Mutagenetix > Incidental Mutation

Incidental Mutation 'R4646:Kdm5a'

350233

Institutional Source

Beutler Lab

Gene Symbol

Kdm5a

Ensembl Gene

ENSMUSG00000030180

Gene Name

lysine demethylase 5A

Synonyms

Rbbp2, Jarid1a, RBP2

MMRRC Submission

041907-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4646 (G1)

Quality Score

220

Status

Not validated

Chromosome

Chromosomal Location

120341085-120421535 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 120351938 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glycine at position 176 (V176G)

Ref Sequence

ENSEMBL: ENSMUSP00000005108 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000005108] [ENSMUST00000132009] [ENSMUST00000135802] [ENSMUST00000203373]

AlphaFold

Q3UXZ9

Predicted Effect

possibly damaging
Transcript: ENSMUST00000005108
AA Change: V176G

PolyPhen 2 Score 0.553 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: V176G

Domain	Start	End	E-Value	Type
JmjN	18	59	4.06e-20	SMART
ARID	81	170	4.76e-35	SMART
BRIGHT	85	175	2.48e-31	SMART
PHD	295	341	1.16e-14	SMART
Blast:JmjC	384	436	2e-22	BLAST
JmjC	437	603	5.88e-73	SMART
low complexity region	638	651	N/A	INTRINSIC
Pfam:zf-C5HC2	676	729	1.3e-21	PFAM
Pfam:PLU-1	740	1072	1.2e-104	PFAM
low complexity region	1091	1119	N/A	INTRINSIC
PHD	1163	1216	1.37e-11	SMART
low complexity region	1269	1280	N/A	INTRINSIC
low complexity region	1337	1351	N/A	INTRINSIC
low complexity region	1403	1414	N/A	INTRINSIC
low complexity region	1494	1512	N/A	INTRINSIC
coiled coil region	1534	1579	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000132009
AA Change: V176G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000145375
Gene: ENSMUSG00000030180
AA Change: V176G

Domain	Start	End	E-Value	Type
JmjN	18	59	4.06e-20	SMART
ARID	81	170	4.76e-35	SMART
BRIGHT	85	175	2.48e-31	SMART
PHD	295	341	1.16e-14	SMART
JmjC	437	603	1.47e-64	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000135802
AA Change: V176G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000145021
Gene: ENSMUSG00000030180
AA Change: V176G

Domain	Start	End	E-Value	Type
JmjN	18	59	1.7e-22	SMART
ARID	81	170	3.6e-39	SMART
BRIGHT	85	175	1.2e-33	SMART
PHD	295	341	7.3e-17	SMART
Blast:JmjC	384	436	2e-22	BLAST
JmjC	437	603	2.2e-75	SMART
low complexity region	638	651	N/A	INTRINSIC
Pfam:zf-C5HC2	676	728	6.3e-15	PFAM
Pfam:PLU-1	741	811	9.8e-16	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000203373
AA Change: V54G

PolyPhen 2 Score 0.373 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000144720
Gene: ENSMUSG00000030180
AA Change: V54G

Domain	Start	End	E-Value	Type
BRIGHT	1	53	8.4e-4	SMART
Blast:JmjC	58	153	3e-56	BLAST
PDB:2E6R\|A	121	152	4e-9	PDB

Coding Region Coverage

1x: 99.0%
3x: 98.6%
10x: 97.4%
20x: 95.6%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the Jumonji, AT-rich interactive domain 1 (JARID1) histone demethylase protein family. The encoded protein plays a role in gene regulation through the histone code by specifically demethylating lysine 4 of histone H3. The encoded protein interacts with many other proteins, including retinoblastoma protein, and is implicated in the transcriptional regulation of Hox genes and cytokines. This gene may play a role in tumor progression. [provided by RefSeq, Aug 2013]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit reduced body size, abnormal involuntary movement and quantitative changes in the hematopoietic stem cell and myeloid progenitor compartments, consistent with enhanced survival and increased cycling. Neonatalsurvival is sensitive to genetic background. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 102 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700031F05Rik	G	T	X: 101,904,515 (GRCm39)	N132K	possibly damaging	Het
2010315B03Rik	T	A	9: 124,056,228 (GRCm39)	Y232F	probably benign	Het
Acadl	A	T	1: 66,870,602 (GRCm39)	S428R	probably benign	Het
Adamts10	A	G	17: 33,764,529 (GRCm39)	D683G	probably damaging	Het
Angptl4	G	A	17: 34,000,273 (GRCm39)	P32S	probably benign	Het
Apob	A	G	12: 8,062,759 (GRCm39)	N134S	probably benign	Het
Atr	G	A	9: 95,753,250 (GRCm39)		probably null	Het
B4galnt1	G	A	10: 127,003,705 (GRCm39)	V223M	probably damaging	Het
Bbs10	A	G	10: 111,136,995 (GRCm39)	K703E	probably benign	Het
C1galt1c1	A	T	X: 37,720,349 (GRCm39)	S216T	probably benign	Het
C2cd3	A	C	7: 100,021,657 (GRCm39)		probably benign	Het
Clca4b	A	C	3: 144,634,286 (GRCm39)	H102Q	probably benign	Het
Cntrl	T	C	2: 35,039,473 (GRCm39)	I557T	probably damaging	Het
Col26a1	G	A	5: 136,876,404 (GRCm39)	S72F	probably damaging	Het
Crocc2	G	A	1: 93,096,516 (GRCm39)	V24M	possibly damaging	Het
Csmd1	T	C	8: 15,982,511 (GRCm39)	I2719V	possibly damaging	Het
Cul9	C	T	17: 46,849,943 (GRCm39)	W502*	probably null	Het
Dazl	A	T	17: 50,595,183 (GRCm39)	F84I	probably damaging	Het
Dcaf1	G	T	9: 106,724,006 (GRCm39)	R478L	probably benign	Het
Dock5	T	G	14: 68,080,228 (GRCm39)	I198L	probably benign	Het
Dock9	A	T	14: 121,823,658 (GRCm39)	L1428H	probably damaging	Het
Dync1li1	T	A	9: 114,538,237 (GRCm39)	V198E	probably damaging	Het
Egf	A	T	3: 129,513,925 (GRCm39)	C429S	probably damaging	Het
Ehmt1	T	C	2: 24,781,696 (GRCm39)	E7G	probably null	Het
Ercc4	G	T	16: 12,965,438 (GRCm39)	R690L	probably damaging	Het
Erich5	T	C	15: 34,471,112 (GRCm39)	C114R	possibly damaging	Het
Etv1	T	C	12: 38,915,685 (GRCm39)	S428P	possibly damaging	Het
Fbxo31	G	T	8: 122,286,755 (GRCm39)	F174L	probably benign	Het
Fbxo33	T	A	12: 59,251,217 (GRCm39)	I433L	probably benign	Het
Fez2	A	T	17: 78,720,357 (GRCm39)	V99E	probably damaging	Het
Gabarapl2	A	C	8: 112,669,185 (GRCm39)	K48Q	probably damaging	Het
Gfi1b	T	A	2: 28,500,149 (GRCm39)	H294L	probably damaging	Het
Gk2	A	G	5: 97,604,056 (GRCm39)	S261P	probably damaging	Het
Gpr158	T	C	2: 21,831,864 (GRCm39)	I988T	probably benign	Het
Grk3	G	C	5: 113,077,586 (GRCm39)	H394D	probably benign	Het
Grm6	A	G	11: 50,748,033 (GRCm39)	E381G	probably benign	Het
Gtf3c1	A	T	7: 125,258,266 (GRCm39)	M1268K	possibly damaging	Het
Hikeshi	A	T	7: 89,572,854 (GRCm39)	I113N	probably damaging	Het
Hmg20b	T	A	10: 81,184,416 (GRCm39)	Q129L	probably damaging	Het
Hunk	C	A	16: 90,272,791 (GRCm39)	T365K	probably damaging	Het
Ints15	A	T	5: 143,293,740 (GRCm39)	W246R	probably damaging	Het
Kif2a	T	A	13: 107,098,693 (GRCm39)	E691V	probably damaging	Het
Ly6e	T	C	15: 74,830,510 (GRCm39)		probably null	Het
Map1b	G	T	13: 99,568,977 (GRCm39)	P1248Q	unknown	Het
Mettl25	A	G	10: 105,662,416 (GRCm39)	S185P	probably damaging	Het
Mfap3l	T	A	8: 61,124,184 (GRCm39)	V142D	probably damaging	Het
Mip	T	A	10: 128,062,922 (GRCm39)	H122Q	probably benign	Het
Mkx	G	A	18: 6,992,040 (GRCm39)	T280I	probably benign	Het
Msi1	A	T	5: 115,589,514 (GRCm39)		probably null	Het
Mtcl2	T	C	2: 156,862,426 (GRCm39)	E1501G	probably damaging	Het
Muc5b	A	G	7: 141,416,377 (GRCm39)	M3108V	probably benign	Het
Mybl1	A	G	1: 9,742,511 (GRCm39)	S625P	probably damaging	Het
Myo7b	C	A	18: 32,127,422 (GRCm39)	V627F	probably benign	Het
Ndst3	A	T	3: 123,465,684 (GRCm39)	I96N	probably damaging	Het
Nrp1	A	T	8: 129,184,425 (GRCm39)	T357S	probably benign	Het
Obscn	G	T	11: 59,015,396 (GRCm39)	Y1050*	probably null	Het
Or2ak7	A	G	11: 58,575,556 (GRCm39)	N286D	probably damaging	Het
Or2d4	A	T	7: 106,543,547 (GRCm39)	N220K	probably benign	Het
Or2y1c	A	C	11: 49,361,451 (GRCm39)	I158L	probably benign	Het
Or4c107	T	A	2: 88,789,556 (GRCm39)	F249I	probably damaging	Het
Or5d47	A	T	2: 87,804,142 (GRCm39)	I289K	probably benign	Het
Or5i1	T	C	2: 87,613,565 (GRCm39)	V227A	possibly damaging	Het
Otof	T	C	5: 30,540,914 (GRCm39)	E875G	possibly damaging	Het
Pick1	A	T	15: 79,133,137 (GRCm39)	D399V	probably benign	Het
Pik3c2g	T	A	6: 139,665,744 (GRCm39)	S22T	probably benign	Het
Pnpla2	A	G	7: 141,038,574 (GRCm39)	E276G	possibly damaging	Het
Pomk	A	T	8: 26,473,633 (GRCm39)	S107T	probably damaging	Het
Rbm46	A	T	3: 82,771,765 (GRCm39)	D283E	probably benign	Het
Rimbp3	A	G	16: 17,030,962 (GRCm39)	D1462G	probably damaging	Het
Rnf112	T	A	11: 61,342,936 (GRCm39)	E230V	probably damaging	Het
Rock1	T	C	18: 10,112,391 (GRCm39)	T455A	probably benign	Het
Rtp4	A	T	16: 23,428,790 (GRCm39)	M18L	probably benign	Het
Scaf11	A	T	15: 96,317,981 (GRCm39)		probably null	Het
Schip1	T	C	3: 67,972,297 (GRCm39)	V8A	probably benign	Het
Sec31b	T	C	19: 44,515,060 (GRCm39)	H351R	probably benign	Het
Sh3bp5l	A	G	11: 58,237,177 (GRCm39)	D378G	probably benign	Het
Sowahb	T	C	5: 93,190,715 (GRCm39)	D668G	probably damaging	Het
Spam1	A	G	6: 24,800,586 (GRCm39)	T442A	probably benign	Het
Syt14	T	A	1: 192,615,633 (GRCm39)	Y451F	probably damaging	Het
Tafa5	T	G	15: 87,604,783 (GRCm39)	S115A	probably damaging	Het
Tdh	A	G	14: 63,731,205 (GRCm39)	L323P	possibly damaging	Het
Tet2	A	T	3: 133,193,843 (GRCm39)	M197K	probably benign	Het
Thbs1	G	A	2: 117,948,810 (GRCm39)	A489T	probably benign	Het
Tnfaip1	C	T	11: 78,420,008 (GRCm39)	R88Q	probably damaging	Het
Tnn	T	C	1: 159,973,612 (GRCm39)	M252V	probably benign	Het
Trdn	G	T	10: 33,071,977 (GRCm39)	E215*	probably null	Het
Trim55	T	C	3: 19,725,286 (GRCm39)	F268L	probably benign	Het
Trmt112	T	A	19: 6,887,816 (GRCm39)	V55E	possibly damaging	Het
Tube1	A	G	10: 39,018,363 (GRCm39)	M147V	possibly damaging	Het
Ubn1	A	G	16: 4,895,851 (GRCm39)	T966A	probably damaging	Het
Unc80	A	G	1: 66,708,394 (GRCm39)	I2651V	probably benign	Het
Vmn1r172	G	A	7: 23,359,919 (GRCm39)	R268H	probably benign	Het
Vmn1r231	T	A	17: 21,110,571 (GRCm39)	I115F	probably damaging	Het
Vmn1r237	A	G	17: 21,534,400 (GRCm39)	K41R	probably benign	Het
Vmn2r58	A	T	7: 41,509,935 (GRCm39)	N547K	probably damaging	Het
Vmn2r74	T	C	7: 85,606,782 (GRCm39)	D188G	probably benign	Het
Vwa5b2	A	G	16: 20,415,079 (GRCm39)	K367R	probably damaging	Het
Washc4	T	A	10: 83,410,407 (GRCm39)	M665K	possibly damaging	Het
Wbp11	T	A	6: 136,798,189 (GRCm39)	Y236F	probably benign	Het
Wbp4	T	A	14: 79,709,801 (GRCm39)	I145F	possibly damaging	Het
Wwc2	C	A	8: 48,373,636 (GRCm39)	D77Y	probably damaging	Het
Zpld2	G	A	4: 133,929,459 (GRCm39)	A282V	probably benign	Het

Other mutations in Kdm5a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00540:Kdm5a	APN	6	120,362,680 (GRCm39)	critical splice donor site	probably null	0.00
IGL00706:Kdm5a	APN	6	120,383,597 (GRCm39)	missense	possibly damaging	0.44
IGL01361:Kdm5a	APN	6	120,375,977 (GRCm39)	missense	probably damaging	1.00
IGL01402:Kdm5a	APN	6	120,367,640 (GRCm39)	nonsense	probably null	0.00
IGL01924:Kdm5a	APN	6	120,371,216 (GRCm39)	critical splice donor site	probably null	0.00
IGL01935:Kdm5a	APN	6	120,385,284 (GRCm39)	missense	probably benign	0.02
IGL02165:Kdm5a	APN	6	120,392,251 (GRCm39)	missense	probably damaging	1.00
IGL02472:Kdm5a	APN	6	120,383,691 (GRCm39)	splice site	probably benign
IGL02506:Kdm5a	APN	6	120,409,110 (GRCm39)	missense	probably damaging	0.99
IGL02604:Kdm5a	APN	6	120,408,941 (GRCm39)	missense	probably benign
IGL02633:Kdm5a	APN	6	120,341,680 (GRCm39)	missense	probably damaging	1.00
IGL02876:Kdm5a	APN	6	120,367,605 (GRCm39)	unclassified	probably benign
IGL03009:Kdm5a	APN	6	120,407,047 (GRCm39)	missense	probably damaging	0.98
IGL03027:Kdm5a	APN	6	120,351,951 (GRCm39)	splice site	probably null
IGL03164:Kdm5a	APN	6	120,415,980 (GRCm39)	missense	probably damaging	1.00
IGL03236:Kdm5a	APN	6	120,415,949 (GRCm39)	missense	probably damaging	0.98
IGL03276:Kdm5a	APN	6	120,379,669 (GRCm39)	splice site	probably benign
Anastasia	UTSW	6	120,407,192 (GRCm39)	nonsense	probably null
Augmented	UTSW	6	120,406,977 (GRCm39)	intron	probably benign
Calla_lily	UTSW	6	120,381,983 (GRCm39)	missense	probably damaging	1.00
crocus	UTSW	6	120,375,999 (GRCm39)	missense	probably null	0.98
Magnolia	UTSW	6	120,375,939 (GRCm39)	missense	probably damaging	0.99
Saffron	UTSW	6	120,366,581 (GRCm39)	missense	probably benign	0.19
Selbst	UTSW	6	120,365,066 (GRCm39)	nonsense	probably null
R0320:Kdm5a	UTSW	6	120,366,581 (GRCm39)	missense	probably benign	0.19
R0462:Kdm5a	UTSW	6	120,379,561 (GRCm39)	missense	probably damaging	1.00
R0601:Kdm5a	UTSW	6	120,379,632 (GRCm39)	missense	possibly damaging	0.76
R0628:Kdm5a	UTSW	6	120,392,200 (GRCm39)	missense	probably damaging	1.00
R1024:Kdm5a	UTSW	6	120,375,999 (GRCm39)	missense	probably null	0.98
R2013:Kdm5a	UTSW	6	120,408,951 (GRCm39)	missense	probably benign	0.09
R2015:Kdm5a	UTSW	6	120,408,951 (GRCm39)	missense	probably benign	0.09
R2061:Kdm5a	UTSW	6	120,358,578 (GRCm39)	missense	probably benign
R2188:Kdm5a	UTSW	6	120,383,601 (GRCm39)	missense	possibly damaging	0.59
R3923:Kdm5a	UTSW	6	120,358,625 (GRCm39)	missense	probably benign	0.01
R4013:Kdm5a	UTSW	6	120,371,067 (GRCm39)	missense	probably damaging	1.00
R4016:Kdm5a	UTSW	6	120,371,067 (GRCm39)	missense	probably damaging	1.00
R4017:Kdm5a	UTSW	6	120,371,067 (GRCm39)	missense	probably damaging	1.00
R4030:Kdm5a	UTSW	6	120,382,074 (GRCm39)	nonsense	probably null
R4737:Kdm5a	UTSW	6	120,382,976 (GRCm39)	intron	probably benign
R4779:Kdm5a	UTSW	6	120,346,060 (GRCm39)	unclassified	probably benign
R4836:Kdm5a	UTSW	6	120,389,363 (GRCm39)	missense	probably damaging	1.00
R5129:Kdm5a	UTSW	6	120,381,983 (GRCm39)	missense	probably damaging	1.00
R5182:Kdm5a	UTSW	6	120,365,066 (GRCm39)	nonsense	probably null
R5183:Kdm5a	UTSW	6	120,406,977 (GRCm39)	intron	probably benign
R5572:Kdm5a	UTSW	6	120,389,336 (GRCm39)	missense	possibly damaging	0.69
R6110:Kdm5a	UTSW	6	120,389,267 (GRCm39)	missense	probably damaging	1.00
R6132:Kdm5a	UTSW	6	120,351,892 (GRCm39)	missense	probably damaging	1.00
R6198:Kdm5a	UTSW	6	120,415,958 (GRCm39)	missense	probably benign	0.37
R6246:Kdm5a	UTSW	6	120,408,871 (GRCm39)	missense	probably damaging	0.97
R6336:Kdm5a	UTSW	6	120,375,939 (GRCm39)	missense	probably damaging	0.99
R6343:Kdm5a	UTSW	6	120,359,894 (GRCm39)	missense	probably benign	0.01
R6612:Kdm5a	UTSW	6	120,407,189 (GRCm39)	missense	probably damaging	0.99
R6647:Kdm5a	UTSW	6	120,389,422 (GRCm39)	missense	probably benign	0.25
R7068:Kdm5a	UTSW	6	120,407,176 (GRCm39)	missense	probably benign	0.40
R7369:Kdm5a	UTSW	6	120,408,965 (GRCm39)	missense	possibly damaging	0.67
R7380:Kdm5a	UTSW	6	120,382,879 (GRCm39)	missense	probably benign	0.35
R7411:Kdm5a	UTSW	6	120,403,776 (GRCm39)	missense	probably damaging	1.00
R7521:Kdm5a	UTSW	6	120,409,148 (GRCm39)	nonsense	probably null
R7570:Kdm5a	UTSW	6	120,404,803 (GRCm39)	missense	probably damaging	0.99
R7647:Kdm5a	UTSW	6	120,404,747 (GRCm39)	missense	probably benign	0.01
R7704:Kdm5a	UTSW	6	120,404,025 (GRCm39)	missense	probably damaging	1.00
R7796:Kdm5a	UTSW	6	120,367,724 (GRCm39)	missense	probably damaging	1.00
R7875:Kdm5a	UTSW	6	120,375,979 (GRCm39)	nonsense	probably null
R8265:Kdm5a	UTSW	6	120,383,557 (GRCm39)	missense	possibly damaging	0.72
R8297:Kdm5a	UTSW	6	120,358,516 (GRCm39)	missense	probably benign	0.00
R8336:Kdm5a	UTSW	6	120,396,407 (GRCm39)	missense	probably benign	0.00
R8471:Kdm5a	UTSW	6	120,407,192 (GRCm39)	nonsense	probably null
R8872:Kdm5a	UTSW	6	120,365,101 (GRCm39)	missense	probably damaging	1.00
R8890:Kdm5a	UTSW	6	120,366,624 (GRCm39)	missense	probably damaging	1.00
R9028:Kdm5a	UTSW	6	120,416,092 (GRCm39)	missense	probably benign
R9064:Kdm5a	UTSW	6	120,403,869 (GRCm39)	small deletion	probably benign
R9114:Kdm5a	UTSW	6	120,382,887 (GRCm39)	nonsense	probably null
R9316:Kdm5a	UTSW	6	120,381,973 (GRCm39)	missense	probably damaging	1.00
R9353:Kdm5a	UTSW	6	120,404,730 (GRCm39)	missense	probably benign	0.01
R9412:Kdm5a	UTSW	6	120,365,991 (GRCm39)	missense	probably damaging	1.00
R9416:Kdm5a	UTSW	6	120,365,056 (GRCm39)	missense	probably damaging	1.00
R9431:Kdm5a	UTSW	6	120,392,253 (GRCm39)	missense	probably damaging	1.00
R9711:Kdm5a	UTSW	6	120,367,658 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TTTTCCAGATTGTTGCCAGC -3'
(R):5'- GATTCCAGTTGGCTATGCATAAGC -3'

Sequencing Primer
(F):5'- TTCCAGATTGTTGCCAGCAAAGG -3'
(R):5'- GAGAAACCCTGTCTCGAA -3'

Posted On

2015-10-08