Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01361:Kdm5a'

75739

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 #

IGL01361

Quality Score

Status

Chromosome

Chromosomal Location

120341085-120421535 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 120375977 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Asparagine at position 578 (Y578N)

Gene Model

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

AlphaFold

Q3UXZ9

Predicted Effect

probably benign
Transcript: ENSMUST00000005108
AA Change: Y578N

PolyPhen 2 Score 0.264 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: Y578N

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

probably damaging
Transcript: ENSMUST00000100996
AA Change: Y578N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000098558
Gene: ENSMUSG00000030180
AA Change: Y578N

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	728	3.6e-17	PFAM
Pfam:PLU-1	741	1072	5e-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
PHD	1614	1659	1.27e-6	SMART
low complexity region	1662	1674	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000132009
AA Change: Y578N

PolyPhen 2 Score 0.905 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000145375
Gene: ENSMUSG00000030180
AA Change: Y578N

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

possibly damaging
Transcript: ENSMUST00000135802
AA Change: Y578N

PolyPhen 2 Score 0.869 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000145021
Gene: ENSMUSG00000030180
AA Change: Y578N

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

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: 36 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Ankrd36	T	A	11: 5,546,706 (GRCm39)		probably benign	Het
C1qtnf3	G	A	15: 10,960,768 (GRCm39)	G157D	probably damaging	Het
Cacna1b	T	C	2: 24,569,107 (GRCm39)	E940G	possibly damaging	Het
Camta1	A	G	4: 151,229,149 (GRCm39)	L561P	probably damaging	Het
Car15	T	C	16: 17,655,718 (GRCm39)	Y27C	probably damaging	Het
Catsper1	G	T	19: 5,389,507 (GRCm39)	S474I	probably damaging	Het
Cps1	A	G	1: 67,234,304 (GRCm39)	D897G	probably benign	Het
Crtc1	A	G	8: 70,840,253 (GRCm39)	L540P	probably damaging	Het
Fdps	A	G	3: 89,001,749 (GRCm39)		probably benign	Het
Gprc6a	A	G	10: 51,491,526 (GRCm39)	I741T	probably damaging	Het
Hdac7	A	C	15: 97,709,323 (GRCm39)	M47R	possibly damaging	Het
Kalrn	T	C	16: 33,996,092 (GRCm39)		probably benign	Het
Kat14	C	A	2: 144,248,540 (GRCm39)		probably null	Het
Kcnu1	T	C	8: 26,376,796 (GRCm39)	V390A	possibly damaging	Het
Lrp1b	T	C	2: 41,000,763 (GRCm39)		probably benign	Het
Mpc2	G	T	1: 165,307,092 (GRCm39)	A98S	probably benign	Het
Nek10	T	C	14: 14,850,957 (GRCm38)	I334T	probably damaging	Het
Nufip2	T	A	11: 77,583,196 (GRCm39)	V370E	possibly damaging	Het
Nup160	C	A	2: 90,514,356 (GRCm39)	Y101*	probably null	Het
Obscn	T	A	11: 58,919,715 (GRCm39)	Y6174F	probably damaging	Het
Omp	A	T	7: 97,794,489 (GRCm39)	I46N	probably benign	Het
Pcbp4	A	T	9: 106,340,448 (GRCm39)		probably null	Het
Pctp	A	G	11: 89,879,552 (GRCm39)	V103A	probably damaging	Het
Pla2r1	A	G	2: 60,309,814 (GRCm39)	Y590H	probably damaging	Het
Ppfibp2	T	C	7: 107,343,508 (GRCm39)		probably null	Het
Reln	G	A	5: 22,124,019 (GRCm39)	T2829M	probably benign	Het
Sh3yl1	T	A	12: 30,989,563 (GRCm39)		probably benign	Het
Sipa1l3	A	T	7: 29,048,112 (GRCm39)	Y210N	probably damaging	Het
Slc33a1	C	A	3: 63,850,833 (GRCm39)	C497F	probably damaging	Het
Srp9	G	A	1: 181,958,902 (GRCm39)	C25Y	probably damaging	Het
Traf4	C	A	11: 78,056,226 (GRCm39)	R14L	possibly damaging	Het
Tut7	A	T	13: 59,933,614 (GRCm39)	I894K	probably damaging	Het
Usf3	C	A	16: 44,033,000 (GRCm39)		probably null	Het
Vmn2r85	T	C	10: 130,254,690 (GRCm39)	T665A	probably benign	Het
Vps13a	C	T	19: 16,720,371 (GRCm39)	A405T	probably damaging	Het
Zan	A	T	5: 137,412,604 (GRCm39)		probably benign	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
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
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

2013-10-07