Mutagenetix > Incidental Mutation

Incidental Mutation 'R8956:Kdm4a'

681995

Institutional Source

Beutler Lab

Gene Symbol

Kdm4a

Ensembl Gene

ENSMUSG00000033326

Gene Name

lysine (K)-specific demethylase 4A

Synonyms

D4Ertd222e, JHDM3A, Jmjd2a, Jmjd2

MMRRC Submission

068792-MU

Accession Numbers

Essential gene?

Possibly essential (E-score: 0.643) question?

Stock #

R8956 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

117994154-118037240 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 118019013 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 401 (V401A)

Ref Sequence

ENSEMBL: ENSMUSP00000102014 (fasta)

Gene Model

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

AlphaFold

Q8BW72

Predicted Effect

probably benign
Transcript: ENSMUST00000050288
AA Change: V401A

PolyPhen 2 Score 0.297 (Sensitivity: 0.91; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000062910
Gene: ENSMUSG00000033326
AA Change: V401A

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: V401A

PolyPhen 2 Score 0.692 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000095524
Gene: ENSMUSG00000033326
AA Change: V401A

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: ENSMUST00000106403
AA Change: V401A

PolyPhen 2 Score 0.692 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000102011
Gene: ENSMUSG00000033326
AA Change: V401A

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: V401A

PolyPhen 2 Score 0.692 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000102014
Gene: ENSMUSG00000033326
AA Change: V401A

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

98% (87/89)

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: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acan	C	T	7: 78,750,713 (GRCm39)	T1828I	probably benign	Het
Acsf2	A	G	11: 94,461,211 (GRCm39)	S322P	probably benign	Het
Acss2	T	A	2: 155,391,438 (GRCm39)	I170N	probably damaging	Het
Adam22	G	A	5: 8,142,343 (GRCm39)	T814I	probably damaging	Het
Agrn	G	T	4: 156,250,995 (GRCm39)	D1914E	probably damaging	Het
Akap6	T	C	12: 53,187,127 (GRCm39)	S1514P	probably benign	Het
Akap9	T	C	5: 3,998,805 (GRCm39)	L58P	possibly damaging	Het
Apof	A	G	10: 128,105,712 (GRCm39)	I289V	probably benign	Het
Arhgap35	G	A	7: 16,348,404 (GRCm39)		probably benign	Het
Atad3a	A	C	4: 155,838,054 (GRCm39)	F239L	probably damaging	Het
Atf6	T	C	1: 170,621,576 (GRCm39)	T482A	probably damaging	Het
Atg9b	T	C	5: 24,591,850 (GRCm39)		probably benign	Het
Atp8b4	T	A	2: 126,167,327 (GRCm39)		probably null	Het
B4galt5	T	C	2: 167,143,260 (GRCm39)	Y388C	probably damaging	Het
Bahd1	T	C	2: 118,749,689 (GRCm39)	L495P	probably damaging	Het
Bcl6	T	C	16: 23,793,716 (GRCm39)	E77G	probably damaging	Het
Bst1	C	A	5: 43,982,716 (GRCm39)	S187*	probably null	Het
Car4	A	G	11: 84,855,377 (GRCm39)	N170S	probably null	Het
Cdk14	A	T	5: 5,277,182 (GRCm39)	V131E	probably damaging	Het
Cdk4	T	A	10: 126,900,546 (GRCm39)		probably benign	Het
Cebpe	T	C	14: 54,949,121 (GRCm39)	R99G	probably damaging	Het
Col9a1	G	A	1: 24,276,300 (GRCm39)	G736D	probably damaging	Het
Copa	T	A	1: 171,937,480 (GRCm39)	V477D	possibly damaging	Het
Coq9	G	A	8: 95,576,886 (GRCm39)	G166D	probably benign	Het
Cttnbp2	A	T	6: 18,434,165 (GRCm39)	N564K	possibly damaging	Het
Dgkq	T	C	5: 108,798,095 (GRCm39)	N721S	probably benign	Het
Dnhd1	A	T	7: 105,341,852 (GRCm39)	Y1217F	probably damaging	Het
Eef1akmt4	G	T	16: 20,437,398 (GRCm39)	E247*	probably null	Het
Elovl7	A	T	13: 108,393,320 (GRCm39)	I18F	probably benign	Het
Eml5	T	C	12: 98,818,952 (GRCm39)	K785E	possibly damaging	Het
Faap100	C	A	11: 120,268,185 (GRCm39)	C196F	probably damaging	Het
Fat2	G	A	11: 55,173,729 (GRCm39)	T2328M	probably damaging	Het
Gcnt2	T	A	13: 41,041,204 (GRCm39)	I121N	probably benign	Het
Gm12253	A	G	11: 58,327,605 (GRCm39)	K152E	probably benign	Het
Gm16440	T	A	14: 17,574,527 (GRCm39)	R167*	probably null	Het
Gm43302	T	A	5: 105,425,602 (GRCm39)	I276F	possibly damaging	Het
Gys2	A	G	6: 142,374,267 (GRCm39)	S593P	probably damaging	Het
H2-M10.4	T	A	17: 36,772,245 (GRCm39)	N168Y	probably benign	Het
Hpca	C	A	4: 129,012,287 (GRCm39)	R83L	probably damaging	Het
Igkv8-28	A	G	6: 70,121,109 (GRCm39)	F13L	probably benign	Het
Il17ra	A	T	6: 120,458,465 (GRCm39)	I539F	probably damaging	Het
Krt86	A	T	15: 101,375,157 (GRCm39)	T351S	probably benign	Het
Lig4	A	G	8: 10,021,378 (GRCm39)	C801R	probably benign	Het
Lrrn4	G	A	2: 132,714,011 (GRCm39)	P312S	probably damaging	Het
Macf1	T	A	4: 123,368,641 (GRCm39)	H2040L	probably benign	Het
Madcam1	A	G	10: 79,502,466 (GRCm39)	K317E	possibly damaging	Het
Maip1	T	C	1: 57,450,961 (GRCm39)	I201T	probably damaging	Het
Map4k4	C	A	1: 40,039,840 (GRCm39)	D513E	probably benign	Het
Mideas	T	A	12: 84,209,102 (GRCm39)	I667L	probably benign	Het
Mpped1	G	A	15: 83,740,469 (GRCm39)	G137R	probably damaging	Het
Mrgprd	T	G	7: 144,875,923 (GRCm39)	F265V	probably benign	Het
Myct1	C	T	10: 5,554,208 (GRCm39)	T25I	probably damaging	Het
Mylk	A	G	16: 34,791,779 (GRCm39)	T1484A	probably benign	Het
Nbas	C	T	12: 13,482,923 (GRCm39)	S1400L	possibly damaging	Het
Nedd4	T	A	9: 72,633,708 (GRCm39)	S405T	probably benign	Het
Neil2	A	G	14: 63,429,227 (GRCm39)	V22A	probably damaging	Het
Nrip1	G	C	16: 76,089,193 (GRCm39)	A788G	probably benign	Het
Ogfr	AGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCAAAAGGCCAGGTGGAGCCAGAGGACCCAAAAGGCCAGGTGGGGCCAGAAGACCCAAAAGGCCAGGTGGGGCCAGAGGACCCAAAAGGCCAGGTGGGGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGGGGCCAGAG	AGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCAAAAGGCCAGGTGGAGCCAGAGGACCCAAAAGGCCAGGTGGGGCCAGAAGACCCAAAAGGCCAGGTGGGGCCAGAGGACCCAAAAGGCCAGGTGGGGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGAGCCAGAGGACCCCAAAAGCCAGGTGGGGCCAGAGGACCCCCAAAGCCAGGTGGGGCCAGAG	2: 180,236,850 (GRCm39)		probably benign	Het
Or10ab4	A	G	7: 107,655,160 (GRCm39)	T324A	probably benign	Het
Or10d4c	C	T	9: 39,558,496 (GRCm39)	T158I	probably damaging	Het
Or2b7	T	C	13: 21,740,169 (GRCm39)	I8V	probably benign	Het
Or2bd2	G	A	7: 6,442,020 (GRCm39)		probably benign	Het
Or2r2	T	A	6: 42,463,830 (GRCm39)	Q99L	probably damaging	Het
Or6c215	C	T	10: 129,638,222 (GRCm39)	M57I	possibly damaging	Het
Orc2	T	C	1: 58,505,221 (GRCm39)	N478S	probably damaging	Het
Oxct1	A	G	15: 4,064,806 (GRCm39)	E48G	possibly damaging	Het
Pcca	A	G	14: 122,975,324 (GRCm39)	I28V	probably benign	Het
Pcdha8	T	C	18: 37,126,241 (GRCm39)	V241A	probably benign	Het
Pgap6	T	A	17: 26,339,374 (GRCm39)	S563T	possibly damaging	Het
Pkd1l3	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	8: 110,350,827 (GRCm39)		probably benign	Het
Pkd2	T	A	5: 104,631,090 (GRCm39)	W505R	probably damaging	Het
Plxnc1	C	T	10: 94,746,448 (GRCm39)	V430I	probably benign	Het
Prkd3	A	G	17: 79,278,883 (GRCm39)	M401T	probably damaging	Het
Rgmb	A	G	17: 16,027,748 (GRCm39)	C324R	probably benign	Het
Rsph6a	A	T	7: 18,799,364 (GRCm39)		probably benign	Het
Sclt1	A	T	3: 41,636,209 (GRCm39)	M264K	probably benign	Het
Serhl	T	A	15: 82,985,899 (GRCm39)	V30D	possibly damaging	Het
Sfrp1	T	C	8: 23,902,159 (GRCm39)	V120A	probably damaging	Het
Slc22a8	C	T	19: 8,587,030 (GRCm39)	Q408*	probably null	Het
Slc35b2	A	G	17: 45,877,673 (GRCm39)	T218A	probably damaging	Het
Slco4c1	A	T	1: 96,765,242 (GRCm39)	F403I	probably damaging	Het
Sorbs1	T	A	19: 40,351,660 (GRCm39)	H250L	probably damaging	Het
Sorcs3	T	A	19: 48,737,810 (GRCm39)	C742*	probably null	Het
Tnc	T	C	4: 63,918,970 (GRCm39)	Y1151C	probably damaging	Het
Tor1aip1	T	A	1: 155,909,582 (GRCm39)		probably benign	Het
Trim9	T	C	12: 70,393,665 (GRCm39)	Q93R	probably damaging	Het
Tsnaxip1	A	G	8: 106,570,813 (GRCm39)	Y613C	probably damaging	Het
Ttc6	C	T	12: 57,775,196 (GRCm39)	Q1631*	probably null	Het
Ubr5	A	G	15: 38,015,367 (GRCm39)	L881P	probably damaging	Het
Upp2	C	T	2: 58,457,454 (GRCm39)		probably benign	Het
Vmn1r203	T	A	13: 22,709,004 (GRCm39)	S262T	possibly damaging	Het
Vmn2r116	A	T	17: 23,605,736 (GRCm39)	D216V	probably damaging	Het
Vps52	A	G	17: 34,177,049 (GRCm39)	Q96R	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
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
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'- CTCCGACAGACAGTTGTCAG -3'
(R):5'- AGCACTGTTCAGATGATGGAATG -3'

Sequencing Primer
(F):5'- TGGACCAACCAGTCTGTCAG -3'
(R):5'- CTGTTCAGATGATGGAATGAATGAC -3'

Posted On

2021-08-31