Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL03164:Kdm5a'

411561

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Kdm5a

Ensembl Gene

ENSMUSG00000030180

Gene Name

lysine demethylase 5A

Synonyms

Rbbp2, Jarid1a, RBP2

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

IGL03164

Quality Score

Status

Chromosome

Chromosomal Location

120341085-120421535 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 120415980 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 1633 (D1633E)

Ref Sequence

ENSEMBL: ENSMUSP00000005108 (fasta)

Gene Model

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

AlphaFold

Q3UXZ9

Predicted Effect

probably damaging
Transcript: ENSMUST00000005108
AA Change: D1633E

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: D1633E

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: ENSMUST00000142791

Coding Region Coverage

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: 43 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadac	A	G	3: 59,947,070 (GRCm39)	D256G	probably damaging	Het
Abcb11	A	T	2: 69,122,343 (GRCm39)	L380*	probably null	Het
Aco1	A	T	4: 40,167,116 (GRCm39)	N110I	probably benign	Het
Adamts9	T	C	6: 92,866,918 (GRCm39)	D126G	probably damaging	Het
Anks1b	T	G	10: 89,878,554 (GRCm39)	V121G	probably damaging	Het
Ap1s3	A	G	1: 79,602,887 (GRCm39)	L40P	probably damaging	Het
Cd19	C	A	7: 126,012,681 (GRCm39)	M237I	possibly damaging	Het
Chil6	T	C	3: 106,301,714 (GRCm39)	T129A	probably benign	Het
Chtf18	A	G	17: 25,945,816 (GRCm39)	M94T	probably benign	Het
Clstn2	G	T	9: 97,681,462 (GRCm39)	D59E	possibly damaging	Het
Cplx3	T	C	9: 57,517,278 (GRCm39)	T369A	probably damaging	Het
Ctnnbl1	A	C	2: 157,659,681 (GRCm39)	M253L	probably benign	Het
Erg	T	C	16: 95,210,730 (GRCm39)	T41A	possibly damaging	Het
Gjd3	T	A	11: 102,691,547 (GRCm39)	N152I	possibly damaging	Het
Ints1	A	G	5: 139,738,490 (GRCm39)	L2084P	probably damaging	Het
Isoc1	C	T	18: 58,806,404 (GRCm39)	S238L	probably damaging	Het
Krt76	T	C	15: 101,795,886 (GRCm39)	D428G	possibly damaging	Het
Lrp2	G	T	2: 69,295,043 (GRCm39)	T3425K	probably damaging	Het
Lta4h	T	C	10: 93,306,659 (GRCm39)		probably benign	Het
Nap1l4	C	T	7: 143,091,953 (GRCm39)		probably null	Het
Nlrp5	T	A	7: 23,117,798 (GRCm39)	Y507*	probably null	Het
Nps	T	C	7: 134,874,039 (GRCm39)	S53P	probably damaging	Het
Oprk1	A	T	1: 5,669,087 (GRCm39)	I178F	probably damaging	Het
Or2a12	C	T	6: 42,905,064 (GRCm39)	R300*	probably null	Het
Or5p1	T	C	7: 107,916,901 (GRCm39)	S267P	probably damaging	Het
Osgin2	G	T	4: 16,001,938 (GRCm39)	S204R	probably benign	Het
Otop1	G	T	5: 38,445,306 (GRCm39)	G155*	probably null	Het
Peli3	A	G	19: 4,986,144 (GRCm39)		probably null	Het
Pex7	T	A	10: 19,770,461 (GRCm39)		probably benign	Het
Pfkm	T	C	15: 98,029,843 (GRCm39)	L749P	probably damaging	Het
Pwp1	T	A	10: 85,714,367 (GRCm39)	F103Y	probably benign	Het
Rhod	T	C	19: 4,482,829 (GRCm39)	K63E	possibly damaging	Het
Rtl1	T	C	12: 109,559,367 (GRCm39)	E824G	probably damaging	Het
Sema4d	A	G	13: 51,862,958 (GRCm39)	F467L	possibly damaging	Het
Septin10	T	C	10: 59,016,921 (GRCm39)	E201G	probably damaging	Het
Slc37a3	G	A	6: 39,322,237 (GRCm39)	T389I	probably benign	Het
Slco2b1	C	T	7: 99,334,743 (GRCm39)	A243T	probably damaging	Het
Sorbs2	A	G	8: 46,235,911 (GRCm39)	T187A	probably benign	Het
Supt20	T	A	3: 54,620,609 (GRCm39)	D389E	probably benign	Het
Tchh	A	G	3: 93,352,699 (GRCm39)	D713G	unknown	Het
Trappc10	T	C	10: 78,056,076 (GRCm39)	R209G	probably damaging	Het
Unc119	A	G	11: 78,239,002 (GRCm39)	D176G	probably damaging	Het
Usb1	G	A	8: 96,060,112 (GRCm39)	R21Q	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
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
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

Posted On

2016-08-02