,454 (GRCm38)	D2231G	probably benign	Het
Wbp1	C	T	6: 83,119,932 (GRCm38)	C118Y	unknown	Het
Zdhhc20	C	T	14: 57,890,214 (GRCm38)		probably benign	Het
Zfp217	T	A	2: 170,114,471 (GRCm38)	N869I	probably benign	Het
Zfp677	T	C	17: 21,398,088 (GRCm38)	I469T	probably benign	Het
Zmym2	T	A	14: 56,947,872 (GRCm38)		probably benign	Het
Zzef1	T	G	11: 72,796,576 (GRCm38)	S94A	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
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
R9616:Kdm1b	UTSW	13	47,080,554 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ATGTGGAGACAGATCACGTG -3'
(R):5'- GGGCAACTGTTCCTGGATAAC -3'

Sequencing Primer
(F):5'- ATCACGTGGAGATGTGGTAGCTC -3'
(R):5'- GGCAACTGTTCCTGGATAACTAAATC -3'

Posted On

2021-08-02