Mutagenetix > Incidental Mutation

Incidental Mutation 'R7647:Kdm5a'

590587

Institutional Source

Beutler Lab

Gene Symbol

Kdm5a

Ensembl Gene

ENSMUSG00000030180

Gene Name

lysine demethylase 5A

Synonyms

Rbbp2, Jarid1a, RBP2

MMRRC Submission

045725-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7647 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

120341085-120421535 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 120404747 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 1330 (S1330T)

Ref Sequence

ENSEMBL: ENSMUSP00000005108 (fasta)

Gene Model

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

AlphaFold

Q3UXZ9

Predicted Effect

probably benign
Transcript: ENSMUST00000005108
AA Change: S1330T

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: S1330T

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: 99.6%
20x: 98.8%

Validation Efficiency

100% (43/43)

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: 45 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5730507C01Rik	C	A	12: 18,564,803 (GRCm39)	T22K	possibly damaging	Het
Abca7	G	T	10: 79,836,656 (GRCm39)	M344I	probably benign	Het
Alg14	T	C	3: 121,155,334 (GRCm39)	S185P	probably damaging	Het
Atg13	A	T	2: 91,519,006 (GRCm39)	H146Q	possibly damaging	Het
Atmin	T	G	8: 117,684,661 (GRCm39)	F774V	possibly damaging	Het
Ccdc150	A	G	1: 54,395,863 (GRCm39)	D782G	probably damaging	Het
Ccdc86	A	G	19: 10,926,363 (GRCm39)	S79P	unknown	Het
Cd180	A	T	13: 102,842,451 (GRCm39)	E499V	probably damaging	Het
Cd24a	C	T	10: 43,458,747 (GRCm39)	H73Y	unknown	Het
Cdh17	C	T	4: 11,814,698 (GRCm39)	P751L	probably damaging	Het
Chil3	A	G	3: 106,056,122 (GRCm39)	L344S	possibly damaging	Het
Cspp1	A	G	1: 10,206,162 (GRCm39)	D1129G	probably benign	Het
Cyth1	C	A	11: 118,068,114 (GRCm39)	V288L	probably benign	Het
Ddx19a	A	T	8: 111,703,259 (GRCm39)		probably null	Het
Dpysl4	T	A	7: 138,679,689 (GRCm39)	Y520N	possibly damaging	Het
Eif4b	T	A	15: 101,997,129 (GRCm39)	M249K	unknown	Het
Enam	G	A	5: 88,650,884 (GRCm39)	D798N	probably benign	Het
Fcgbpl1	A	G	7: 27,839,470 (GRCm39)	K428E	probably benign	Het
Gldc	A	G	19: 30,096,067 (GRCm39)	V648A	probably damaging	Het
Gm7995	A	G	14: 42,133,308 (GRCm39)	I62V	possibly damaging	Het
Ice1	A	G	13: 70,737,916 (GRCm39)	V2177A	possibly damaging	Het
Mon2	G	T	10: 122,841,931 (GRCm39)	P1553Q	probably benign	Het
Mylk	G	C	16: 34,699,894 (GRCm39)	S419T	probably benign	Het
Nphs1	T	A	7: 30,181,390 (GRCm39)		probably null	Het
Nsd1	A	G	13: 55,447,648 (GRCm39)	T1924A	probably damaging	Het
Obscn	T	A	11: 58,888,113 (GRCm39)		probably null	Het
Or11l3	A	T	11: 58,516,029 (GRCm39)	V281D	probably damaging	Het
Or52h9	T	C	7: 104,202,893 (GRCm39)	F256L	probably benign	Het
Or6c213	A	T	10: 129,574,070 (GRCm39)	C239S	probably damaging	Het
Or6c6	T	C	10: 129,187,326 (GRCm39)	V298A	probably benign	Het
Pcsk1	A	G	13: 75,280,329 (GRCm39)	D718G	possibly damaging	Het
Pitrm1	A	T	13: 6,605,444 (GRCm39)	N158I	probably damaging	Het
Pkd1l1	C	T	11: 8,897,296 (GRCm39)	V538M		Het
Prkdc	G	T	16: 15,555,807 (GRCm39)	G2194C	probably damaging	Het
Psmc5	T	C	11: 106,152,433 (GRCm39)	M150T	possibly damaging	Het
Rint1	T	C	5: 24,005,800 (GRCm39)	Y161H	probably damaging	Het
Sdk2	T	C	11: 113,684,563 (GRCm39)	K1966R	probably damaging	Het
Sgcb	A	T	5: 73,796,720 (GRCm39)		probably null	Het
Slc4a7	G	A	14: 14,773,348 (GRCm38)	E773K	probably benign	Het
Sp100	A	G	1: 85,619,764 (GRCm39)	K353E	possibly damaging	Het
Ssh1	T	C	5: 114,081,019 (GRCm39)	T804A	probably benign	Het
Vipr1	T	C	9: 121,482,905 (GRCm39)	L40P	possibly damaging	Het
Vmn1r7	A	G	6: 57,002,255 (GRCm39)	S2P	probably benign	Het
Vwa8	T	C	14: 79,172,669 (GRCm39)	S304P	probably damaging	Het
Zbed4	T	C	15: 88,665,924 (GRCm39)	M664T	probably damaging	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
R4646:Kdm5a	UTSW	6	120,351,938 (GRCm39)	missense	possibly damaging	0.55
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
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'- CTCTGTTGAAGAAGTCTGTTAGC -3'
(R):5'- ACATAATCGCCATGGCAGGG -3'

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

Posted On

2019-10-24