Mutagenetix > Incidental Mutation

Incidental Mutation 'R2188:Kdm5a'

237919

Institutional Source

Beutler Lab

Gene Symbol

Kdm5a

Ensembl Gene

ENSMUSG00000030180

Gene Name

lysine demethylase 5A

Synonyms

Rbbp2, Jarid1a, RBP2

MMRRC Submission

040190-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2188 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

120341085-120421535 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 120383601 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Isoleucine at position 781 (F781I)

Ref Sequence

ENSEMBL: ENSMUSP00000005108 (fasta)

Gene Model

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

AlphaFold

Q3UXZ9

Predicted Effect

possibly damaging
Transcript: ENSMUST00000005108
AA Change: F781I

PolyPhen 2 Score 0.590 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: F781I

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

possibly damaging
Transcript: ENSMUST00000100996
AA Change: F781I

PolyPhen 2 Score 0.590 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000098558
Gene: ENSMUSG00000030180
AA Change: F781I

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

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
AA Change: F781I

PolyPhen 2 Score 0.012 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000145021
Gene: ENSMUSG00000030180
AA Change: F781I

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

1x: 99.3%
3x: 98.6%
10x: 97.3%
20x: 95.1%

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: 38 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca7	T	C	10: 79,838,367 (GRCm39)	L547P	probably damaging	Het
Arhgap29	A	C	3: 121,784,658 (GRCm39)	D195A	probably damaging	Het
Atad3a	A	T	4: 155,835,976 (GRCm39)	I274N	probably damaging	Het
Ccdc12	G	T	9: 110,485,699 (GRCm39)	K23N	possibly damaging	Het
Ccpg1	A	G	9: 72,920,388 (GRCm39)	T668A	probably benign	Het
Cdc34b	T	C	11: 94,632,998 (GRCm39)	I66T	probably benign	Het
Dnah1	A	G	14: 31,001,121 (GRCm39)	I2408T	probably damaging	Het
Fam91a1	A	C	15: 58,302,512 (GRCm39)	N284T	probably damaging	Het
Gbp2b	A	T	3: 142,314,040 (GRCm39)	E440V	probably benign	Het
Gm5134	T	C	10: 75,831,670 (GRCm39)	S370P	probably damaging	Het
Hmcn2	G	A	2: 31,309,947 (GRCm39)	A3238T	probably benign	Het
Hmg20a	A	G	9: 56,384,584 (GRCm39)	E118G	possibly damaging	Het
Itprid2	T	C	2: 79,475,267 (GRCm39)	S409P	probably benign	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Kmt2d	A	G	15: 98,737,181 (GRCm39)		probably benign	Het
Lrp1b	T	C	2: 41,298,971 (GRCm39)	T857A	probably benign	Het
Mucl2	T	A	15: 103,927,840 (GRCm39)	N39I	probably damaging	Het
Myl6	A	G	10: 128,328,566 (GRCm39)	I27T	possibly damaging	Het
Ndor1	A	T	2: 25,141,765 (GRCm39)		probably null	Het
Nlrp9a	A	G	7: 26,264,354 (GRCm39)	E758G	probably damaging	Het
Or52h7	G	A	7: 104,213,883 (GRCm39)	A152T	probably benign	Het
Or8u8	A	T	2: 86,011,780 (GRCm39)	I225N	probably damaging	Het
Parp3	G	A	9: 106,353,051 (GRCm39)	R42W	probably damaging	Het
Pik3c2g	A	G	6: 139,798,600 (GRCm39)	I495V	probably damaging	Het
Qrfprl	C	A	6: 65,418,260 (GRCm39)	H143N	probably damaging	Het
Sdsl	C	T	5: 120,596,485 (GRCm39)	G310S	probably damaging	Het
Sec24a	A	G	11: 51,614,411 (GRCm39)	L531P	probably damaging	Het
Slc2a12	C	T	10: 22,540,736 (GRCm39)	S197F	probably benign	Het
Snapc1	T	A	12: 74,017,001 (GRCm39)	I213N	probably damaging	Het
Srpk1	A	T	17: 28,813,163 (GRCm39)	I527N	probably damaging	Het
Steap2	G	T	5: 5,723,643 (GRCm39)	Y412*	probably null	Het
Tbk1	A	C	10: 121,399,836 (GRCm39)	Y329*	probably null	Het
Tekt5	T	C	16: 10,176,189 (GRCm39)	E452G	probably damaging	Het
Tmc5	G	T	7: 118,254,178 (GRCm39)	C672F	probably damaging	Het
Trim27	T	C	13: 21,367,987 (GRCm39)	L201S	probably damaging	Het
Vil1	A	C	1: 74,466,724 (GRCm39)	D638A	probably benign	Het
Vmn2r68	TCC	TC	7: 84,870,758 (GRCm39)		probably null	Het
Zfp583	C	T	7: 6,320,610 (GRCm39)	R134H	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
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
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

Predicted Primers

PCR Primer
(F):5'- GTCATCTGTTGGGAATAAACATCTG -3'
(R):5'- AGAAACATGGCCACTGGAGC -3'

Sequencing Primer
(F):5'- CTGTTGGGAATAAACATCTGATCAG -3'
(R):5'- TGGAGCAAAATATAAAATAGGGCCTC -3'

Posted On

2014-10-02