Mutagenetix > Incidental Mutation

Incidental Mutation 'R5700:Kdm4b'

450872

Institutional Source

Beutler Lab

Gene Symbol

Kdm4b

Ensembl Gene

ENSMUSG00000024201

Gene Name

lysine (K)-specific demethylase 4B

Synonyms

Jmjd2b, 4732474L06Rik

MMRRC Submission

043328-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5700 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

56326062-56402870 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 56351700 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 15 (I15T)

Ref Sequence

ENSEMBL: ENSMUSP00000118089 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025036] [ENSMUST00000086835] [ENSMUST00000139679]

AlphaFold

Q91VY5

Predicted Effect

possibly damaging
Transcript: ENSMUST00000025036
AA Change: I15T

PolyPhen 2 Score 0.715 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000025036
Gene: ENSMUSG00000024201
AA Change: I15T

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

possibly damaging
Transcript: ENSMUST00000086835
AA Change: I15T

PolyPhen 2 Score 0.551 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000084045
Gene: ENSMUSG00000024201
AA Change: I15T

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

possibly damaging
Transcript: ENSMUST00000139679
AA Change: I15T

PolyPhen 2 Score 0.927 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000118089
Gene: ENSMUSG00000024201
AA Change: I15T

Domain	Start	End	E-Value	Type
JmjN	14	56	5.88e-17	SMART
low complexity region	61	68	N/A	INTRINSIC
Pfam:JmjC	176	208	5.8e-13	PFAM

Meta Mutation Damage Score

0.9501

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.4%

Validation Efficiency

98% (50/51)

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: 49 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc2	A	T	19: 43,798,194	Q155L	probably benign	Het
Acadvl	A	C	11: 70,013,203	Y242D	probably damaging	Het
Armc8	A	G	9: 99,496,149		probably null	Het
Barx2	A	T	9: 31,858,765	F156I	probably damaging	Het
Best1	T	C	19: 9,997,199		probably benign	Het
Btbd8	T	C	5: 107,503,648	S136P	possibly damaging	Het
Btla	T	A	16: 45,250,573	Y298*	probably null	Het
Casr	T	A	16: 36,509,617	I452F	probably damaging	Het
Ccser1	C	A	6: 61,311,276	P141H	probably benign	Het
Cr2	A	G	1: 195,159,757	V296A	probably damaging	Het
Csl	T	A	10: 99,759,015	I63F	probably damaging	Het
Dbt	G	A	3: 116,520,303	V40M	probably damaging	Het
Fam53b	A	T	7: 132,760,020	L93Q	probably damaging	Het
Fdps	T	C	3: 89,095,649	I105V	probably damaging	Het
Gm4884	A	G	7: 41,043,219	D204G	probably benign	Het
Gm5592	A	G	7: 41,158,579		probably benign	Het
Gm7367	A	T	7: 60,155,762		noncoding transcript	Het
Grid2	T	A	6: 64,094,432	V413D	possibly damaging	Het
Hgf	C	T	5: 16,610,124	P471L	probably damaging	Het
Hoxc9	T	C	15: 102,981,881	Y77H	possibly damaging	Het
Hs6st3	C	T	14: 119,138,787	R125*	probably null	Het
Klhl1	T	C	14: 96,518,040	N93S	probably benign	Het
Klhl6	G	A	16: 19,957,218	Q197*	probably null	Het
Medag	T	C	5: 149,422,217	V7A	probably benign	Het
Mptx2	G	A	1: 173,274,847	L92F	probably benign	Het
Nckap5	C	T	1: 125,976,925		probably null	Het
Obscn	T	C	11: 59,133,194	K550R	probably benign	Het
Olfr1369-ps1	T	A	13: 21,116,001	V103E	probably damaging	Het
Olfr193	T	A	16: 59,109,993	I206F	probably damaging	Het
Olfr716	A	G	7: 107,147,541	N75S	probably benign	Het
Olfr8	T	C	10: 78,955,484	I93T	probably damaging	Het
Parp6	T	C	9: 59,624,727	S101P	probably damaging	Het
Plcd3	T	C	11: 103,073,763	N594S	probably benign	Het
Plscr5	A	T	9: 92,205,511	K178*	probably null	Het
Ppp2r1b	T	C	9: 50,878,157	Y443H	probably damaging	Het
Pqlc2	C	T	4: 139,300,254	S259N	probably damaging	Het
Prnd	G	A	2: 131,953,343	V128I	probably benign	Het
Rftn1	G	T	17: 50,002,669	P156Q	probably damaging	Het
Scmh1	T	C	4: 120,516,946	V445A	probably benign	Het
Serpinb6c	A	T	13: 33,899,308	M41K	probably damaging	Het
Spns1	A	G	7: 126,372,469	V303A	possibly damaging	Het
Ston1	T	A	17: 88,644,339	S639R	probably damaging	Het
Thbs4	T	C	13: 92,776,953	D153G	probably benign	Het
Timm44	T	C	8: 4,274,171	Y36C	probably damaging	Het
Trim34b	G	T	7: 104,336,411	V418F	probably damaging	Het
Vmn1r72	C	T	7: 11,670,423	V33M	probably damaging	Het
Zcchc7	T	C	4: 44,931,084	V412A	probably benign	Het
Zfand1	T	A	3: 10,341,019	N210I	probably damaging	Het
Zfhx3	A	G	8: 108,933,867	H1251R	probably damaging	Het

Other mutations in Kdm4b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01293:Kdm4b	APN	17	56353019	missense	probably benign	0.28
IGL01408:Kdm4b	APN	17	56353518	splice site	probably benign
IGL01610:Kdm4b	APN	17	56353522	splice site	probably benign
IGL01936:Kdm4b	APN	17	56397355	missense	probably damaging	1.00
IGL01964:Kdm4b	APN	17	56389256	splice site	probably null
IGL02151:Kdm4b	APN	17	56396234	missense	probably benign	0.05
IGL02596:Kdm4b	APN	17	56399706	missense	probably benign	0.14
IGL02975:Kdm4b	APN	17	56375996	splice site	probably null
IGL03172:Kdm4b	APN	17	56401649	missense	probably damaging	0.98
Coelestinum	UTSW	17	56353091	missense	probably benign	0.31
mistflower	UTSW	17	56389564	missense	possibly damaging	0.65
R0193:Kdm4b	UTSW	17	56393952	missense	probably benign	0.04
R0311:Kdm4b	UTSW	17	56386200	missense	probably benign	0.42
R0331:Kdm4b	UTSW	17	56386289	splice site	probably benign
R1109:Kdm4b	UTSW	17	56399430	missense	probably damaging	0.99
R1499:Kdm4b	UTSW	17	56400025	missense	probably damaging	1.00
R1895:Kdm4b	UTSW	17	56397340	missense	probably damaging	1.00
R1985:Kdm4b	UTSW	17	56401302	missense	probably damaging	1.00
R2087:Kdm4b	UTSW	17	56389564	missense	possibly damaging	0.65
R2185:Kdm4b	UTSW	17	56393750	missense	probably benign	0.00
R2904:Kdm4b	UTSW	17	56355884	missense	probably benign	0.03
R3792:Kdm4b	UTSW	17	56355944	missense	probably damaging	1.00
R3897:Kdm4b	UTSW	17	56396955	missense	probably damaging	1.00
R4661:Kdm4b	UTSW	17	56399459	missense	probably damaging	1.00
R4685:Kdm4b	UTSW	17	56401675	missense	probably benign	0.06
R4716:Kdm4b	UTSW	17	56386178	missense	probably benign	0.10
R4790:Kdm4b	UTSW	17	56401618	missense	probably damaging	0.97
R4864:Kdm4b	UTSW	17	56353091	missense	probably benign	0.31
R5963:Kdm4b	UTSW	17	56399732	missense	probably damaging	1.00
R6003:Kdm4b	UTSW	17	56396916	missense	probably damaging	1.00
R6029:Kdm4b	UTSW	17	56396576	missense	probably damaging	0.98
R6769:Kdm4b	UTSW	17	56351754	missense	possibly damaging	0.54
R6771:Kdm4b	UTSW	17	56351754	missense	possibly damaging	0.54
R6927:Kdm4b	UTSW	17	56399435	missense	probably damaging	1.00
R7041:Kdm4b	UTSW	17	56396592	missense	probably damaging	0.96
R7230:Kdm4b	UTSW	17	56369155	missense	probably damaging	1.00
R7275:Kdm4b	UTSW	17	56396333	missense	probably damaging	0.99
R7454:Kdm4b	UTSW	17	56389639	missense	probably benign	0.00
R7455:Kdm4b	UTSW	17	56396657	missense	probably damaging	0.98
R7457:Kdm4b	UTSW	17	56396319	missense	probably damaging	1.00
R8171:Kdm4b	UTSW	17	56389534	missense	probably damaging	0.99
R8367:Kdm4b	UTSW	17	56355875	missense	probably damaging	1.00
R8524:Kdm4b	UTSW	17	56399384	missense	probably damaging	1.00
R8810:Kdm4b	UTSW	17	56399771	missense	probably damaging	1.00
R9260:Kdm4b	UTSW	17	56394775	missense	probably benign
R9459:Kdm4b	UTSW	17	56399509	missense	probably benign	0.15
R9466:Kdm4b	UTSW	17	56389548	missense	probably benign	0.04
R9559:Kdm4b	UTSW	17	56386228	missense	probably damaging	1.00
X0024:Kdm4b	UTSW	17	56401278	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TACTCAACCGGTGTCACCTTG -3'
(R):5'- TCCATGTTTAAGAAGGTCGGGG -3'

Sequencing Primer
(F):5'- CGGTGTCACCTTGGCTTTTGAC -3'
(R):5'- TTTAAGAAGGTCGGGGAGGCAG -3'

Posted On

2017-01-03