Mutagenetix > Incidental Mutation

Incidental Mutation 'R7260:Kdm4d'

564547

Institutional Source

Beutler Lab

Gene Symbol

Kdm4d

Ensembl Gene

ENSMUSG00000053914

Gene Name

lysine (K)-specific demethylase 4D

Synonyms

Jmjd2d

MMRRC Submission

045352-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7260 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

14373844-14411778 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 14374454 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 468 (D468G)

Ref Sequence

ENSEMBL: ENSMUSP00000061632 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000058796] [ENSMUST00000115647]

AlphaFold

Q3U2K5

Predicted Effect

probably benign
Transcript: ENSMUST00000058796
AA Change: D468G

PolyPhen 2 Score 0.049 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000061632
Gene: ENSMUSG00000053914
AA Change: D468G

Domain	Start	End	E-Value	Type
Pfam:JmjN	16	50	3.3e-15	PFAM
JmjC	143	309	2.3e-57	SMART
low complexity region	370	383	N/A	INTRINSIC
low complexity region	417	434	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000115647

SMART Domains

Protein: ENSMUSP00000111311
Gene: ENSMUSG00000053914

Domain	Start	End	E-Value	Type
Pfam:JmjN	16	50	1.1e-16	PFAM
JmjC	143	309	2.3e-57	SMART
low complexity region	370	383	N/A	INTRINSIC
low complexity region	417	434	N/A	INTRINSIC

Coding Region Coverage

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

Validation Efficiency

98% (78/80)

MGI Phenotype

PHENOTYPE: Mice homozygous for a knock-out allele exhibit accumulation of histone 3 methylation in spermatids, a transient increase in testes size, wider tubules, occasional male germ cell apoptosis, and decreased body weight. However, fertility is normal. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310057J18Rik	A	G	10: 28,849,882 (GRCm39)	S293P	probably benign	Het
Actn2	T	C	13: 12,291,376 (GRCm39)	N676S	probably benign	Het
Amfr	C	T	8: 94,702,776 (GRCm39)	M463I	possibly damaging	Het
Ankdd1a	G	T	9: 65,411,834 (GRCm39)	A325D	probably damaging	Het
Apba2	A	G	7: 64,389,493 (GRCm39)	D463G	probably damaging	Het
Arid5b	A	G	10: 67,933,637 (GRCm39)	V755A	probably damaging	Het
Boc	A	T	16: 44,310,533 (GRCm39)	F796I		Het
Ccnt1	G	A	15: 98,463,005 (GRCm39)	Q56*	probably null	Het
Cd248	T	A	19: 5,119,383 (GRCm39)	Y410*	probably null	Het
Chd9	T	A	8: 91,721,171 (GRCm39)	N986K	unknown	Het
Col6a6	T	C	9: 105,661,168 (GRCm39)	T314A	probably benign	Het
Cpped1	A	G	16: 11,646,327 (GRCm39)	F142L	possibly damaging	Het
Csmd1	C	T	8: 16,050,574 (GRCm39)	A2221T	probably damaging	Het
Cyp2c69	C	A	19: 39,831,344 (GRCm39)	V490L	probably benign	Het
Cyrib	A	T	15: 63,829,438 (GRCm39)	F23L	possibly damaging	Het
Dcst2	T	C	3: 89,273,593 (GRCm39)	F157S	probably damaging	Het
Ddx54	G	T	5: 120,764,985 (GRCm39)	R788L	probably benign	Het
Dnah1	T	C	14: 30,991,343 (GRCm39)	Y3145C	probably damaging	Het
Dnah14	A	T	1: 181,534,309 (GRCm39)	R2320W	probably damaging	Het
Dnai3	T	A	3: 145,752,295 (GRCm39)	M794L	probably benign	Het
Emilin2	T	C	17: 71,581,785 (GRCm39)	T314A	probably benign	Het
Eml2	A	G	7: 18,934,515 (GRCm39)	S405G	probably benign	Het
Ephb2	A	G	4: 136,498,885 (GRCm39)	F65L	probably damaging	Het
Fbn2	T	C	18: 58,199,188 (GRCm39)	D1360G	probably benign	Het
Fbxo22	A	G	9: 55,125,754 (GRCm39)	T206A	probably benign	Het
Filip1l	A	G	16: 57,391,287 (GRCm39)	E625G	probably damaging	Het
Gen1	A	C	12: 11,306,849 (GRCm39)	M172R	probably damaging	Het
Gk5	A	G	9: 96,001,663 (GRCm39)	K54E	probably benign	Het
Glis3	T	C	19: 28,508,802 (GRCm39)	E394G	probably benign	Het
Helq	T	A	5: 100,939,793 (GRCm39)	E373D	probably damaging	Het
Ighv1-74	A	G	12: 115,766,372 (GRCm39)	F83L	probably benign	Het
Ints15	A	G	5: 143,297,594 (GRCm39)	V151A	probably benign	Het
Iqcn	T	C	8: 71,161,397 (GRCm39)	Y197H	probably benign	Het
Kif20b	A	G	19: 34,927,610 (GRCm39)	I957M	probably damaging	Het
Ldhal6b	A	G	17: 5,468,535 (GRCm39)	F133S	possibly damaging	Het
Loxhd1	T	C	18: 77,420,338 (GRCm39)	Y321H	possibly damaging	Het
Ltbp1	A	T	17: 75,373,139 (GRCm39)	M261L	probably benign	Het
Mical2	A	T	7: 111,919,001 (GRCm39)	Q430L	probably benign	Het
Mroh4	A	T	15: 74,479,978 (GRCm39)	N885K	possibly damaging	Het
Ms4a7	A	G	19: 11,299,710 (GRCm39)	Y231H	probably damaging	Het
Msh2	G	T	17: 88,025,047 (GRCm39)	V642F	probably damaging	Het
Muc5b	G	T	7: 141,396,385 (GRCm39)	A166S	unknown	Het
Myo18b	T	C	5: 112,923,154 (GRCm39)	I1868V	probably benign	Het
Nfatc3	T	C	8: 106,835,578 (GRCm39)	S975P	probably benign	Het
Oacyl	T	C	18: 65,831,438 (GRCm39)	L25P	probably damaging	Het
Or12e10	A	G	2: 87,640,731 (GRCm39)	N189S	probably damaging	Het
Or5b109	T	C	19: 13,212,388 (GRCm39)	F258S	probably damaging	Het
Or5w15	T	C	2: 87,568,852 (GRCm39)		probably null	Het
Or6c69	T	A	10: 129,748,156 (GRCm39)		probably benign	Het
Or8a1	T	A	9: 37,642,049 (GRCm39)	I77F	probably damaging	Het
Patj	A	G	4: 98,304,970 (GRCm39)	I275V	possibly damaging	Het
Pdcd11	G	A	19: 47,117,673 (GRCm39)	R1674Q	possibly damaging	Het
Peg10	CCACATCAGGATCCACATCAGGATGCACATCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAG	CCACATCAGGATCCACATCAGGATGCACATCAG	6: 4,756,398 (GRCm39)		probably benign	Het
Phkb	T	A	8: 86,604,759 (GRCm39)	Y55N	probably benign	Het
Pias4	A	G	10: 80,993,302 (GRCm39)	V207A	possibly damaging	Het
Plxna4	C	A	6: 32,216,455 (GRCm39)	R540L	possibly damaging	Het
Psapl1	G	A	5: 36,362,556 (GRCm39)	V383M	probably benign	Het
Rars1	C	A	11: 35,725,281 (GRCm39)	A10S	probably benign	Het
Rhobtb1	A	T	10: 69,106,610 (GRCm39)	K454*	probably null	Het
Rmnd1	A	T	10: 4,364,803 (GRCm39)		probably null	Het
Rnf213	A	G	11: 119,343,401 (GRCm39)	I3589V		Het
Rngtt	T	C	4: 33,356,176 (GRCm39)	S338P	possibly damaging	Het
Sh3bgr	A	G	16: 96,025,681 (GRCm39)	E189G	unknown	Het
Slc30a3	G	A	5: 31,245,690 (GRCm39)	T281I	probably damaging	Het
Smok3c	T	A	5: 138,063,885 (GRCm39)	D457E	possibly damaging	Het
Stard9	C	A	2: 120,537,419 (GRCm39)	Q4274K	possibly damaging	Het
Syne2	G	T	12: 75,991,853 (GRCm39)	L1938F	probably damaging	Het
Tmem70	C	A	1: 16,735,590 (GRCm39)	T20K	possibly damaging	Het
Tnrc6a	A	G	7: 122,785,813 (GRCm39)	E1502G	probably benign	Het
Tpp1	A	T	7: 105,396,704 (GRCm39)	S438T	probably benign	Het
Tubb2a	T	A	13: 34,259,397 (GRCm39)	Q131L	probably damaging	Het
Ube2v1	A	G	2: 167,471,114 (GRCm39)	S26P	probably benign	Het
Unc13a	G	T	8: 72,113,229 (GRCm39)	S207R	possibly damaging	Het
Usp35	T	G	7: 96,969,286 (GRCm39)	D362A	probably damaging	Het
Utp20	A	G	10: 88,587,334 (GRCm39)	I2487T	probably benign	Het
Vmn2r111	T	C	17: 22,778,032 (GRCm39)	N549S	possibly damaging	Het
Vmn2r117	T	A	17: 23,694,359 (GRCm39)	H496L	probably benign	Het
Vmn2r92	C	T	17: 18,387,138 (GRCm39)	A159V	probably damaging	Het
Wiz	T	C	17: 32,578,085 (GRCm39)	K467E	probably damaging	Het
Zfp534	T	C	4: 147,759,461 (GRCm39)	T403A	probably benign	Het
Zswim5	T	C	4: 116,819,843 (GRCm39)	L416P	probably damaging	Het

Other mutations in Kdm4d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01011:Kdm4d	APN	9	14,375,515 (GRCm39)	missense	probably benign	0.10
IGL01114:Kdm4d	APN	9	14,375,493 (GRCm39)	missense	probably damaging	1.00
IGL01609:Kdm4d	APN	9	14,375,714 (GRCm39)	missense	probably damaging	0.99
IGL02342:Kdm4d	APN	9	14,374,860 (GRCm39)	missense	probably damaging	0.99
IGL02513:Kdm4d	APN	9	14,375,850 (GRCm39)	missense	probably benign	0.00
IGL03276:Kdm4d	APN	9	14,375,838 (GRCm39)	missense	probably benign	0.04
IGL03379:Kdm4d	APN	9	14,375,139 (GRCm39)	missense	probably damaging	1.00
R0220:Kdm4d	UTSW	9	14,374,418 (GRCm39)	missense	probably benign
R0755:Kdm4d	UTSW	9	14,375,591 (GRCm39)	missense	probably damaging	0.99
R1195:Kdm4d	UTSW	9	14,374,395 (GRCm39)	missense	probably benign
R1195:Kdm4d	UTSW	9	14,374,395 (GRCm39)	missense	probably benign
R1195:Kdm4d	UTSW	9	14,374,395 (GRCm39)	missense	probably benign
R1455:Kdm4d	UTSW	9	14,375,691 (GRCm39)	missense	probably damaging	0.98
R1552:Kdm4d	UTSW	9	14,375,325 (GRCm39)	missense	probably damaging	1.00
R1692:Kdm4d	UTSW	9	14,375,807 (GRCm39)	missense	probably benign	0.43
R1871:Kdm4d	UTSW	9	14,375,679 (GRCm39)	missense	probably damaging	1.00
R1892:Kdm4d	UTSW	9	14,375,613 (GRCm39)	missense	probably benign	0.14
R4792:Kdm4d	UTSW	9	14,374,686 (GRCm39)	missense	probably benign
R5113:Kdm4d	UTSW	9	14,375,409 (GRCm39)	missense	probably damaging	1.00
R5211:Kdm4d	UTSW	9	14,374,400 (GRCm39)	missense	probably benign	0.04
R5352:Kdm4d	UTSW	9	14,375,654 (GRCm39)	missense	probably damaging	1.00
R6692:Kdm4d	UTSW	9	14,374,361 (GRCm39)	missense	probably benign
R7014:Kdm4d	UTSW	9	14,375,475 (GRCm39)	missense	probably damaging	0.99
R7198:Kdm4d	UTSW	9	14,375,316 (GRCm39)	missense	probably damaging	1.00
R8116:Kdm4d	UTSW	9	14,375,237 (GRCm39)	missense	probably damaging	1.00
R8134:Kdm4d	UTSW	9	14,374,532 (GRCm39)	missense	probably damaging	1.00
R8354:Kdm4d	UTSW	9	14,375,235 (GRCm39)	missense	possibly damaging	0.80
R9006:Kdm4d	UTSW	9	14,374,833 (GRCm39)	missense	probably benign	0.01
R9197:Kdm4d	UTSW	9	14,375,537 (GRCm39)	missense	probably damaging	1.00
R9298:Kdm4d	UTSW	9	14,375,336 (GRCm39)	missense	probably damaging	1.00
R9300:Kdm4d	UTSW	9	14,375,336 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AACTGACCAGGAGCTCTCTCAG -3'
(R):5'- TCCAGAAGTCTGACTCAGCC -3'

Sequencing Primer
(F):5'- AGCTCTCTCAGGTATGGCCAATG -3'
(R):5'- CAGAAGTCTGACTCAGCCAGAGC -3'

Posted On

2019-06-26