Mutagenetix > Incidental Mutation

Incidental Mutation 'R7454:Kdm4b'

578035

Institutional Source

Beutler Lab

Gene Symbol

Kdm4b

Ensembl Gene

ENSMUSG00000024201

Gene Name

lysine (K)-specific demethylase 4B

Synonyms

Jmjd2b, 4732474L06Rik

MMRRC Submission

045528-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7454 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

56633062-56709870 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 56696639 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Threonine at position 452 (P452T)

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: P452T

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000025036
Gene: ENSMUSG00000024201
AA Change: P452T

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: P452T

PolyPhen 2 Score 0.783 (Sensitivity: 0.85; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000084045
Gene: ENSMUSG00000024201
AA Change: P452T

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

probably benign
Transcript: ENSMUST00000141507

SMART Domains

Protein: ENSMUSP00000116789
Gene: ENSMUSG00000024201

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: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

100% (90/90)

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: 89 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2510002D24Rik	A	G	16: 18,655,601 (GRCm39)	E57G	possibly damaging	Het
4932414N04Rik	C	A	2: 68,518,648 (GRCm39)	T159K	unknown	Het
Adamts10	T	A	17: 33,763,979 (GRCm39)	F616L	possibly damaging	Het
Adtrp	G	A	13: 41,981,791 (GRCm39)	S26L	unknown	Het
Alpk3	A	C	7: 80,728,310 (GRCm39)	E480A	probably benign	Het
Anks6	T	C	4: 47,038,919 (GRCm39)	T529A	unknown	Het
Arl4d	A	G	11: 101,557,486 (GRCm39)	H4R	probably benign	Het
Ash1l	A	G	3: 88,891,172 (GRCm39)	H1017R	probably benign	Het
Bbs12	T	C	3: 37,375,102 (GRCm39)	S517P	possibly damaging	Het
Bcl11b	C	A	12: 107,882,467 (GRCm39)	R616L	possibly damaging	Het
Bean1	G	A	8: 104,937,658 (GRCm39)	G79D	probably damaging	Het
Bicra	C	G	7: 15,706,059 (GRCm39)	G1461R	probably benign	Het
Bptf	T	C	11: 106,935,466 (GRCm39)	T124A	probably benign	Het
Btnl4	A	T	17: 34,691,348 (GRCm39)	V312E	probably benign	Het
Ccdc7a	A	G	8: 129,670,997 (GRCm39)	M503T	unknown	Het
Celf5	T	C	10: 81,318,357 (GRCm39)	E28G	probably damaging	Het
Cilp2	G	A	8: 70,336,040 (GRCm39)	L350F	probably damaging	Het
Clec4a2	T	C	6: 123,119,411 (GRCm39)	I245T	probably damaging	Het
Ctnnal1	A	T	4: 56,844,544 (GRCm39)	V140D	probably damaging	Het
Dennd4a	A	C	9: 64,759,852 (GRCm39)	H319P	probably damaging	Het
Dlgap3	G	T	4: 127,128,852 (GRCm39)	L857F	probably null	Het
Dnah6	T	A	6: 73,189,475 (GRCm39)	T58S	probably damaging	Het
Dnah7a	T	A	1: 53,557,923 (GRCm39)	M2164L	probably benign	Het
Dspp	T	A	5: 104,323,476 (GRCm39)	H206Q	probably benign	Het
Dzip1l	G	A	9: 99,541,727 (GRCm39)	V443M	possibly damaging	Het
Erc2	A	G	14: 28,024,948 (GRCm39)	H939R	possibly damaging	Het
Fam149a	G	T	8: 45,801,583 (GRCm39)	H513N	probably benign	Het
Fam171a2	T	C	11: 102,330,543 (GRCm39)	T280A	possibly damaging	Het
Fkbp5	A	C	17: 28,634,999 (GRCm39)	V170G	probably damaging	Het
Fnbp4	ACCACCTCCACCTCCACCTCC	ACCACCTCCACCTCCACCTCCACCTCC	2: 90,608,159 (GRCm39)		probably benign	Het
Fzd2	T	C	11: 102,495,955 (GRCm39)	F133S	probably damaging	Het
Galm	A	G	17: 80,445,550 (GRCm39)	N100S	possibly damaging	Het
Gbp2b	T	A	3: 142,303,920 (GRCm39)	I5N	possibly damaging	Het
Gga2	T	C	7: 121,601,369 (GRCm39)	R245G	probably benign	Het
Gm10053	A	G	19: 24,853,264 (GRCm39)	T50A	probably benign	Het
Gm1110	T	C	9: 26,831,945 (GRCm39)	T69A	probably benign	Het
Heatr5a	T	C	12: 52,008,326 (GRCm39)	S6G	probably benign	Het
Hmcn1	A	G	1: 150,439,355 (GRCm39)	S5610P	probably damaging	Het
Hmgb4	A	G	4: 128,154,199 (GRCm39)	V123A	probably damaging	Het
Itgal	C	A	7: 126,926,936 (GRCm39)	Q943K	probably benign	Het
Jakmip1	C	A	5: 37,332,498 (GRCm39)	D1059E	probably damaging	Het
Jazf1	T	C	6: 52,870,929 (GRCm39)		probably null	Het
Kat6a	A	G	8: 23,425,788 (GRCm39)	E1111G	possibly damaging	Het
Krit1	T	C	5: 3,862,474 (GRCm39)	Y210H	probably damaging	Het
Krtap6-2	A	T	16: 89,216,800 (GRCm39)	Y56N	unknown	Het
Lig1	A	T	7: 13,022,647 (GRCm39)	D158V	probably damaging	Het
Lmo1	A	T	7: 108,739,873 (GRCm39)	L94Q	probably benign	Het
Lrrc30	A	T	17: 67,939,238 (GRCm39)	L114H	probably damaging	Het
Ltn1	T	C	16: 87,194,700 (GRCm39)	I1400V	probably benign	Het
Mark3	T	C	12: 111,570,961 (GRCm39)	I87T	probably damaging	Het
Mfrp	G	T	9: 44,016,480 (GRCm39)	V392F	possibly damaging	Het
Mrgprg	A	G	7: 143,318,872 (GRCm39)	L80P	probably damaging	Het
Ndufaf3	A	T	9: 108,444,125 (GRCm39)	M1K	probably null	Het
Nme7	T	A	1: 164,208,217 (GRCm39)	L295*	probably null	Het
Noct	G	T	3: 51,157,151 (GRCm39)	C163F	probably damaging	Het
Or11h4b	T	A	14: 50,918,281 (GRCm39)	Q270L	possibly damaging	Het
Or13a26	A	T	7: 140,284,547 (GRCm39)	I128F	probably damaging	Het
Or4b1	T	A	2: 89,979,763 (GRCm39)	I196F	possibly damaging	Het
Or5ak22	T	A	2: 85,229,955 (GRCm39)	K307N	probably damaging	Het
Or6c203	T	A	10: 129,010,324 (GRCm39)	T189S	probably damaging	Het
Or8g2	A	G	9: 39,821,200 (GRCm39)	I34V	probably benign	Het
Patz1	C	T	11: 3,248,297 (GRCm39)		probably benign	Het
Per3	A	G	4: 151,097,185 (GRCm39)	L780P	probably benign	Het
Pira1	T	G	7: 3,738,509 (GRCm39)	E622D	probably benign	Het
Pla2g4a	T	C	1: 149,748,441 (GRCm39)	M256V	possibly damaging	Het
Pnliprp1	A	G	19: 58,729,532 (GRCm39)	K395R	probably benign	Het
Poc5	G	T	13: 96,537,340 (GRCm39)	G242V	possibly damaging	Het
Ppfia4	A	G	1: 134,251,873 (GRCm39)	S434P	possibly damaging	Het
Prss42	A	G	9: 110,627,897 (GRCm39)	N110S	probably benign	Het
Ralgapb	T	A	2: 158,274,822 (GRCm39)	I241N	possibly damaging	Het
Rbak	A	C	5: 143,159,528 (GRCm39)	Y508*	probably null	Het
S1pr2	G	T	9: 20,878,845 (GRCm39)	R328S	possibly damaging	Het
Sap130	T	C	18: 31,783,565 (GRCm39)	M214T	probably benign	Het
Slc46a1	T	A	11: 78,357,337 (GRCm39)	V130E	probably damaging	Het
Smc4	A	T	3: 68,925,457 (GRCm39)	H343L	probably benign	Het
Tarbp1	C	A	8: 127,184,416 (GRCm39)	R500L	probably benign	Het
Tasor2	A	G	13: 3,635,332 (GRCm39)	S492P	probably benign	Het
Tgfbr3	A	T	5: 107,362,894 (GRCm39)	H39Q	probably damaging	Het
Tpp2	T	C	1: 43,993,819 (GRCm39)	S235P	probably benign	Het
Trbc2	G	T	6: 41,523,763 (GRCm39)	R33M		Het
Trim3	C	T	7: 105,268,765 (GRCm39)	R63Q	probably damaging	Het
Ttc28	T	C	5: 111,433,350 (GRCm39)	V2128A	probably benign	Het
Ttn	C	T	2: 76,556,162 (GRCm39)	R30281H	probably damaging	Het
Ttn	T	A	2: 76,774,483 (GRCm39)	Q2187L	unknown	Het
Ttyh3	T	C	5: 140,615,180 (GRCm39)	S403G	possibly damaging	Het
Vmn2r112	A	T	17: 22,822,288 (GRCm39)	D322V	probably benign	Het
Wdr38	C	T	2: 38,888,352 (GRCm39)		probably benign	Het
Xrn1	T	A	9: 95,930,411 (GRCm39)	S1543R	probably benign	Het
Zbtb8b	G	A	4: 129,326,562 (GRCm39)	T201I	possibly damaging	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
R4685:Kdm4b	UTSW	17	56,708,675 (GRCm39)	missense	probably benign	0.06
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
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'- AGCATTCTGCCCATCCTGTG -3'
(R):5'- CCTGTGCAGCACAAGAAAGC -3'

Sequencing Primer
(F):5'- CCACCCTAGACTGCGTCTG -3'
(R):5'- AAGCTGGGACACGGTGC -3'

Posted On

2019-10-07