Mutagenetix > Incidental Mutation

Incidental Mutation 'R7570:Kdm5a'

585705

Institutional Source

Beutler Lab

Gene Symbol

Kdm5a

Ensembl Gene

ENSMUSG00000030180

Gene Name

lysine (K)-specific demethylase 5A

Synonyms

Jarid1a, Rbbp2, RBP2

MMRRC Submission

045631-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7570 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

120364124-120444574 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 120427842 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 1348 (D1348E)

Ref Sequence

ENSEMBL: ENSMUSP00000005108 (fasta)

Gene Model

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

AlphaFold

Q3UXZ9

Predicted Effect

probably damaging
Transcript: ENSMUST00000005108
AA Change: D1348E

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: D1348E

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

98% (104/106)

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: 106 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930590J08Rik	C	T	6: 91,934,610	T613I	probably benign	Het
9130019O22Rik	T	A	7: 127,385,283	S216C	probably benign	Het
Ajuba	T	C	14: 54,576,402	E288G	probably damaging	Het
Ankrd12	C	T	17: 65,985,360	R1026K	probably benign	Het
Apol7b	T	C	15: 77,423,474	T274A	probably benign	Het
Arid4a	A	T	12: 71,063,142	R86*	probably null	Het
Asnsd1	C	T	1: 53,348,258	G70D	probably damaging	Het
Atg4c	T	A	4: 99,228,560	V313D	possibly damaging	Het
Atp13a5	A	C	16: 29,266,963	C885G	probably damaging	Het
Bpifb9a	A	T	2: 154,262,263	I209F	possibly damaging	Het
Bsn	T	C	9: 108,113,543	D1670G	probably damaging	Het
Cct8	T	A	16: 87,491,322	I121F	probably benign	Het
Cd209a	T	G	8: 3,744,151	D217A	probably damaging	Het
Cdk19	C	T	10: 40,477,958	S456L	possibly damaging	Het
Chd9	C	T	8: 90,994,580	H999Y	unknown	Het
Col5a1	G	A	2: 27,951,383	V339M	unknown	Het
Cr2	G	A	1: 195,169,340	R115*	probably null	Het
Cyb561	A	T	11: 105,937,644	F62I	probably damaging	Het
Cyp2c38	A	T	19: 39,404,743	N293K	possibly damaging	Het
Cyp2c69	A	T	19: 39,859,898	D293E	probably damaging	Het
Dcbld2	T	A	16: 58,424,569	C69S	possibly damaging	Het
Dcdc2a	T	C	13: 25,119,373	S296P	probably benign	Het
Dmxl1	T	A	18: 49,893,957	I2044K	possibly damaging	Het
Dnah5	A	G	15: 28,346,952	D2527G	probably damaging	Het
Dnah6	T	C	6: 73,149,430	T1305A	probably benign	Het
Dnajc9	A	G	14: 20,388,644	V47A	probably benign	Het
Dnmt3b	A	G	2: 153,676,699	Y594C	probably damaging	Het
Dph7	A	G	2: 24,965,630	D147G	probably damaging	Het
Drap1	T	C	19: 5,423,352	H164R	possibly damaging	Het
Dsg3	T	A	18: 20,527,780	V392E	possibly damaging	Het
Dxo	A	G	17: 34,837,640	D81G	probably benign	Het
E230025N22Rik	G	T	18: 36,695,592	T11K	probably benign	Het
Esyt1	A	G	10: 128,518,932	V533A	possibly damaging	Het
Etv3	T	A	3: 87,536,031	C307*	probably null	Het
Fam114a1	T	A	5: 65,030,059		probably null	Het
Fam208b	A	G	13: 3,573,621	Y2110H	probably damaging	Het
Fam3c	T	A	6: 22,326,405		probably benign	Het
Fbn1	G	T	2: 125,397,852	T305K	probably benign	Het
Ggt1	A	T	10: 75,585,594	I484F	probably damaging	Het
Gm10639	A	T	9: 78,304,469	D171V	possibly damaging	Het
Gpatch1	T	C	7: 35,293,812	D536G	probably damaging	Het
Gpx4	T	C	10: 80,055,041	I189T	probably damaging	Het
Gsr	T	A	8: 33,669,165	C85S	probably damaging	Het
Havcr1	T	A	11: 46,770,542		probably null	Het
Heatr4	T	C	12: 83,979,644	T280A	probably benign	Het
Hmcn2	A	T	2: 31,423,911	E3532D	probably benign	Het
Hnrnpc	T	C	14: 52,075,099	N308S	possibly damaging	Het
Ighv8-9	A	G	12: 115,468,738	V13A	probably benign	Het
Itgb2l	A	T	16: 96,426,239	F535I	probably benign	Het
Kndc1	CT	C	7: 139,923,775		probably null	Het
Ky	A	G	9: 102,542,329	I512V	probably benign	Het
Lamc1	A	T	1: 153,243,275	F866Y	possibly damaging	Het
Lbx1	C	A	19: 45,235,248		probably benign	Het
Magel2	A	G	7: 62,378,910	T521A	possibly damaging	Het
Mgam	A	T	6: 40,746,433	I491L	probably benign	Het
Mitd1	T	C	1: 37,890,192	E40G	probably damaging	Het
Mpzl3	A	G	9: 45,070,687	T218A	probably benign	Het
Mrpl42	A	G	10: 95,480,965	S77P	probably benign	Het
Mup5	C	T	4: 61,834,674	W37*	probably null	Het
Myh14	T	C	7: 44,632,426	I803V	probably benign	Het
Ncor2	T	A	5: 125,030,089	T744S		Het
Ndufv3	A	G	17: 31,527,622	D162G	probably damaging	Het
Nostrin	A	G	2: 69,175,806	E278G	probably damaging	Het
Nrxn1	T	G	17: 90,162,379	E1288A	probably benign	Het
Olfr1205	A	G	2: 88,831,128	N4D	possibly damaging	Het
Olfr623	C	A	7: 103,660,881	R123L	probably damaging	Het
Olfr648	T	A	7: 104,179,748	Y220F	probably damaging	Het
Olfr972	A	T	9: 39,873,455	Y60F	possibly damaging	Het
Patj	T	A	4: 98,424,500		probably null	Het
Pcm1	T	G	8: 41,267,344	I314R	possibly damaging	Het
Pcsk6	A	G	7: 66,033,898	T754A	probably benign	Het
Pde2a	A	T	7: 101,502,834	N326I	probably benign	Het
Plekhg4	T	C	8: 105,378,684	S594P	possibly damaging	Het
Plekhm3	T	C	1: 64,937,906	D135G	probably damaging	Het
Plin4	A	T	17: 56,106,776	M283K	probably benign	Het
Ppfia3	T	C	7: 45,340,748		probably null	Het
Prdm9	T	C	17: 15,555,652	N179S	probably benign	Het
Prrt3	T	C	6: 113,494,488	S908G	probably damaging	Het
Psg22	C	A	7: 18,722,735	S181Y	possibly damaging	Het
Rcor3	C	A	1: 192,137,876	G8V	probably damaging	Het
Rp1l1	T	A	14: 64,031,574	C1536*	probably null	Het
Rpp25l	T	C	4: 41,712,529	H82R	probably damaging	Het
Rps3a1	T	A	3: 86,139,089	M172L	probably benign	Het
Rtbdn	T	C	8: 84,952,927	L110P	probably damaging	Het
Ryr1	T	A	7: 29,078,585	Q2169L	probably damaging	Het
Scn4a	A	T	11: 106,320,473	C1573S	possibly damaging	Het
Sec16b	A	T	1: 157,531,395		probably null	Het
Serpina1a	A	T	12: 103,853,837	D383E	possibly damaging	Het
Sh3gl3	T	C	7: 82,285,077	M262T	probably benign	Het
Sos2	G	A	12: 69,590,880	T1052M	probably damaging	Het
Spag16	G	A	1: 69,996,841	V343I	probably benign	Het
Spocd1	T	G	4: 129,930,164	D251E		Het
Stc2	G	T	11: 31,367,798	N74K	probably damaging	Het
Thbs3	C	T	3: 89,219,052	Q227*	probably null	Het
Tmem92	A	C	11: 94,778,990	I105R	probably benign	Het
Tmod1	T	A	4: 46,083,632	N20K	probably benign	Het
Tns1	T	C	1: 73,953,479	D53G	probably damaging	Het
Tspan33	T	A	6: 29,717,338	L246Q	probably damaging	Het
Ttc16	A	G	2: 32,768,968	L392P	probably damaging	Het
Uggt1	T	A	1: 36,185,838	T572S	probably benign	Het
Usp17la	A	T	7: 104,860,397	T70S	probably damaging	Het
Usp31	C	T	7: 121,674,963	R370H	probably damaging	Het
Wdr83	C	T	8: 85,079,834	V112M	probably damaging	Het
Zbtb25	T	A	12: 76,369,592		probably benign	Het
Zfp110	T	A	7: 12,849,340	N638K	possibly damaging	Het
Zfp820	T	C	17: 21,819,013	T445A	probably benign	Het

Other mutations in Kdm5a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00540:Kdm5a	APN	6	120,385,719 (GRCm38)	critical splice donor site	probably null	0.00
IGL00706:Kdm5a	APN	6	120,406,636 (GRCm38)	missense	possibly damaging	0.44
IGL01361:Kdm5a	APN	6	120,399,016 (GRCm38)	missense	probably damaging	1.00
IGL01402:Kdm5a	APN	6	120,390,679 (GRCm38)	nonsense	probably null	0.00
IGL01924:Kdm5a	APN	6	120,394,255 (GRCm38)	critical splice donor site	probably null	0.00
IGL01935:Kdm5a	APN	6	120,408,323 (GRCm38)	missense	probably benign	0.02
IGL02165:Kdm5a	APN	6	120,415,290 (GRCm38)	missense	probably damaging	1.00
IGL02472:Kdm5a	APN	6	120,406,730 (GRCm38)	splice site	probably benign
IGL02506:Kdm5a	APN	6	120,432,149 (GRCm38)	missense	probably damaging	0.99
IGL02604:Kdm5a	APN	6	120,431,980 (GRCm38)	missense	probably benign
IGL02633:Kdm5a	APN	6	120,364,719 (GRCm38)	missense	probably damaging	1.00
IGL02876:Kdm5a	APN	6	120,390,644 (GRCm38)	unclassified	probably benign
IGL03009:Kdm5a	APN	6	120,430,086 (GRCm38)	missense	probably damaging	0.98
IGL03027:Kdm5a	APN	6	120,374,990 (GRCm38)	splice site	probably null
IGL03164:Kdm5a	APN	6	120,439,019 (GRCm38)	missense	probably damaging	1.00
IGL03236:Kdm5a	APN	6	120,438,988 (GRCm38)	missense	probably damaging	0.98
IGL03276:Kdm5a	APN	6	120,402,708 (GRCm38)	splice site	probably benign
Anastasia	UTSW	6	120,430,231 (GRCm38)	nonsense	probably null
Augmented	UTSW	6	120,430,016 (GRCm38)	intron	probably benign
Calla_lily	UTSW	6	120,405,022 (GRCm38)	missense	probably damaging	1.00
crocus	UTSW	6	120,399,038 (GRCm38)	missense	probably null	0.98
Magnolia	UTSW	6	120,398,978 (GRCm38)	missense	probably damaging	0.99
Saffron	UTSW	6	120,389,620 (GRCm38)	missense	probably benign	0.19
Selbst	UTSW	6	120,388,105 (GRCm38)	nonsense	probably null
R0320:Kdm5a	UTSW	6	120,389,620 (GRCm38)	missense	probably benign	0.19
R0462:Kdm5a	UTSW	6	120,402,600 (GRCm38)	missense	probably damaging	1.00
R0601:Kdm5a	UTSW	6	120,402,671 (GRCm38)	missense	possibly damaging	0.76
R0628:Kdm5a	UTSW	6	120,415,239 (GRCm38)	missense	probably damaging	1.00
R1024:Kdm5a	UTSW	6	120,399,038 (GRCm38)	missense	probably null	0.98
R2013:Kdm5a	UTSW	6	120,431,990 (GRCm38)	missense	probably benign	0.09
R2015:Kdm5a	UTSW	6	120,431,990 (GRCm38)	missense	probably benign	0.09
R2061:Kdm5a	UTSW	6	120,381,617 (GRCm38)	missense	probably benign
R2188:Kdm5a	UTSW	6	120,406,640 (GRCm38)	missense	possibly damaging	0.59
R3923:Kdm5a	UTSW	6	120,381,664 (GRCm38)	missense	probably benign	0.01
R4013:Kdm5a	UTSW	6	120,394,106 (GRCm38)	missense	probably damaging	1.00
R4016:Kdm5a	UTSW	6	120,394,106 (GRCm38)	missense	probably damaging	1.00
R4017:Kdm5a	UTSW	6	120,394,106 (GRCm38)	missense	probably damaging	1.00
R4030:Kdm5a	UTSW	6	120,405,113 (GRCm38)	nonsense	probably null
R4646:Kdm5a	UTSW	6	120,374,977 (GRCm38)	missense	possibly damaging	0.55
R4737:Kdm5a	UTSW	6	120,406,015 (GRCm38)	intron	probably benign
R4779:Kdm5a	UTSW	6	120,369,099 (GRCm38)	unclassified	probably benign
R4836:Kdm5a	UTSW	6	120,412,402 (GRCm38)	missense	probably damaging	1.00
R5129:Kdm5a	UTSW	6	120,405,022 (GRCm38)	missense	probably damaging	1.00
R5182:Kdm5a	UTSW	6	120,388,105 (GRCm38)	nonsense	probably null
R5183:Kdm5a	UTSW	6	120,430,016 (GRCm38)	intron	probably benign
R5572:Kdm5a	UTSW	6	120,412,375 (GRCm38)	missense	possibly damaging	0.69
R6110:Kdm5a	UTSW	6	120,412,306 (GRCm38)	missense	probably damaging	1.00
R6132:Kdm5a	UTSW	6	120,374,931 (GRCm38)	missense	probably damaging	1.00
R6198:Kdm5a	UTSW	6	120,438,997 (GRCm38)	missense	probably benign	0.37
R6246:Kdm5a	UTSW	6	120,431,910 (GRCm38)	missense	probably damaging	0.97
R6336:Kdm5a	UTSW	6	120,398,978 (GRCm38)	missense	probably damaging	0.99
R6343:Kdm5a	UTSW	6	120,382,933 (GRCm38)	missense	probably benign	0.01
R6612:Kdm5a	UTSW	6	120,430,228 (GRCm38)	missense	probably damaging	0.99
R6647:Kdm5a	UTSW	6	120,412,461 (GRCm38)	missense	probably benign	0.25
R7068:Kdm5a	UTSW	6	120,430,215 (GRCm38)	missense	probably benign	0.40
R7369:Kdm5a	UTSW	6	120,432,004 (GRCm38)	missense	possibly damaging	0.67
R7380:Kdm5a	UTSW	6	120,405,918 (GRCm38)	missense	probably benign	0.35
R7411:Kdm5a	UTSW	6	120,426,815 (GRCm38)	missense	probably damaging	1.00
R7521:Kdm5a	UTSW	6	120,432,187 (GRCm38)	nonsense	probably null
R7647:Kdm5a	UTSW	6	120,427,786 (GRCm38)	missense	probably benign	0.01
R7704:Kdm5a	UTSW	6	120,427,064 (GRCm38)	missense	probably damaging	1.00
R7796:Kdm5a	UTSW	6	120,390,763 (GRCm38)	missense	probably damaging	1.00
R7875:Kdm5a	UTSW	6	120,399,018 (GRCm38)	nonsense	probably null
R8265:Kdm5a	UTSW	6	120,406,596 (GRCm38)	missense	possibly damaging	0.72
R8297:Kdm5a	UTSW	6	120,381,555 (GRCm38)	missense	probably benign	0.00
R8336:Kdm5a	UTSW	6	120,419,446 (GRCm38)	missense	probably benign	0.00
R8471:Kdm5a	UTSW	6	120,430,231 (GRCm38)	nonsense	probably null
R8872:Kdm5a	UTSW	6	120,388,140 (GRCm38)	missense	probably damaging	1.00
R8890:Kdm5a	UTSW	6	120,389,663 (GRCm38)	missense	probably damaging	1.00
R9028:Kdm5a	UTSW	6	120,439,131 (GRCm38)	missense	probably benign
R9064:Kdm5a	UTSW	6	120,426,908 (GRCm38)	small deletion	probably benign
R9114:Kdm5a	UTSW	6	120,405,926 (GRCm38)	nonsense	probably null
R9316:Kdm5a	UTSW	6	120,405,012 (GRCm38)	missense	probably damaging	1.00
R9353:Kdm5a	UTSW	6	120,427,769 (GRCm38)	missense	probably benign	0.01
R9412:Kdm5a	UTSW	6	120,389,030 (GRCm38)	missense	probably damaging	1.00
R9416:Kdm5a	UTSW	6	120,388,095 (GRCm38)	missense	probably damaging	1.00
R9431:Kdm5a	UTSW	6	120,415,292 (GRCm38)	missense	probably damaging	1.00
R9711:Kdm5a	UTSW	6	120,390,697 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GTTGAAGAAGTCTGTTAGCTGC -3'
(R):5'- ACATAATCGCCATGGCAGGG -3'

Sequencing Primer
(F):5'- AGAAGTCTGTTAGCTGCTTTTTAAG -3'
(R):5'- CCACCCTCAGTCCTTAAGTA -3'

Posted On

2019-10-17