Mutagenetix > Incidental Mutation

Incidental Mutation 'R9028:Kdm5a'

686869

Institutional Source

Beutler Lab

Gene Symbol

Kdm5a

Ensembl Gene

ENSMUSG00000030180

Gene Name

lysine (K)-specific demethylase 5A

Synonyms

Jarid1a, Rbbp2, RBP2

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9028 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

120364124-120444574 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 120439131 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Proline to Serine at position 1671 (P1671S)

Ref Sequence

ENSEMBL: ENSMUSP00000005108 (fasta)

Gene Model

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

AlphaFold

Q3UXZ9

Predicted Effect

probably benign
Transcript: ENSMUST00000005108
AA Change: P1671S

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

SMART Domains

Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: P1671S

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: 100.0%
10x: 99.8%
20x: 99.2%

Validation Efficiency

99% (74/75)

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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5330417C22Rik	G	A	3: 108,463,503	T687I	probably benign	Het
Aasdh	A	G	5: 76,876,130	V1066A	probably damaging	Het
Abca5	T	A	11: 110,298,078	H851L	probably damaging	Het
Actn2	T	C	13: 12,300,978	I218M	possibly damaging	Het
Afmid	G	A	11: 117,836,663	E338K	probably benign	Het
Amer3	G	A	1: 34,588,677	V666I	probably benign	Het
Apol7b	A	G	15: 77,423,416	V293A	probably damaging	Het
Bag6	T	A	17: 35,144,154	S657T	probably benign	Het
Btaf1	T	C	19: 36,969,108	L438P	probably damaging	Het
Cdc20	T	C	4: 118,436,560	E126G	probably benign	Het
Cep97	C	T	16: 55,919,552	W248*	probably null	Het
Cfap69	A	T	5: 5,646,958	S113T	probably benign	Het
Cgrrf1	C	A	14: 46,853,743	D241E	probably benign	Het
Cnksr1	T	C	4: 134,233,297	T280A	possibly damaging	Het
Cox4i1	T	A	8: 120,671,283		probably benign	Het
Cpm	T	A	10: 117,683,509	F441I	probably benign	Het
Cs	A	C	10: 128,353,083	M154L		Het
Dmrta1	T	A	4: 89,691,677	N291K	probably damaging	Het
Dnah7a	T	C	1: 53,521,138	T2125A	probably benign	Het
Dock10	A	T	1: 80,606,295		probably benign	Het
Dok7	A	G	5: 35,079,475	Y369C	probably damaging	Het
E130311K13Rik	T	C	3: 63,915,548	Y225C	probably damaging	Het
F7	T	C	8: 13,026,087	L10P	possibly damaging	Het
Faf1	C	A	4: 109,890,908	T470K	possibly damaging	Het
Fam83h	A	T	15: 76,003,889	L533Q	possibly damaging	Het
Far1	T	A	7: 113,547,422	V129E	probably damaging	Het
Fgfr4	T	C	13: 55,159,154	Y219H	probably damaging	Het
Fryl	A	T	5: 73,098,266	S807R	probably benign	Het
Gaa	T	A	11: 119,270,381	D83E	probably benign	Het
Gm6970	T	C	19: 47,170,690	K149E	unknown	Het
Grm2	A	G	9: 106,651,185	S167P	possibly damaging	Het
Hibch	T	C	1: 52,853,709	L26P	possibly damaging	Het
Hspa9	T	C	18: 34,942,031	E415G	probably damaging	Het
Ipo4	T	C	14: 55,628,951	Y757C	probably damaging	Het
Itk	T	A	11: 46,344,883		probably benign	Het
Kif13a	G	A	13: 46,798,365	P811S	probably damaging	Het
Kif23	T	C	9: 61,921,059	E857G	probably damaging	Het
Kif2b	A	G	11: 91,577,185	S91P	probably benign	Het
Letm1	G	T	5: 33,752,503	Q396K	probably damaging	Het
Map2k6	T	A	11: 110,497,973	M247K		Het
Mga	A	G	2: 119,947,589	I1872V	probably benign	Het
Mmp15	A	T	8: 95,369,688	N369I	probably benign	Het
Myo3a	T	A	2: 22,600,087	S1487T	possibly damaging	Het
Ncam1	T	C	9: 49,507,436	T855A		Het
Ncoa2	A	G	1: 13,152,855	V1182A	probably benign	Het
Nhlrc3	A	T	3: 53,453,571	C254*	probably null	Het
Nlrp1a	C	T	11: 71,122,993	R477H	probably benign	Het
Nox3	T	A	17: 3,665,910	T407S	possibly damaging	Het
Olfr1229	T	A	2: 89,282,332	D267V	probably damaging	Het
Olfr1375	C	T	11: 51,048,833	T242M	probably damaging	Het
Olfr411	T	C	11: 74,346,921	Y101C	probably damaging	Het
Pfkp	T	A	13: 6,605,689	I303F	probably damaging	Het
Pgc	T	C	17: 47,733,058	Y292H	possibly damaging	Het
Phtf2	A	G	5: 20,794,375	Y257H	probably benign	Het
Pkdrej	T	C	15: 85,816,897	N1613D	probably damaging	Het
Prpmp5	C	T	6: 132,312,655	E69K	unknown	Het
Rapgef2	A	G	3: 79,074,344	S1115P	probably damaging	Het
Rbpj	A	G	5: 53,649,690	E260G	possibly damaging	Het
Rrm1	T	A	7: 102,460,398	N476K	probably damaging	Het
Slc9a2	T	A	1: 40,726,452	I334N	probably damaging	Het
Slk	T	G	19: 47,620,073	N488K	probably benign	Het
Smarca5	T	C	8: 80,714,013	I607M	probably damaging	Het
Sspo	G	A	6: 48,496,153	V162M	probably benign	Het
Svep1	T	G	4: 58,145,199	Q422P	possibly damaging	Het
Tcn2	C	T	11: 3,922,111	V339I	probably damaging	Het
Tnfrsf19	T	C	14: 61,005,201	H78R	probably benign	Het
Trav14-3	C	A	14: 53,763,430	Q33K	unknown	Het
Ubtd2	T	C	11: 32,499,432	I93T	possibly damaging	Het
Uhrf2	G	A	19: 30,089,344		probably null	Het
Vmn1r224	T	G	17: 20,419,850	S230A	possibly damaging	Het
Wee2	A	T	6: 40,444,255	H93L	probably benign	Het
Zdhhc17	T	C	10: 110,961,073	E279G	probably damaging	Het
Zfp623	T	A	15: 75,947,500	F102I	probably damaging	Het
Zfpm2	A	C	15: 41,103,362	E1081A	possibly damaging	Het
Zscan18	A	T	7: 12,772,189		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
Anastasia	UTSW	6	120430231	nonsense	probably null
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
Saffron	UTSW	6	120389620	missense	probably benign	0.19
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
R5572:Kdm5a	UTSW	6	120412375	missense	possibly damaging	0.69
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
R8872:Kdm5a	UTSW	6	120388140	missense	probably damaging	1.00
R8890:Kdm5a	UTSW	6	120389663	missense	probably damaging	1.00
R9064:Kdm5a	UTSW	6	120426908	small deletion	probably benign
R9114:Kdm5a	UTSW	6	120405926	nonsense	probably null
R9316:Kdm5a	UTSW	6	120405012	missense	probably damaging	1.00
R9353:Kdm5a	UTSW	6	120427769	missense	probably benign	0.01
R9412:Kdm5a	UTSW	6	120389030	missense	probably damaging	1.00
R9416:Kdm5a	UTSW	6	120388095	missense	probably damaging	1.00
R9431:Kdm5a	UTSW	6	120415292	missense	probably damaging	1.00
R9711:Kdm5a	UTSW	6	120390697	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TCTGGCCTTACTGTTATGATGC -3'
(R):5'- CAATCCATGCAGAGAGGAAGCC -3'

Sequencing Primer
(F):5'- CTGGCCTTACTGTTATGATGCTAAAC -3'
(R):5'- GCCAGCACTAAGAGGACTTTTTCTG -3'

Posted On

2021-11-19