Mutagenetix > Incidental Mutations

Incidental Mutation 'R5572:Kdm5a'

435725

Institutional Source

Beutler Lab

Gene Symbol

Kdm5a

Ensembl Gene

ENSMUSG00000030180

Gene Name

lysine (K)-specific demethylase 5A

Synonyms

Jarid1a, Rbbp2, RBP2

MMRRC Submission

043266-MU

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R5572 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

120364124-120444574 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 120412375 bp

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 921 (V921A)

Ref Sequence

ENSEMBL: ENSMUSP00000005108 (fasta)

Gene Model

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000005108
AA Change: V921A

PolyPhen 2 Score 0.688 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: V921A

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

noncoding transcript
Transcript: ENSMUST00000124847

Predicted Effect

probably benign
Transcript: ENSMUST00000132009

SMART Domains

Protein: ENSMUSP00000145375
Gene: ENSMUSG00000030180

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

SMART Domains

Protein: ENSMUSP00000145021
Gene: ENSMUSG00000030180

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

Meta Mutation Damage Score

0.0761

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.4%
20x: 95.2%

Validation Efficiency

100% (64/64)

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: 56 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610507B11Rik	A	T	11: 78,264,567	D167V	probably damaging	Het
Abcb1a	C	T	5: 8,715,108		probably null	Het
Abcd4	T	C	12: 84,606,276	D380G	probably benign	Het
Actr3b	T	A	5: 25,809,888	D68E	probably benign	Het
Apol10a	T	C	15: 77,488,634	S157P	probably damaging	Het
Arap3	A	T	18: 37,991,066	I327N	probably damaging	Het
Arnt	G	T	3: 95,474,704	V198L	possibly damaging	Het
Baiap3	T	A	17: 25,251,475	D86V	possibly damaging	Het
Bcl9l	G	T	9: 44,500,798	R27L	possibly damaging	Het
C1qc	T	C	4: 136,892,462	Y34C	probably benign	Het
C1rb	T	C	6: 124,580,799	S632P	probably benign	Het
C3	A	G	17: 57,224,673	S284P	probably damaging	Het
Cfap44	T	G	16: 44,481,305	V1802G	possibly damaging	Het
Cfhr1	A	G	1: 139,556,427	V117A	possibly damaging	Het
Clca3b	T	C	3: 144,827,309	D654G	probably damaging	Het
Col17a1	A	T	19: 47,650,729	S1126T	probably benign	Het
Cts3	T	A	13: 61,564,968	I313F	probably damaging	Het
Egfl7	T	C	2: 26,591,691	V6A	possibly damaging	Het
Eif2s3y	G	A	Y: 1,016,631	D272N	probably damaging	Het
Fam129a	T	C	1: 151,709,190	S513P	probably benign	Het
Foxp4	A	G	17: 47,880,879	V111A	unknown	Het
Hmcn2	A	T	2: 31,414,525		probably null	Het
Hmcn2	G	A	2: 31,414,526		probably null	Het
Igsf11	C	T	16: 39,024,932	R283C	probably damaging	Het
Il1a	A	G	2: 129,307,918	Y21H	possibly damaging	Het
Il6ra	A	T	3: 89,871,282	V420D	probably damaging	Het
Kirrel3	G	A	9: 35,000,948	A196T	probably damaging	Het
Klra1	T	A	6: 130,372,839	D212V	possibly damaging	Het
N4bp2l2	G	A	5: 150,662,290	T75I	probably benign	Het
Nnmt	A	G	9: 48,592,147	L193P	probably damaging	Het
Npdc1	G	A	2: 25,408,945	D284N	probably damaging	Het
Ntm	A	G	9: 29,014,216	I191T	probably damaging	Het
Olfr318	A	G	11: 58,720,229	V273A	probably benign	Het
Olfr607	A	C	7: 103,460,698	L170R	probably benign	Het
Olfr652	A	T	7: 104,564,994	T258S	probably benign	Het
Pam	A	C	1: 97,854,744		probably benign	Het
Pomk	T	A	8: 25,983,190	H245L	possibly damaging	Het
Rapgef4	G	A	2: 72,034,120		probably null	Het
Rasip1	G	T	7: 45,636,729	R792L	probably benign	Het
Ret	T	C	6: 118,155,431	Y1016C	probably damaging	Het
Rhbdd1	A	T	1: 82,340,810	N138I	possibly damaging	Het
Snx13	T	G	12: 35,103,120	V383G	probably damaging	Het
Syt3	A	G	7: 44,390,718	H125R	probably benign	Het
Tlr6	A	T	5: 64,955,018	L182Q	probably damaging	Het
Tlr9	T	C	9: 106,225,637	V709A	possibly damaging	Het
Tmprss6	T	C	15: 78,442,422	Y655C	probably damaging	Het
Ttn	A	T	2: 76,853,628		probably benign	Het
Ube3a	T	C	7: 59,288,777	I761T	probably damaging	Het
Ube3b	G	A	5: 114,406,179	D546N	probably damaging	Het
Ugt2b36	A	G	5: 87,089,482	V188A	possibly damaging	Het
Usp29	A	G	7: 6,962,192	I345V	probably benign	Het
Vmn2r78	A	G	7: 86,915,512	K55R	probably benign	Het
Wdsub1	A	G	2: 59,862,707	F288L	possibly damaging	Het
Zan	C	T	5: 137,394,431	V4601M	unknown	Het
Zbtb8b	T	C	4: 129,428,541	K376E	probably damaging	Het
Zfp619	A	T	7: 39,535,239	Y231F	probably benign	Het

Other mutations in Kdm5a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00540:Kdm5a	APN	6	120385719	critical splice donor site	probably null	0.00
IGL00706:Kdm5a	APN	6	120406636	missense	possibly damaging	0.44
IGL01361:Kdm5a	APN	6	120399016	missense	probably damaging	1.00
IGL01402:Kdm5a	APN	6	120390679	nonsense	probably null	0.00
IGL01924:Kdm5a	APN	6	120394255	critical splice donor site	probably null	0.00
IGL01935:Kdm5a	APN	6	120408323	missense	probably benign	0.02
IGL02165:Kdm5a	APN	6	120415290	missense	probably damaging	1.00
IGL02472:Kdm5a	APN	6	120406730	splice site	probably benign
IGL02506:Kdm5a	APN	6	120432149	missense	probably damaging	0.99
IGL02604:Kdm5a	APN	6	120431980	missense	probably benign
IGL02633:Kdm5a	APN	6	120364719	missense	probably damaging	1.00
IGL02876:Kdm5a	APN	6	120390644	unclassified	probably benign
IGL03009:Kdm5a	APN	6	120430086	missense	probably damaging	0.98
IGL03027:Kdm5a	APN	6	120374990	splice site	probably null
IGL03164:Kdm5a	APN	6	120439019	missense	probably damaging	1.00
IGL03236:Kdm5a	APN	6	120438988	missense	probably damaging	0.98
IGL03276:Kdm5a	APN	6	120402708	splice site	probably benign
Augmented	UTSW	6	120430016	intron	probably benign
Calla_lily	UTSW	6	120405022	missense	probably damaging	1.00
crocus	UTSW	6	120399038	missense	probably null	0.98
Magnolia	UTSW	6	120398978	missense	probably damaging	0.99
Selbst	UTSW	6	120388105	nonsense	probably null
R0320:Kdm5a	UTSW	6	120389620	missense	probably benign	0.19
R0462:Kdm5a	UTSW	6	120402600	missense	probably damaging	1.00
R0601:Kdm5a	UTSW	6	120402671	missense	possibly damaging	0.76
R0628:Kdm5a	UTSW	6	120415239	missense	probably damaging	1.00
R1024:Kdm5a	UTSW	6	120399038	missense	probably null	0.98
R2013:Kdm5a	UTSW	6	120431990	missense	probably benign	0.09
R2015:Kdm5a	UTSW	6	120431990	missense	probably benign	0.09
R2061:Kdm5a	UTSW	6	120381617	missense	probably benign
R2188:Kdm5a	UTSW	6	120406640	missense	possibly damaging	0.59
R3923:Kdm5a	UTSW	6	120381664	missense	probably benign	0.01
R4013:Kdm5a	UTSW	6	120394106	missense	probably damaging	1.00
R4016:Kdm5a	UTSW	6	120394106	missense	probably damaging	1.00
R4017:Kdm5a	UTSW	6	120394106	missense	probably damaging	1.00
R4030:Kdm5a	UTSW	6	120405113	nonsense	probably null
R4646:Kdm5a	UTSW	6	120374977	missense	possibly damaging	0.55
R4737:Kdm5a	UTSW	6	120406015	intron	probably benign
R4779:Kdm5a	UTSW	6	120369099	unclassified	probably benign
R4836:Kdm5a	UTSW	6	120412402	missense	probably damaging	1.00
R5129:Kdm5a	UTSW	6	120405022	missense	probably damaging	1.00
R5182:Kdm5a	UTSW	6	120388105	nonsense	probably null
R5183:Kdm5a	UTSW	6	120430016	intron	probably benign
R6110:Kdm5a	UTSW	6	120412306	missense	probably damaging	1.00
R6132:Kdm5a	UTSW	6	120374931	missense	probably damaging	1.00
R6198:Kdm5a	UTSW	6	120438997	missense	probably benign	0.37
R6246:Kdm5a	UTSW	6	120431910	missense	probably damaging	0.97
R6336:Kdm5a	UTSW	6	120398978	missense	probably damaging	0.99
R6343:Kdm5a	UTSW	6	120382933	missense	probably benign	0.01
R6612:Kdm5a	UTSW	6	120430228	missense	probably damaging	0.99
R6647:Kdm5a	UTSW	6	120412461	missense	probably benign	0.25
R7068:Kdm5a	UTSW	6	120430215	missense	probably benign	0.40
R7369:Kdm5a	UTSW	6	120432004	missense	possibly damaging	0.67
R7380:Kdm5a	UTSW	6	120405918	missense	probably benign	0.35
R7411:Kdm5a	UTSW	6	120426815	missense	probably damaging	1.00
R7521:Kdm5a	UTSW	6	120432187	nonsense	probably null
R7570:Kdm5a	UTSW	6	120427842	missense	probably damaging	0.99
R7647:Kdm5a	UTSW	6	120427786	missense	probably benign	0.01
R7704:Kdm5a	UTSW	6	120427064	missense	probably damaging	1.00
R7796:Kdm5a	UTSW	6	120390763	missense	probably damaging	1.00
R7875:Kdm5a	UTSW	6	120399018	nonsense	probably null
R8265:Kdm5a	UTSW	6	120406596	missense	possibly damaging	0.72
R8297:Kdm5a	UTSW	6	120381555	missense	probably benign	0.00
R8336:Kdm5a	UTSW	6	120419446	missense	probably benign	0.00
R8471:Kdm5a	UTSW	6	120430231	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- GCCATGATGGATGAAACCCC -3'
(R):5'- AAATGGGCTTTATGTTCCTCCAC -3'

Sequencing Primer
(F):5'- TGATGGATGAAACCCCAGATTCTTCC -3'
(R):5'- GCCACTTGTGCTGAAACTTGAAC -3'

Posted On

2016-10-24