Mutagenetix > Incidental Mutation

Incidental Mutation 'R8134:Kdm4d'

632177

Institutional Source

Beutler Lab

Gene Symbol

Kdm4d

Ensembl Gene

ENSMUSG00000053914

Gene Name

lysine (K)-specific demethylase 4D

Synonyms

Jmjd2d

MMRRC Submission

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8134 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

14462548-14500482 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 14463236 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Histidine at position 442 (R442H)

Ref Sequence

ENSEMBL: ENSMUSP00000061632 (fasta)

Gene Model

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

AlphaFold

Q3U2K5

Predicted Effect

probably damaging
Transcript: ENSMUST00000058796
AA Change: R442H

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000061632
Gene: ENSMUSG00000053914
AA Change: R442H

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 damaging
Transcript: ENSMUST00000115647
AA Change: R442H

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000111311
Gene: ENSMUSG00000053914
AA Change: R442H

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

Meta Mutation Damage Score

0.1719

Coding Region Coverage

1x: 99.8%
3x: 99.6%
10x: 98.5%
20x: 93.5%

Validation Efficiency

99% (71/72)

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: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abce1	G	A	8: 79,699,353	P265L	probably benign	Het
Adam20	A	G	8: 40,796,064	T404A	probably benign	Het
Anp32a	G	T	9: 62,377,581	R237L	unknown	Het
Ascc3	A	G	10: 50,767,458	D1835G	probably benign	Het
Atg9b	A	G	5: 24,385,222		probably null	Het
Bard1	A	T	1: 71,067,138	N443K	probably damaging	Het
Btnl1	A	G	17: 34,385,673	D476G	possibly damaging	Het
C2cd3	A	T	7: 100,418,504	I487F		Het
Cadm4	A	G	7: 24,503,605	E384G	possibly damaging	Het
Camsap3	A	G	8: 3,598,075	K128E	probably benign	Het
Casz1	C	T	4: 148,943,035	P1005S	probably damaging	Het
Cd38	C	A	5: 43,901,448	L135M	probably damaging	Het
Cdk20	A	G	13: 64,437,920	E244G	probably benign	Het
Cfap54	A	T	10: 92,878,516	V2667D	unknown	Het
Col11a1	A	G	3: 114,218,786	K1792E	unknown	Het
Cpne9	A	T	6: 113,295,042	D377V	probably benign	Het
Csmd1	A	T	8: 15,932,550	C2706S	probably damaging	Het
Ctnnbl1	T	C	2: 157,809,471	V222A	probably benign	Het
Frmpd2	T	C	14: 33,505,495	S277P	probably benign	Het
Gm15922	A	G	7: 3,735,839	S590P	probably damaging	Het
Herc2	C	T	7: 56,085,136	T158I	probably benign	Het
Hoxa4	G	T	6: 52,190,557	H215N	possibly damaging	Het
Hpd	G	T	5: 123,174,380	Q309K	probably benign	Het
Il20ra	A	G	10: 19,750,704	T159A	probably damaging	Het
Ints10	T	A	8: 68,802,986	Y209*	probably null	Het
Ints2	A	G	11: 86,212,660	I1190T	probably damaging	Het
Jhy	A	G	9: 40,960,892	V107A	probably null	Het
Kif1bp	T	C	10: 62,577,977	Y134C	probably benign	Het
Klb	A	T	5: 65,383,615	H1017L	probably benign	Het
Kndc1	T	A	7: 139,901,369		probably null	Het
Krtap4-1	GGCAGCAGGGGCTGCAGCAAGGGCTGCAGCAGGGGC	GGCAGCAGGGGCTGCAGCAAGGGCTGCAGCAGGGGCTGCAGCAAGGGCTGCAGCAGGGGC	11: 99,627,834		probably benign	Het
Lrrn3	T	C	12: 41,453,048	I423M	probably damaging	Het
Magi2	T	G	5: 20,391,367	F274L	probably damaging	Het
Magi2	T	A	5: 20,391,394	D283E	probably benign	Het
Map3k19	A	C	1: 127,823,755	S620A	probably damaging	Het
Meis2	C	T	2: 115,866,888	M388I	probably benign	Het
Ms4a3	G	C	19: 11,638,249	H54Q	probably benign	Het
Nfe2l1	A	T	11: 96,819,759	M548K	possibly damaging	Het
Ninl	C	T	2: 150,950,314	C763Y	probably benign	Het
Numa1	T	C	7: 102,001,627	F1522L	probably benign	Het
Olfr1344	T	C	7: 6,438,923		probably benign	Het
Olfr539	T	A	7: 140,667,767	I153N	possibly damaging	Het
Pcdhgc3	G	A	18: 37,806,863	V106I	probably benign	Het
Phf3	A	G	1: 30,824,471	V152A	unknown	Het
Plcg2	A	T	8: 117,557,318	D118V	probably damaging	Het
Pnpla1	A	G	17: 28,878,469	D203G	probably damaging	Het
Ppip5k2	A	T	1: 97,745,163	M474K	probably benign	Het
Ppp1r12b	T	C	1: 134,886,542	E341G	possibly damaging	Het
Rictor	C	T	15: 6,772,154	S441L	probably benign	Het
Rrs1	C	T	1: 9,545,420		probably benign	Het
Scaf11	T	C	15: 96,420,711	N324S	probably damaging	Het
Spaca1	T	A	4: 34,042,157		probably null	Het
Sun3	G	T	11: 9,029,346	D118E	probably benign	Het
Svop	C	T	5: 114,042,931	V215I	probably benign	Het
Tbc1d15	A	T	10: 115,209,569	C497S	probably damaging	Het
Tdrd6	A	T	17: 43,626,173	I1328N	probably damaging	Het
Tuba8	T	A	6: 121,221,422	D116E	probably benign	Het
Ube2z	A	G	11: 96,058,374	I213T	possibly damaging	Het
Ubqln4	G	A	3: 88,555,490		probably null	Het
Vps13a	A	G	19: 16,654,354	I2639T	possibly damaging	Het
Zfp217	G	A	2: 170,119,651	S252F	possibly damaging	Het
Zfp94	A	T	7: 24,303,741	V92E	probably benign	Het

Other mutations in Kdm4d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01011:Kdm4d	APN	9	14464219	missense	probably benign	0.10
IGL01114:Kdm4d	APN	9	14464197	missense	probably damaging	1.00
IGL01609:Kdm4d	APN	9	14464418	missense	probably damaging	0.99
IGL02342:Kdm4d	APN	9	14463564	missense	probably damaging	0.99
IGL02513:Kdm4d	APN	9	14464554	missense	probably benign	0.00
IGL03276:Kdm4d	APN	9	14464542	missense	probably benign	0.04
IGL03379:Kdm4d	APN	9	14463843	missense	probably damaging	1.00
R0220:Kdm4d	UTSW	9	14463122	missense	probably benign
R0755:Kdm4d	UTSW	9	14464295	missense	probably damaging	0.99
R1195:Kdm4d	UTSW	9	14463099	missense	probably benign
R1195:Kdm4d	UTSW	9	14463099	missense	probably benign
R1195:Kdm4d	UTSW	9	14463099	missense	probably benign
R1455:Kdm4d	UTSW	9	14464395	missense	probably damaging	0.98
R1552:Kdm4d	UTSW	9	14464029	missense	probably damaging	1.00
R1692:Kdm4d	UTSW	9	14464511	missense	probably benign	0.43
R1871:Kdm4d	UTSW	9	14464383	missense	probably damaging	1.00
R1892:Kdm4d	UTSW	9	14464317	missense	probably benign	0.14
R4792:Kdm4d	UTSW	9	14463390	missense	probably benign
R5113:Kdm4d	UTSW	9	14464113	missense	probably damaging	1.00
R5211:Kdm4d	UTSW	9	14463104	missense	probably benign	0.04
R5352:Kdm4d	UTSW	9	14464358	missense	probably damaging	1.00
R6692:Kdm4d	UTSW	9	14463065	missense	probably benign
R7014:Kdm4d	UTSW	9	14464179	missense	probably damaging	0.99
R7198:Kdm4d	UTSW	9	14464020	missense	probably damaging	1.00
R7260:Kdm4d	UTSW	9	14463158	missense	probably benign	0.05
R8116:Kdm4d	UTSW	9	14463941	missense	probably damaging	1.00
R8354:Kdm4d	UTSW	9	14463939	missense	possibly damaging	0.80
R9006:Kdm4d	UTSW	9	14463537	missense	probably benign	0.01
R9197:Kdm4d	UTSW	9	14464241	missense	probably damaging	1.00
R9298:Kdm4d	UTSW	9	14464040	missense	probably damaging	1.00
R9300:Kdm4d	UTSW	9	14464040	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CAGGACATAGGTTTAGGGGTCG -3'
(R):5'- TCTGCCTATAGCCACGGTAAG -3'

Sequencing Primer
(F):5'- CCTTCAGAAGCTGTCATAAGATGCTG -3'
(R):5'- TAGCCACGGTAAGTAACGTTCCTTG -3'

Posted On

2020-06-30