Mutagenetix > Incidental Mutation

Incidental Mutation 'R8265:Kdm5a'

639673

Institutional Source

Beutler Lab

Gene Symbol

Kdm5a

Ensembl Gene

ENSMUSG00000030180

Gene Name

lysine demethylase 5A

Synonyms

Rbbp2, Jarid1a, RBP2

MMRRC Submission

067690-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8265 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

120341085-120421535 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 120383557 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 766 (M766K)

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: M766K

PolyPhen 2 Score 0.722 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000005108
Gene: ENSMUSG00000030180
AA Change: M766K

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 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

possibly damaging
Transcript: ENSMUST00000135802
AA Change: M766K

PolyPhen 2 Score 0.460 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000145021
Gene: ENSMUSG00000030180
AA Change: M766K

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: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

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: 45 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1810055G02Rik	A	G	19: 3,766,568 (GRCm39)	T52A	probably benign	Het
Adam9	T	C	8: 25,457,202 (GRCm39)	Y642C	probably damaging	Het
Atp2c1	T	C	9: 105,347,315 (GRCm39)	E47G	probably benign	Het
Btbd9	T	A	17: 30,553,278 (GRCm39)	T395S	possibly damaging	Het
Cacna1s	G	A	1: 136,020,364 (GRCm39)	W800*	probably null	Het
Cdr1	AAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCAGAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCAGAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCAGAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCAGAAGTCCAAGTCTTCCCAGAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCAGAAGTCCAAGTCTTCCCAGAAGTCCAAGTCTTCCCGAAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCC	AAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCAGAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCAGAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCAGAAGTCCAAGTCTTCCCAGAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCAGAAGTCCAAGTCTTCCCAGAAGTCCAAGTCTTCCCGAAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCCGAAAATCCAAGTCTTCCC	X: 60,228,130 (GRCm39)		probably benign	Het
Ceacam20	G	A	7: 19,708,159 (GRCm39)	V255M	probably damaging	Het
Cit	C	A	5: 116,126,236 (GRCm39)	L1610M	probably damaging	Het
Cped1	A	G	6: 22,222,426 (GRCm39)	T729A	probably benign	Het
Ddx19b	A	T	8: 111,735,824 (GRCm39)	V407E	probably damaging	Het
Dst	A	G	1: 34,217,603 (GRCm39)	K1348E	probably benign	Het
E2f4	T	A	8: 106,027,977 (GRCm39)	S302T	probably damaging	Het
Eif1	A	G	11: 100,211,299 (GRCm39)	E31G	probably benign	Het
G530012D18Rik	C	G	1: 85,504,935 (GRCm39)	D113E	unknown	Het
Herc1	C	T	9: 66,293,986 (GRCm39)	Q443*	probably null	Het
Hmgxb3	A	G	18: 61,300,410 (GRCm39)	V222A	possibly damaging	Het
Hnrnpu	A	T	1: 178,159,725 (GRCm39)	I452N	unknown	Het
Ints1	C	G	5: 139,757,919 (GRCm39)	D260H	probably damaging	Het
Lama4	G	A	10: 38,981,200 (GRCm39)	C1720Y	probably damaging	Het
Mei1	C	A	15: 81,987,508 (GRCm39)	Y433*	probably null	Het
Milr1	A	G	11: 106,654,711 (GRCm39)	K188E	probably benign	Het
Myo7a	A	G	7: 97,734,604 (GRCm39)	F630S	probably benign	Het
Myoz2	A	G	3: 122,800,172 (GRCm39)	F219L	probably benign	Het
Nt5c1a	T	C	4: 123,107,953 (GRCm39)	V212A	possibly damaging	Het
Or51f1e	A	G	7: 102,747,304 (GRCm39)	T119A	probably benign	Het
Or51v14	A	T	7: 103,261,048 (GRCm39)	C171S	possibly damaging	Het
Or8b42	T	C	9: 38,342,469 (GRCm39)	V297A	probably damaging	Het
Pi16	A	G	17: 29,545,947 (GRCm39)	T242A	probably benign	Het
Pigw	C	A	11: 84,770,847 (GRCm39)		probably benign	Het
Pipox	T	A	11: 77,774,793 (GRCm39)	T97S	probably benign	Het
Plagl1	C	A	10: 13,004,625 (GRCm39)	A631E	unknown	Het
Poteg	T	A	8: 27,984,923 (GRCm39)	H427Q	possibly damaging	Het
Prdm14	A	G	1: 13,184,618 (GRCm39)	S518P	probably damaging	Het
Rabep2	A	G	7: 126,043,423 (GRCm39)	E441G	probably benign	Het
Rasal3	A	G	17: 32,614,794 (GRCm39)		probably null	Het
Rbm33	T	C	5: 28,599,322 (GRCm39)	V90A		Het
Sidt1	C	A	16: 44,088,250 (GRCm39)	R381M	possibly damaging	Het
Sppl2b	TGTCACAGGT	TGT	10: 80,701,903 (GRCm39)		probably null	Het
Srsf5	A	G	12: 80,994,110 (GRCm39)	D51G	possibly damaging	Het
Taar8a	T	A	10: 23,952,839 (GRCm39)	S148T	probably damaging	Het
Tmem59l	A	G	8: 70,938,426 (GRCm39)	S149P	probably damaging	Het
Trafd1	T	A	5: 121,511,340 (GRCm39)	I493F	possibly damaging	Het
Trrap	C	T	5: 144,722,344 (GRCm39)	S289L	possibly damaging	Het
Zfp267	T	C	3: 36,213,677 (GRCm39)		probably benign	Het
Zfp955a	C	T	17: 33,463,087 (GRCm39)	V15M	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
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
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'- CTGTTGGGAATAAACATCTGATCAG -3'
(R):5'- TGGAAGAAACATGGCCACTG -3'

Sequencing Primer
(F):5'- CCATTGTAGAATGGCTGTT -3'
(R):5'- CCTCATAGGCCAATTAAAGTGGAAAG -3'

Posted On

2020-07-28