Mutagenetix > Incidental Mutation

Incidental Mutation 'R4013:Kdm5a'

311814

Institutional Source

Beutler Lab

Gene Symbol

Kdm5a

Ensembl Gene

ENSMUSG00000030180

Gene Name

lysine demethylase 5A

Synonyms

Rbbp2, Jarid1a, RBP2

MMRRC Submission

040950-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4013 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

120341085-120421535 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 120371067 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Asparagine at position 504 (Y504N)

Ref Sequence

ENSEMBL: ENSMUSP00000145021 (fasta)

Gene Model

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

AlphaFold

Q3UXZ9

Predicted Effect

probably damaging
Transcript: ENSMUST00000005108
AA Change: Y504N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: Y504N

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: Y504N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000098558
Gene: ENSMUSG00000030180
AA Change: Y504N

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

probably damaging
Transcript: ENSMUST00000132009
AA Change: Y504N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000145375
Gene: ENSMUSG00000030180
AA Change: Y504N

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 damaging
Transcript: ENSMUST00000135802
AA Change: Y504N

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000145021
Gene: ENSMUSG00000030180
AA Change: Y504N

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

Meta Mutation Damage Score

0.9676

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.6%
20x: 92.4%

Validation Efficiency

98% (47/48)

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
Abcc6	T	C	7: 45,668,104 (GRCm39)	Q168R	probably benign	Het
Adgrg3	A	G	8: 95,761,727 (GRCm39)		probably benign	Het
Apold1	A	G	6: 134,960,869 (GRCm39)	I108V	probably benign	Het
Atp6v0a2	G	A	5: 124,789,860 (GRCm39)	V429M	probably damaging	Het
Cbln4	A	T	2: 171,879,477 (GRCm39)	M137K	probably damaging	Het
Cfap57	A	G	4: 118,450,340 (GRCm39)	V594A	probably benign	Het
Chd9	A	G	8: 91,699,797 (GRCm39)	E28G	possibly damaging	Het
Clip4	T	A	17: 72,163,541 (GRCm39)	C704*	probably null	Het
Col8a2	T	A	4: 126,204,908 (GRCm39)		probably benign	Het
Cyp3a59	A	G	5: 146,016,193 (GRCm39)	T17A	probably benign	Het
Cyp4f14	G	A	17: 33,135,853 (GRCm39)	Q3*	probably null	Het
Cysltr2	A	G	14: 73,267,005 (GRCm39)	I235T	probably damaging	Het
Esp34	C	A	17: 38,870,446 (GRCm39)	C45*	probably null	Het
Gabrg2	T	C	11: 41,862,707 (GRCm39)	K126E	possibly damaging	Het
Gm4846	A	C	1: 166,322,249 (GRCm39)		probably null	Het
Igsf21	T	C	4: 139,764,780 (GRCm39)	N165S	possibly damaging	Het
Kcnf1	A	G	12: 17,225,994 (GRCm39)	F76L	probably benign	Het
Kcns1	A	G	2: 164,010,177 (GRCm39)	V194A	probably damaging	Het
Kdm5b	A	G	1: 134,555,067 (GRCm39)	Y1325C	possibly damaging	Het
Kif1a	T	C	1: 93,004,014 (GRCm39)	D156G	probably damaging	Het
Lrp1b	A	G	2: 40,692,996 (GRCm39)	F3401L	possibly damaging	Het
Lrrc63	A	G	14: 75,335,731 (GRCm39)	Y460H	probably damaging	Het
Myo15b	G	T	11: 115,762,282 (GRCm39)	E1201*	probably null	Het
Ndor1	A	T	2: 25,140,162 (GRCm39)	I84K	probably damaging	Het
Ndst4	T	A	3: 125,476,819 (GRCm39)	Y15N	probably damaging	Het
Or51af1	T	C	7: 103,141,840 (GRCm39)	T82A	probably benign	Het
Or5ar1	A	G	2: 85,671,725 (GRCm39)	S137P	probably damaging	Het
Pik3r6	T	A	11: 68,424,347 (GRCm39)	D317E	possibly damaging	Het
Ppp2r1a	G	A	17: 21,171,609 (GRCm39)	R28H	probably damaging	Het
Ptch1	T	G	13: 63,672,773 (GRCm39)	E944A	probably benign	Het
Ptpn12	G	A	5: 21,197,741 (GRCm39)	P700L	probably benign	Het
Setx	GTGGCT	GT	2: 29,044,073 (GRCm39)	1814	probably null	Het
Slc39a13	T	C	2: 90,895,247 (GRCm39)		probably null	Het
Smarca2	G	A	19: 26,661,327 (GRCm39)		probably null	Het
Taok1	A	T	11: 77,450,659 (GRCm39)	L371H	possibly damaging	Het
Tas2r116	A	G	6: 132,833,230 (GRCm39)	H277R	probably damaging	Het
Treml4	G	A	17: 48,571,837 (GRCm39)	R80Q	probably benign	Het
Trim9	G	A	12: 70,393,126 (GRCm39)	H273Y	probably damaging	Het
Tyr	A	G	7: 87,087,148 (GRCm39)	S455P	probably benign	Het
Vmn1r214	G	A	13: 23,219,520 (GRCm39)	C338Y	probably benign	Het
Vmn2r52	G	A	7: 9,904,603 (GRCm39)	T412I	probably benign	Het
Wdr70	A	T	15: 8,108,698 (GRCm39)	C149*	probably null	Het
Wdr93	T	A	7: 79,418,159 (GRCm39)	V294E	possibly 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
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'- TCTGAGGTTCTAGAGAGTTATGTCC -3'
(R):5'- TGACTCATACTTTAAGGATCCCTTC -3'

Sequencing Primer
(F):5'- GGTTCTAGAGAGTTATGTCCATATCC -3'
(R):5'- CCATGAGCACATTTGGGT -3'

Posted On

2015-04-29