Mutagenetix > Incidental Mutation

Incidental Mutation 'R4685:Kdm4b'

353644

Institutional Source

Beutler Lab

Gene Symbol

Kdm4b

Ensembl Gene

ENSMUSG00000024201

Gene Name

lysine (K)-specific demethylase 4B

Synonyms

Jmjd2b, 4732474L06Rik

MMRRC Submission

041936-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4685 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

56633062-56709870 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 56708675 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 1070 (S1070T)

Ref Sequence

ENSEMBL: ENSMUSP00000025036 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025036] [ENSMUST00000086835]

AlphaFold

Q91VY5

Predicted Effect

probably benign
Transcript: ENSMUST00000025036
AA Change: S1070T

PolyPhen 2 Score 0.057 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000025036
Gene: ENSMUSG00000024201
AA Change: S1070T

Domain	Start	End	E-Value	Type
JmjN	14	56	5.88e-17	SMART
low complexity region	61	68	N/A	INTRINSIC
JmjC	143	309	1.19e-59	SMART
low complexity region	349	361	N/A	INTRINSIC
low complexity region	380	399	N/A	INTRINSIC
low complexity region	443	449	N/A	INTRINSIC
low complexity region	481	495	N/A	INTRINSIC
low complexity region	511	537	N/A	INTRINSIC
PHD	719	777	2.5e-5	SMART
PHD	839	895	7.07e-5	SMART
TUDOR	905	962	1.68e-9	SMART
TUDOR	963	1019	7.94e-11	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000086835
AA Change: S1005T

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

SMART Domains

Protein: ENSMUSP00000084045
Gene: ENSMUSG00000024201
AA Change: S1005T

Domain	Start	End	E-Value	Type
JmjN	14	56	5.88e-17	SMART
low complexity region	61	68	N/A	INTRINSIC
JmjC	143	309	1.19e-59	SMART
low complexity region	349	361	N/A	INTRINSIC
low complexity region	380	399	N/A	INTRINSIC
low complexity region	443	449	N/A	INTRINSIC
low complexity region	481	495	N/A	INTRINSIC
low complexity region	511	537	N/A	INTRINSIC
PHD	712	770	2.5e-5	SMART
PHD	832	888	7.07e-5	SMART
TUDOR	898	954	2.31e-12	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000141507
AA Change: S527T

SMART Domains

Protein: ENSMUSP00000116789
Gene: ENSMUSG00000024201
AA Change: S527T

Domain	Start	End	E-Value	Type
PHD	177	235	2.5e-5	SMART
PHD	297	353	7.07e-5	SMART
TUDOR	363	420	1.68e-9	SMART
TUDOR	421	477	7.94e-11	SMART

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 95.0%

Validation Efficiency

97% (71/73)

MGI Phenotype

PHENOTYPE: Mice homozygous for a targeted allele lacking demethylase activity exhibit no gross abnormalities. Mice homozygous for a conditional allele activated in mammary gland epithelial cells exhibit delayed mammary gland development with reduced branching. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2410004P03Rik	T	C	12: 17,057,185 (GRCm39)	D104G	probably damaging	Het
2810021J22Rik	T	C	11: 58,771,750 (GRCm39)	S411P	probably damaging	Het
Adcy2	T	C	13: 68,876,024 (GRCm39)	R493G	probably benign	Het
Adcy8	A	G	15: 64,609,287 (GRCm39)	I874T	probably benign	Het
Ano2	G	T	6: 125,957,087 (GRCm39)	E619*	probably null	Het
Apob	A	G	12: 8,056,456 (GRCm39)	K1613R	probably benign	Het
Arhgef10	T	A	8: 15,006,963 (GRCm39)	F476Y	probably damaging	Het
Bmf	G	A	2: 118,377,283 (GRCm39)	A74V	probably damaging	Het
Cadps	T	C	14: 12,467,139 (GRCm38)	E925G	possibly damaging	Het
Ccdc162	T	C	10: 41,557,682 (GRCm39)	D181G	possibly damaging	Het
Ccdc85c	A	T	12: 108,173,434 (GRCm39)	C387S	probably benign	Het
Cntnap5a	T	C	1: 116,374,410 (GRCm39)	V974A	possibly damaging	Het
Cplx3	T	A	9: 57,516,483 (GRCm39)	I407F	probably damaging	Het
Dnah7b	T	C	1: 46,250,488 (GRCm39)	F1703S	probably damaging	Het
Dsg3	C	A	18: 20,672,793 (GRCm39)	D821E	probably benign	Het
Ecel1	G	T	1: 87,080,668 (GRCm39)		probably null	Het
Edn1	A	T	13: 42,458,729 (GRCm39)		probably null	Het
Egfr	G	A	11: 16,808,980 (GRCm39)	C58Y	probably damaging	Het
Fam184a	T	C	10: 53,574,596 (GRCm39)	N282D	probably benign	Het
Fhit	T	A	14: 9,870,091 (GRCm38)	Q63L	probably damaging	Het
Gabarapl2	T	C	8: 112,669,150 (GRCm39)	V36A	probably benign	Het
Glis1	T	C	4: 107,424,842 (GRCm39)	V151A	probably benign	Het
Gm12695	A	G	4: 96,650,217 (GRCm39)	S210P	probably damaging	Het
Gpat4	TAGAAGA	TAGA	8: 23,672,865 (GRCm39)		probably benign	Het
H2-M10.4	G	A	17: 36,772,688 (GRCm39)	A98V	probably benign	Het
Hhat	C	A	1: 192,277,362 (GRCm39)	G366C	probably damaging	Het
Hydin	C	A	8: 111,189,154 (GRCm39)	A1186E	probably damaging	Het
Itgb2	T	A	10: 77,385,937 (GRCm39)		probably null	Het
Kank1	C	T	19: 25,387,398 (GRCm39)	A329V	possibly damaging	Het
Kyat1	A	G	2: 30,078,277 (GRCm39)	Y101H	probably damaging	Het
Map4k5	T	C	12: 69,858,140 (GRCm39)	K679R	probably benign	Het
Mill1	A	T	7: 17,989,853 (GRCm39)	D45V	probably damaging	Het
Myo3a	T	A	2: 22,412,233 (GRCm39)	Y743N	probably damaging	Het
Nox4	C	G	7: 86,946,716 (GRCm39)	I137M	probably benign	Het
Odf4	A	G	11: 68,813,665 (GRCm39)		probably null	Het
Ostf1	A	T	19: 18,558,652 (GRCm39)	D210E	probably damaging	Het
Paxip1	A	T	5: 27,966,675 (GRCm39)		probably null	Het
Pitrm1	A	G	13: 6,606,578 (GRCm39)	T211A	probably benign	Het
Pla2g4f	A	G	2: 120,135,496 (GRCm39)	S393P	probably damaging	Het
Plppr3	T	C	10: 79,703,359 (GRCm39)	T42A	probably damaging	Het
Plxna4	C	A	6: 32,142,779 (GRCm39)	G1559W	probably damaging	Het
Ppp1r13l	T	C	7: 19,109,308 (GRCm39)		probably null	Het
Prex1	C	T	2: 166,480,252 (GRCm39)	V163M	probably damaging	Het
Prl6a1	A	G	13: 27,500,307 (GRCm39)	T93A	probably benign	Het
Psg16	T	C	7: 16,824,459 (GRCm39)	V81A	probably benign	Het
Rbm33	A	T	5: 28,613,280 (GRCm39)		probably benign	Het
Rest	C	T	5: 77,423,090 (GRCm39)	P298L	possibly damaging	Het
Rhobtb3	G	A	13: 76,027,051 (GRCm39)	R441*	probably null	Het
Rims4	T	A	2: 163,706,914 (GRCm39)	K155*	probably null	Het
Rps6kb1	C	T	11: 86,410,713 (GRCm39)		probably null	Het
Ryr2	T	C	13: 11,707,532 (GRCm39)	D2835G	probably damaging	Het
Sc5d	C	T	9: 42,169,946 (GRCm39)	V92I	probably benign	Het
Sell	A	T	1: 163,893,829 (GRCm39)	I175F	probably damaging	Het
Serpinb6d	A	G	13: 33,855,211 (GRCm39)	D295G	probably damaging	Het
Sphk1	A	G	11: 116,426,106 (GRCm39)	D96G	probably damaging	Het
Spns3	A	T	11: 72,428,096 (GRCm39)	V228D	probably damaging	Het
Sspo	A	G	6: 48,469,828 (GRCm39)	S4500G	probably damaging	Het
Syt9	T	A	7: 107,035,678 (GRCm39)	C232S	possibly damaging	Het
Terf1	A	G	1: 15,889,185 (GRCm39)	I176V	possibly damaging	Het
Tln2	C	T	9: 67,209,854 (GRCm39)	A428T	probably damaging	Het
Tmprss7	T	C	16: 45,499,711 (GRCm39)	N321S	probably benign	Het
Tomm40	A	G	7: 19,435,761 (GRCm39)	I323T	probably benign	Het
Try5	T	A	6: 41,288,233 (GRCm39)	Q240L	possibly damaging	Het
Vmn1r213	A	T	13: 23,195,800 (GRCm39)	I128L	probably benign	Het
Vmn2r80	T	C	10: 79,030,162 (GRCm39)	F663L	possibly damaging	Het
Znfx1	T	A	2: 166,880,950 (GRCm39)	Y278F	probably damaging	Het
Zpbp2	A	G	11: 98,442,117 (GRCm39)		probably benign	Het

Other mutations in Kdm4b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01293:Kdm4b	APN	17	56,660,019 (GRCm39)	missense	probably benign	0.28
IGL01408:Kdm4b	APN	17	56,660,518 (GRCm39)	splice site	probably benign
IGL01610:Kdm4b	APN	17	56,660,522 (GRCm39)	splice site	probably benign
IGL01936:Kdm4b	APN	17	56,704,355 (GRCm39)	missense	probably damaging	1.00
IGL01964:Kdm4b	APN	17	56,696,256 (GRCm39)	splice site	probably null
IGL02151:Kdm4b	APN	17	56,703,234 (GRCm39)	missense	probably benign	0.05
IGL02596:Kdm4b	APN	17	56,706,706 (GRCm39)	missense	probably benign	0.14
IGL02975:Kdm4b	APN	17	56,682,996 (GRCm39)	splice site	probably null
IGL03172:Kdm4b	APN	17	56,708,649 (GRCm39)	missense	probably damaging	0.98
Coelestinum	UTSW	17	56,660,091 (GRCm39)	missense	probably benign	0.31
mistflower	UTSW	17	56,696,564 (GRCm39)	missense	possibly damaging	0.65
R0193:Kdm4b	UTSW	17	56,700,952 (GRCm39)	missense	probably benign	0.04
R0311:Kdm4b	UTSW	17	56,693,200 (GRCm39)	missense	probably benign	0.42
R0331:Kdm4b	UTSW	17	56,693,289 (GRCm39)	splice site	probably benign
R1109:Kdm4b	UTSW	17	56,706,430 (GRCm39)	missense	probably damaging	0.99
R1499:Kdm4b	UTSW	17	56,707,025 (GRCm39)	missense	probably damaging	1.00
R1895:Kdm4b	UTSW	17	56,704,340 (GRCm39)	missense	probably damaging	1.00
R1985:Kdm4b	UTSW	17	56,708,302 (GRCm39)	missense	probably damaging	1.00
R2087:Kdm4b	UTSW	17	56,696,564 (GRCm39)	missense	possibly damaging	0.65
R2185:Kdm4b	UTSW	17	56,700,750 (GRCm39)	missense	probably benign	0.00
R2904:Kdm4b	UTSW	17	56,662,884 (GRCm39)	missense	probably benign	0.03
R3792:Kdm4b	UTSW	17	56,662,944 (GRCm39)	missense	probably damaging	1.00
R3897:Kdm4b	UTSW	17	56,703,955 (GRCm39)	missense	probably damaging	1.00
R4661:Kdm4b	UTSW	17	56,706,459 (GRCm39)	missense	probably damaging	1.00
R4716:Kdm4b	UTSW	17	56,693,178 (GRCm39)	missense	probably benign	0.10
R4790:Kdm4b	UTSW	17	56,708,618 (GRCm39)	missense	probably damaging	0.97
R4864:Kdm4b	UTSW	17	56,660,091 (GRCm39)	missense	probably benign	0.31
R5700:Kdm4b	UTSW	17	56,658,700 (GRCm39)	missense	possibly damaging	0.93
R5963:Kdm4b	UTSW	17	56,706,732 (GRCm39)	missense	probably damaging	1.00
R6003:Kdm4b	UTSW	17	56,703,916 (GRCm39)	missense	probably damaging	1.00
R6029:Kdm4b	UTSW	17	56,703,576 (GRCm39)	missense	probably damaging	0.98
R6769:Kdm4b	UTSW	17	56,658,754 (GRCm39)	missense	possibly damaging	0.54
R6771:Kdm4b	UTSW	17	56,658,754 (GRCm39)	missense	possibly damaging	0.54
R6927:Kdm4b	UTSW	17	56,706,435 (GRCm39)	missense	probably damaging	1.00
R7041:Kdm4b	UTSW	17	56,703,592 (GRCm39)	missense	probably damaging	0.96
R7230:Kdm4b	UTSW	17	56,676,155 (GRCm39)	missense	probably damaging	1.00
R7275:Kdm4b	UTSW	17	56,703,333 (GRCm39)	missense	probably damaging	0.99
R7454:Kdm4b	UTSW	17	56,696,639 (GRCm39)	missense	probably benign	0.00
R7455:Kdm4b	UTSW	17	56,703,657 (GRCm39)	missense	probably damaging	0.98
R7457:Kdm4b	UTSW	17	56,703,319 (GRCm39)	missense	probably damaging	1.00
R8171:Kdm4b	UTSW	17	56,696,534 (GRCm39)	missense	probably damaging	0.99
R8367:Kdm4b	UTSW	17	56,662,875 (GRCm39)	missense	probably damaging	1.00
R8524:Kdm4b	UTSW	17	56,706,384 (GRCm39)	missense	probably damaging	1.00
R8810:Kdm4b	UTSW	17	56,706,771 (GRCm39)	missense	probably damaging	1.00
R9260:Kdm4b	UTSW	17	56,701,775 (GRCm39)	missense	probably benign
R9459:Kdm4b	UTSW	17	56,706,509 (GRCm39)	missense	probably benign	0.15
R9466:Kdm4b	UTSW	17	56,696,548 (GRCm39)	missense	probably benign	0.04
R9559:Kdm4b	UTSW	17	56,693,228 (GRCm39)	missense	probably damaging	1.00
X0024:Kdm4b	UTSW	17	56,708,278 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TATGGTCCCAAGGGGCTTTG -3'
(R):5'- ATCTGTCACAGGAGGCTCTAG -3'

Sequencing Primer
(F):5'- TTTGCCAGGGAGACAACC -3'
(R):5'- CCCTTAGCACCTTTAGGAGAAGAG -3'

Posted On

2015-10-21