Mutagenetix > Incidental Mutation

Incidental Mutation 'R1572:Kdm4a'

170827

Institutional Source

Beutler Lab

Gene Symbol

Kdm4a

Ensembl Gene

ENSMUSG00000033326

Gene Name

lysine (K)-specific demethylase 4A

Synonyms

D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2

MMRRC Submission

039611-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.643) question?

Stock #

R1572 (G1)

Quality Score

154

Status

Validated

Chromosome

Chromosomal Location

117994154-118037240 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 117996146 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 961 (E961G)

Ref Sequence

ENSEMBL: ENSMUSP00000102014 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030263] [ENSMUST00000050288] [ENSMUST00000097911] [ENSMUST00000097912] [ENSMUST00000106403] [ENSMUST00000106406] [ENSMUST00000106410]

AlphaFold

Q8BW72

Predicted Effect

probably benign
Transcript: ENSMUST00000030263

SMART Domains

Protein: ENSMUSP00000030263
Gene: ENSMUSG00000028538

Domain	Start	End	E-Value	Type
transmembrane domain	5	27	N/A	INTRINSIC
low complexity region	37	47	N/A	INTRINSIC
Pfam:Glyco_transf_29	102	373	5.7e-75	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000050288

SMART Domains

Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326

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

possibly damaging
Transcript: ENSMUST00000097911
AA Change: E961G

PolyPhen 2 Score 0.888 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: E961G

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: ENSMUST00000097912

SMART Domains

Protein: ENSMUSP00000095525
Gene: ENSMUSG00000028538

Domain	Start	End	E-Value	Type
transmembrane domain	5	27	N/A	INTRINSIC
Pfam:Glyco_transf_29	86	357	5.4e-75	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000106403
AA Change: E961G

PolyPhen 2 Score 0.888 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: E961G

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

possibly damaging
Transcript: ENSMUST00000106406
AA Change: E961G

PolyPhen 2 Score 0.888 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: E961G

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: ENSMUST00000106410

SMART Domains

Protein: ENSMUSP00000102018
Gene: ENSMUSG00000028538

Domain	Start	End	E-Value	Type
transmembrane domain	5	27	N/A	INTRINSIC
low complexity region	37	47	N/A	INTRINSIC
Pfam:Glyco_transf_29	106	372	4.7e-63	PFAM

Meta Mutation Damage Score

0.2302

Coding Region Coverage

1x: 98.7%
3x: 97.5%
10x: 92.9%
20x: 80.7%

Validation Efficiency

97% (130/134)

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: 112 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310030G06Rik	G	A	9: 50,651,973 (GRCm39)	T85M	probably damaging	Het
Actn1	A	G	12: 80,219,731 (GRCm39)		probably benign	Het
Afap1l1	A	T	18: 61,870,570 (GRCm39)	S603T	probably damaging	Het
Ahcy	T	C	2: 154,910,851 (GRCm39)	Y39C	probably benign	Het
Ankmy2	T	C	12: 36,236,941 (GRCm39)		probably null	Het
Anxa13	A	T	15: 58,220,655 (GRCm39)		noncoding transcript	Het
Aoc1	T	C	6: 48,882,720 (GRCm39)	S221P	possibly damaging	Het
Arhgef10	C	A	8: 15,041,211 (GRCm39)	A770D	possibly damaging	Het
Arhgef19	A	G	4: 140,982,065 (GRCm39)	D707G	probably benign	Het
Arhgef3	G	A	14: 27,123,692 (GRCm39)	R444H	probably damaging	Het
Asphd1	T	C	7: 126,548,271 (GRCm39)	I11V	probably benign	Het
Atp2b1	A	G	10: 98,830,537 (GRCm39)	M333V	probably benign	Het
BC051665	T	C	13: 60,932,841 (GRCm39)	Y40C	probably damaging	Het
Ccdc87	T	A	19: 4,890,341 (GRCm39)	S278T	probably benign	Het
Ccn3	T	A	15: 54,612,648 (GRCm39)	M219K	possibly damaging	Het
Cdcp3	T	A	7: 130,846,560 (GRCm39)	Y777*	probably null	Het
Chaf1b	G	A	16: 93,698,118 (GRCm39)	G463D	possibly damaging	Het
Chrna4	T	C	2: 180,671,100 (GRCm39)	T219A	possibly damaging	Het
Clcnkb	T	G	4: 141,134,406 (GRCm39)	T584P	possibly damaging	Het
Clptm1l	T	C	13: 73,755,866 (GRCm39)	S161P	probably benign	Het
Cmya5	T	C	13: 93,230,777 (GRCm39)	E1437G	possibly damaging	Het
Col13a1	A	T	10: 61,702,205 (GRCm39)		probably null	Het
Col3a1	T	C	1: 45,385,128 (GRCm39)	S82P	possibly damaging	Het
Cpeb3	A	T	19: 37,116,482 (GRCm39)	M383K	probably benign	Het
Cr2	T	A	1: 194,845,622 (GRCm39)	H111L	probably damaging	Het
Cttnbp2	T	C	6: 18,375,974 (GRCm39)	S1522G	possibly damaging	Het
Cul3	T	C	1: 80,260,506 (GRCm39)	D281G	possibly damaging	Het
Cyp2c70	T	G	19: 40,172,426 (GRCm39)	K72T	probably benign	Het
Cyp39a1	A	T	17: 43,991,020 (GRCm39)	I110F	probably damaging	Het
Cyp46a1	T	A	12: 108,318,198 (GRCm39)	M203K	probably null	Het
Cyp8b1	A	T	9: 121,744,024 (GRCm39)	V436D	possibly damaging	Het
Ddx17	T	C	15: 79,422,766 (GRCm39)	D324G	probably damaging	Het
Dop1b	A	G	16: 93,567,041 (GRCm39)	N1274S	probably damaging	Het
Dscaml1	G	A	9: 45,632,631 (GRCm39)	V1166I	probably benign	Het
Dsp	T	C	13: 38,379,714 (GRCm39)	V1554A	probably damaging	Het
Efr3a	T	A	15: 65,726,641 (GRCm39)		probably null	Het
Egfem1	A	T	3: 29,702,420 (GRCm39)	N223I	probably benign	Het
Egr2	T	C	10: 67,375,805 (GRCm39)	S147P	probably damaging	Het
Elmo3	A	G	8: 106,034,933 (GRCm39)	T408A	probably benign	Het
Flnb	A	G	14: 7,883,908 (GRCm38)	D378G	probably damaging	Het
Foxj2	T	A	6: 122,810,220 (GRCm39)	M193K	probably benign	Het
Gm6327	A	G	16: 12,578,020 (GRCm39)		noncoding transcript	Het
Gm7694	T	C	1: 170,130,335 (GRCm39)	H21R	probably benign	Het
Gpr107	A	G	2: 31,057,037 (GRCm39)	D43G	probably damaging	Het
Grid2	T	A	6: 64,406,678 (GRCm39)	Y679*	probably null	Het
Grin2c	G	A	11: 115,146,900 (GRCm39)	P432S	possibly damaging	Het
H2-M10.1	A	G	17: 36,636,625 (GRCm39)	F60L	possibly damaging	Het
Hectd4	A	G	5: 121,439,941 (GRCm39)	D1147G	possibly damaging	Het
Idua	G	T	5: 108,828,455 (GRCm39)	A223S	probably benign	Het
Ifi206	T	C	1: 173,314,419 (GRCm39)	Q7R	probably benign	Het
Itgad	T	A	7: 127,802,406 (GRCm39)	V986E	probably damaging	Het
Itsn2	G	A	12: 4,700,044 (GRCm39)	R670H	probably benign	Het
Klra5	T	A	6: 129,883,585 (GRCm39)	I91L	probably damaging	Het
Kntc1	A	G	5: 123,910,176 (GRCm39)	T525A	probably damaging	Het
Lct	A	G	1: 128,221,932 (GRCm39)	F1536L	probably benign	Het
Lmod1	T	A	1: 135,291,671 (GRCm39)	D175E	probably benign	Het
Lonrf1	A	C	8: 36,701,126 (GRCm39)	D361E	probably benign	Het
Lrrc19	T	C	4: 94,526,666 (GRCm39)	Y297C	probably damaging	Het
Mast4	T	C	13: 102,873,431 (GRCm39)	E1787G	possibly damaging	Het
Mpp2	G	A	11: 101,951,374 (GRCm39)	A452V	probably benign	Het
Msh2	T	C	17: 88,026,080 (GRCm39)	V686A	possibly damaging	Het
Mthfd1	C	T	12: 76,317,193 (GRCm39)	Q15*	probably null	Het
Mtnr1b	A	T	9: 15,774,438 (GRCm39)	I207N	probably damaging	Het
Nid2	A	G	14: 19,855,480 (GRCm39)	T1207A	probably benign	Het
Nin	A	T	12: 70,085,524 (GRCm39)	V1569D	probably damaging	Het
Nrcam	T	A	12: 44,584,147 (GRCm39)		probably benign	Het
Nsd1	T	A	13: 55,394,782 (GRCm39)	H897Q	probably damaging	Het
Or10g9	A	G	9: 39,912,490 (GRCm39)	F11S	probably benign	Het
Or12d2	A	T	17: 37,624,371 (GRCm39)	N301K	probably benign	Het
Or2w2	T	A	13: 21,758,480 (GRCm39)	I49F	possibly damaging	Het
Or7d10	G	T	9: 19,832,208 (GRCm39)	K234N	probably benign	Het
Paip1	T	C	13: 119,588,320 (GRCm39)		probably benign	Het
Pcnx3	G	A	19: 5,735,375 (GRCm39)	R484*	probably null	Het
Pdxk	A	G	10: 78,283,814 (GRCm39)	Y127H	probably damaging	Het
Phf20	T	A	2: 156,129,754 (GRCm39)	V442E	probably benign	Het
Phlpp1	G	A	1: 106,320,519 (GRCm39)	D1505N	probably damaging	Het
Pkhd1	T	C	1: 20,417,664 (GRCm39)	T2496A	probably benign	Het
Pkhd1l1	A	G	15: 44,406,869 (GRCm39)	T2369A	probably benign	Het
Plod2	T	A	9: 92,485,120 (GRCm39)		probably benign	Het
Pnpla7	T	A	2: 24,905,263 (GRCm39)	M617K	possibly damaging	Het
Ppp1r16a	C	T	15: 76,577,869 (GRCm39)	Q328*	probably null	Het
Prkch	T	A	12: 73,696,131 (GRCm39)		probably null	Het
Prr12	G	A	7: 44,678,224 (GRCm39)	H1974Y	unknown	Het
Prr16	A	G	18: 51,436,042 (GRCm39)	I174V	probably benign	Het
Prss45	A	T	9: 110,667,497 (GRCm39)	T39S	probably benign	Het
Pum1	T	A	4: 130,445,515 (GRCm39)	D161E	probably damaging	Het
Rad51ap2	A	G	12: 11,507,113 (GRCm39)	D345G	probably damaging	Het
Ralgapb	A	G	2: 158,288,119 (GRCm39)		probably benign	Het
Rasgrp3	A	G	17: 75,807,729 (GRCm39)	H262R	possibly damaging	Het
Rnf213	T	A	11: 119,327,437 (GRCm39)	I1809N	probably damaging	Het
Ryr1	A	G	7: 28,761,616 (GRCm39)	L3177P	probably damaging	Het
Scyl2	C	A	10: 89,486,818 (GRCm39)	R230L	probably damaging	Het
Sfxn2	T	C	19: 46,570,915 (GRCm39)		probably benign	Het
Slc18b1	T	C	10: 23,674,639 (GRCm39)		probably benign	Het
Spata31d1d	T	C	13: 59,876,005 (GRCm39)	H510R	probably benign	Het
Stab1	A	T	14: 30,872,780 (GRCm39)	N1109K	probably damaging	Het
Styxl2	C	T	1: 165,927,024 (GRCm39)	V863M	possibly damaging	Het
Sult3a2	A	G	10: 33,657,973 (GRCm39)	S47P	probably damaging	Het
Tenm3	T	C	8: 48,682,028 (GRCm39)	N2518S	possibly damaging	Het
Tex21	G	T	12: 76,253,665 (GRCm39)	P416Q	probably benign	Het
Tex38	T	C	4: 115,637,503 (GRCm39)	N100S	probably benign	Het
Thsd4	A	C	9: 60,301,836 (GRCm39)		probably benign	Het
Ticrr	T	C	7: 79,331,572 (GRCm39)	V723A	probably damaging	Het
Tmprss15	A	G	16: 78,887,717 (GRCm39)	V30A	probably benign	Het
Uba3	A	G	6: 97,162,298 (GRCm39)		probably benign	Het
Ubr1	T	C	2: 120,765,800 (GRCm39)		probably benign	Het
Uchl4	A	T	9: 64,143,013 (GRCm39)	I165L	probably benign	Het
Vmn2r112	A	T	17: 22,822,125 (GRCm39)	T268S	possibly damaging	Het
Wfdc3	T	C	2: 164,586,114 (GRCm39)		probably benign	Het
Zfp282	T	A	6: 47,869,801 (GRCm39)	L282Q	probably damaging	Het
Zfp422	A	T	6: 116,603,745 (GRCm39)	C85S	probably damaging	Het
Zfp790	A	T	7: 29,527,564 (GRCm39)	Q83L	probably benign	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
R0652:Kdm4a	UTSW	4	118,032,886 (GRCm39)	missense	probably benign	0.05
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
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'- AGAGCAAAGACAAGCTTCTTGCCC -3'
(R):5'- TTCCTCCATAGCAGAGCAGCTCAG -3'

Sequencing Primer
(F):5'- AGCTTCTTGCCCGAGGAAAC -3'
(R):5'- AGACCTTGTTTGACGGACC -3'

Posted On

2014-04-13