Mutagenetix > Incidental Mutation

Incidental Mutation 'R0652:Kdm4a'

62278

Institutional Source

Beutler Lab

Gene Symbol

Kdm4a

Ensembl Gene

ENSMUSG00000033326

Gene Name

lysine (K)-specific demethylase 4A

Synonyms

D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2

MMRRC Submission

038837-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.631) question?

Stock #

R0652 (G1)

Quality Score

177

Status

Not validated

Chromosome

Chromosomal Location

117994154-118037240 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 118032886 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 60 (D60G)

Ref Sequence

ENSEMBL: ENSMUSP00000062910 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000050288] [ENSMUST00000097911] [ENSMUST00000106403] [ENSMUST00000106406]

AlphaFold

Q8BW72

Predicted Effect

probably benign
Transcript: ENSMUST00000050288
AA Change: D60G

PolyPhen 2 Score 0.052 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326
AA Change: D60G

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.87e-8	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000097911
AA Change: D60G

PolyPhen 2 Score 0.038 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: D60G

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.41e-10	SMART
TUDOR	955	1011	4.77e-14	SMART
low complexity region	1032	1044	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000106403
AA Change: D60G

PolyPhen 2 Score 0.038 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: D60G

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.41e-10	SMART
TUDOR	955	1011	4.77e-14	SMART
low complexity region	1032	1044	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000106406
AA Change: D60G

PolyPhen 2 Score 0.038 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: D60G

Domain	Start	End	E-Value	Type
JmjN	13	55	1.01e-20	SMART
JmjC	142	308	3.57e-63	SMART
low complexity region	461	487	N/A	INTRINSIC
low complexity region	502	525	N/A	INTRINSIC
low complexity region	619	637	N/A	INTRINSIC
PHD	709	767	4.93e-4	SMART
PHD	829	885	1.54e-5	SMART
TUDOR	897	954	2.41e-10	SMART
TUDOR	955	1011	4.77e-14	SMART
low complexity region	1032	1044	N/A	INTRINSIC

Meta Mutation Damage Score

0.2360

Coding Region Coverage

1x: 99.3%
3x: 98.5%
10x: 96.3%
20x: 90.1%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the Jumonji domain 2 (JMJD2) family and encodes a protein containing a JmjN domain, a JmjC domain, a JD2H domain, two TUDOR domains, and two PHD-type zinc fingers. This nuclear protein functions as a trimethylation-specific demethylase, converting specific trimethylated histone residues to the dimethylated form, and as a transcriptional repressor. [provided by RefSeq, Apr 2009]

Allele List at MGI

Other mutations in this stock

Total: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca9	T	C	11: 110,042,889 (GRCm39)	N387D	probably benign	Het
Adgrg5	T	A	8: 95,660,785 (GRCm39)		probably null	Het
Ahi1	C	A	10: 20,855,360 (GRCm39)	H556Q	probably damaging	Het
Amph	A	G	13: 19,270,791 (GRCm39)		probably null	Het
Apol7a	T	C	15: 77,274,055 (GRCm39)		probably benign	Het
Apoo-ps	A	T	13: 107,550,910 (GRCm39)		noncoding transcript	Het
Arpc1b	A	G	5: 145,063,670 (GRCm39)	D306G	probably damaging	Het
Astn2	T	C	4: 65,712,795 (GRCm39)	D615G	probably damaging	Het
Atm	A	G	9: 53,397,314 (GRCm39)	V1673A	probably damaging	Het
B3gnt3	A	T	8: 72,146,466 (GRCm39)	V21E	probably benign	Het
Bco1	A	G	8: 117,832,435 (GRCm39)	D77G	probably damaging	Het
Brinp2	A	T	1: 158,074,191 (GRCm39)	H643Q	probably damaging	Het
Bsn	A	G	9: 107,982,941 (GRCm39)	F3604S	unknown	Het
Cacna1c	A	G	6: 118,579,190 (GRCm39)	F1753L	probably damaging	Het
Cd74	T	C	18: 60,944,957 (GRCm39)	S201P	probably damaging	Het
Cep192	T	A	18: 67,940,336 (GRCm39)	L101Q	probably benign	Het
Cfap161	T	C	7: 83,442,484 (GRCm39)	I110V	probably null	Het
Cnksr3	T	C	10: 7,070,463 (GRCm39)	D257G	probably damaging	Het
Col14a1	A	C	15: 55,208,278 (GRCm39)	E121A	unknown	Het
Cpne3	T	C	4: 19,532,486 (GRCm39)	D309G	probably benign	Het
Ctnnd1	A	G	2: 84,433,240 (GRCm39)	I609T	probably benign	Het
Cyp2s1	A	G	7: 25,508,683 (GRCm39)	V253A	probably damaging	Het
Dock7	T	C	4: 98,943,586 (GRCm39)	D552G	possibly damaging	Het
Dpyd	A	G	3: 119,220,924 (GRCm39)	D965G	probably damaging	Het
Efcab2	T	A	1: 178,308,911 (GRCm39)	M138K	probably damaging	Het
Eml3	T	C	19: 8,910,649 (GRCm39)	S204P	probably damaging	Het
Fbxw16	T	A	9: 109,265,236 (GRCm39)	S432C	possibly damaging	Het
Fbxw20	T	G	9: 109,061,400 (GRCm39)	Q116H	probably damaging	Het
Fech	A	G	18: 64,591,240 (GRCm39)	S395P	probably damaging	Het
Fgf7	A	G	2: 125,877,875 (GRCm39)	K81E	probably benign	Het
Fras1	T	A	5: 96,929,199 (GRCm39)	Y3868N	possibly damaging	Het
Ganab	A	T	19: 8,892,766 (GRCm39)		probably null	Het
Gfra1	T	C	19: 58,288,986 (GRCm39)	N153S	possibly damaging	Het
Gja4	T	A	4: 127,205,920 (GRCm39)	Y281F	probably benign	Het
Gm5141	T	C	13: 62,921,946 (GRCm39)	T407A	probably damaging	Het
Gm5422	T	C	10: 31,125,277 (GRCm39)		noncoding transcript	Het
Greb1	T	C	12: 16,746,457 (GRCm39)	Y1271C	probably damaging	Het
Hp1bp3	C	A	4: 137,956,080 (GRCm39)	N50K	possibly damaging	Het
Hspg2	T	C	4: 137,242,033 (GRCm39)	F589S	probably damaging	Het
Ido1	A	G	8: 25,075,260 (GRCm39)	F183S	probably damaging	Het
Iqgap1	T	A	7: 80,386,143 (GRCm39)	K936I	probably damaging	Het
L3mbtl4	G	A	17: 69,081,286 (GRCm39)	C558Y	probably damaging	Het
Lrrc28	T	C	7: 67,267,833 (GRCm39)	N98S	probably damaging	Het
Lypd11	T	A	7: 24,423,622 (GRCm39)	N14I	possibly damaging	Het
Map1a	A	G	2: 121,133,264 (GRCm39)	D1360G	probably benign	Het
Megf10	C	T	18: 57,410,796 (GRCm39)	P702S	probably benign	Het
Met	A	G	6: 17,491,709 (GRCm39)	E157G	probably benign	Het
Mff	A	G	1: 82,728,285 (GRCm39)	D187G	possibly damaging	Het
Mlph	A	T	1: 90,870,630 (GRCm39)	I514F	possibly damaging	Het
Mroh2a	C	T	1: 88,158,402 (GRCm39)	R150*	probably null	Het
Myo15b	T	C	11: 115,755,468 (GRCm39)	V976A	probably benign	Het
Myo9a	A	G	9: 59,779,209 (GRCm39)	D1655G	probably benign	Het
Ncoa6	C	T	2: 155,233,131 (GRCm39)	G2059D	probably benign	Het
Ndst4	A	T	3: 125,405,188 (GRCm39)	H481L	possibly damaging	Het
Nipbl	A	G	15: 8,332,964 (GRCm39)	S2220P	probably benign	Het
Nom1	C	A	5: 29,640,309 (GRCm39)	P212T	probably damaging	Het
Nsd1	A	G	13: 55,395,399 (GRCm39)	D1000G	possibly damaging	Het
Nudt9	T	C	5: 104,198,467 (GRCm39)	F44S	possibly damaging	Het
Numb	C	T	12: 83,842,566 (GRCm39)	V537I	probably damaging	Het
Or10j3b	T	A	1: 173,043,524 (GRCm39)	I102N	possibly damaging	Het
Or13a27	A	T	7: 139,925,545 (GRCm39)	M119K	probably damaging	Het
Or51q1c	A	G	7: 103,652,446 (GRCm39)		probably null	Het
Or5b109	A	T	19: 13,211,899 (GRCm39)	Y95F	possibly damaging	Het
Or5h17	A	G	16: 58,820,063 (GRCm39)	N5S	probably damaging	Het
Or6c211	T	A	10: 129,506,248 (GRCm39)	T47S	probably benign	Het
Osgin1	A	T	8: 120,172,211 (GRCm39)	Y335F	probably damaging	Het
Pcdh10	T	A	3: 45,334,199 (GRCm39)	V171E	probably damaging	Het
Pira13	T	A	7: 3,825,762 (GRCm39)	Y369F	probably benign	Het
Plxna4	T	C	6: 32,162,436 (GRCm39)	N1359S	probably damaging	Het
Ppp1r16a	C	T	15: 76,574,999 (GRCm39)		probably benign	Het
Prr5l	T	C	2: 101,602,635 (GRCm39)	T2A	possibly damaging	Het
Rbp3	T	A	14: 33,680,605 (GRCm39)	I1069N	possibly damaging	Het
Rnf144b	A	G	13: 47,373,983 (GRCm39)	Y60C	probably damaging	Het
Sbno2	A	T	10: 79,903,128 (GRCm39)	V396E	probably damaging	Het
Sdk1	A	G	5: 141,940,713 (GRCm39)	T494A	probably benign	Het
Serac1	G	T	17: 6,102,031 (GRCm39)	D384E	probably damaging	Het
Sgk1	A	G	10: 21,758,556 (GRCm39)	N7D	probably damaging	Het
Sigirr	A	T	7: 140,672,980 (GRCm39)	V69D	possibly damaging	Het
Slc17a3	C	T	13: 24,039,841 (GRCm39)	S293F	probably damaging	Het
St6gal2	T	C	17: 55,805,290 (GRCm39)	Y396H	probably benign	Het
Ttn	A	T	2: 76,598,956 (GRCm39)	F19319Y	probably damaging	Het
Ubr4	T	A	4: 139,128,637 (GRCm39)	I599N	probably damaging	Het
Vmn1r213	A	G	13: 23,195,564 (GRCm39)		probably benign	Het
Vmn2r96	T	A	17: 18,817,830 (GRCm39)	M469K	probably benign	Het
Wasf1	T	A	10: 40,807,902 (GRCm39)		probably null	Het
Wdr20rt	T	C	12: 65,272,689 (GRCm39)	S51P	probably damaging	Het

Other mutations in Kdm4a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01670:Kdm4a	APN	4	118,017,698 (GRCm39)	missense	probably damaging	1.00
IGL01845:Kdm4a	APN	4	118,017,656 (GRCm39)	missense	possibly damaging	0.85
IGL02009:Kdm4a	APN	4	118,017,366 (GRCm39)	missense	probably benign	0.01
IGL02296:Kdm4a	APN	4	118,034,662 (GRCm39)	missense	probably damaging	1.00
IGL02366:Kdm4a	APN	4	118,017,703 (GRCm39)	critical splice acceptor site	probably null
IGL02606:Kdm4a	APN	4	118,017,486 (GRCm39)	missense	probably benign	0.00
IGL02673:Kdm4a	APN	4	118,025,769 (GRCm39)	missense	probably benign	0.00
R0245:Kdm4a	UTSW	4	118,032,886 (GRCm39)	missense	probably benign	0.05
R0326:Kdm4a	UTSW	4	118,018,903 (GRCm39)	missense	probably benign	0.00
R0551:Kdm4a	UTSW	4	117,995,428 (GRCm39)	makesense	probably null
R0603:Kdm4a	UTSW	4	117,999,708 (GRCm39)	missense	probably damaging	1.00
R0799:Kdm4a	UTSW	4	118,004,189 (GRCm39)	splice site	probably null
R0847:Kdm4a	UTSW	4	118,021,695 (GRCm39)	missense	probably damaging	0.96
R1307:Kdm4a	UTSW	4	118,032,839 (GRCm39)	missense	probably benign	0.02
R1572:Kdm4a	UTSW	4	117,996,146 (GRCm39)	missense	possibly damaging	0.89
R1869:Kdm4a	UTSW	4	117,996,068 (GRCm39)	missense	probably null	1.00
R1902:Kdm4a	UTSW	4	118,017,596 (GRCm39)	missense	probably benign	0.38
R1903:Kdm4a	UTSW	4	118,017,596 (GRCm39)	missense	probably benign	0.38
R2135:Kdm4a	UTSW	4	117,999,656 (GRCm39)	missense	probably damaging	1.00
R3856:Kdm4a	UTSW	4	118,010,428 (GRCm39)	missense	probably damaging	1.00
R4687:Kdm4a	UTSW	4	118,001,280 (GRCm39)	missense	probably damaging	1.00
R4940:Kdm4a	UTSW	4	118,018,951 (GRCm39)	missense	probably benign	0.00
R5115:Kdm4a	UTSW	4	118,019,778 (GRCm39)	missense	possibly damaging	0.75
R5229:Kdm4a	UTSW	4	118,003,802 (GRCm39)	missense	probably damaging	0.99
R5305:Kdm4a	UTSW	4	118,017,698 (GRCm39)	missense	probably damaging	1.00
R5423:Kdm4a	UTSW	4	117,996,105 (GRCm39)	missense	probably damaging	1.00
R5750:Kdm4a	UTSW	4	117,999,396 (GRCm39)	intron	probably benign
R5849:Kdm4a	UTSW	4	118,019,037 (GRCm39)	missense	probably benign	0.17
R5876:Kdm4a	UTSW	4	117,996,073 (GRCm39)	missense	probably damaging	0.98
R6564:Kdm4a	UTSW	4	118,034,636 (GRCm39)	missense	probably benign	0.18
R6772:Kdm4a	UTSW	4	117,999,752 (GRCm39)	critical splice acceptor site	probably null
R6982:Kdm4a	UTSW	4	118,010,636 (GRCm39)	splice site	probably null
R7410:Kdm4a	UTSW	4	118,001,115 (GRCm39)	missense	possibly damaging	0.64
R7418:Kdm4a	UTSW	4	118,017,440 (GRCm39)	missense	probably damaging	0.99
R8808:Kdm4a	UTSW	4	117,999,480 (GRCm39)	missense	unknown
R8956:Kdm4a	UTSW	4	118,019,013 (GRCm39)	missense	possibly damaging	0.69
R8958:Kdm4a	UTSW	4	117,999,573 (GRCm39)	missense	probably benign	0.08
R9233:Kdm4a	UTSW	4	118,004,193 (GRCm39)	critical splice donor site	probably null
R9281:Kdm4a	UTSW	4	117,995,728 (GRCm39)	missense	probably damaging	1.00
R9647:Kdm4a	UTSW	4	118,017,399 (GRCm39)	missense	probably benign
R9647:Kdm4a	UTSW	4	118,003,790 (GRCm39)	missense	probably benign	0.01
Z1176:Kdm4a	UTSW	4	118,034,699 (GRCm39)	missense	probably benign	0.41
Z1176:Kdm4a	UTSW	4	118,010,387 (GRCm39)	missense	probably benign	0.00
Z1177:Kdm4a	UTSW	4	118,004,366 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- GCCAAAGCATCTCCACTCACTTGTC -3'
(R):5'- GGGCTGTTCAAGAACCCACTCTTC -3'

Sequencing Primer
(F):5'- CCACTCACTTGTCGCTATTGG -3'
(R):5'- TTCTCGTGACAGCGTGAC -3'

Posted On

2013-07-30