Mutagenetix > Incidental Mutation

Incidental Mutation 'R0426:Kdm5d'

38704

Institutional Source

Beutler Lab

Gene Symbol

Kdm5d

Ensembl Gene

ENSMUSG00000056673

Gene Name

lysine demethylase 5D

Synonyms

Smcy, HY, Jarid1d

MMRRC Submission

038628-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.071) question?

Stock #

R0426 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

897566-943813 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

T to A at 942437 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000140462 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000055032] [ENSMUST00000186696] [ENSMUST00000186726]

AlphaFold

Q62240

Predicted Effect

probably benign
Transcript: ENSMUST00000055032

SMART Domains

Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673

Domain	Start	End	E-Value	Type
JmjN	13	54	3.45e-23	SMART
ARID	76	165	4.84e-36	SMART
BRIGHT	80	170	4.48e-38	SMART
PHD	325	371	8.56e-13	SMART
JmjC	467	633	2.52e-63	SMART
Pfam:zf-C5HC2	706	758	5.2e-18	PFAM
Pfam:PLU-1	771	1096	1.4e-89	PFAM
low complexity region	1147	1156	N/A	INTRINSIC
low complexity region	1164	1181	N/A	INTRINSIC
PHD	1182	1243	2.54e-6	SMART
coiled coil region	1290	1318	N/A	INTRINSIC
low complexity region	1340	1351	N/A	INTRINSIC
low complexity region	1395	1406	N/A	INTRINSIC
low complexity region	1453	1459	N/A	INTRINSIC
low complexity region	1525	1541	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000186696

SMART Domains

Protein: ENSMUSP00000140663
Gene: ENSMUSG00000056673

Domain	Start	End	E-Value	Type
JmjN	13	54	3.45e-23	SMART
ARID	76	165	4.84e-36	SMART
BRIGHT	80	170	4.48e-38	SMART
PHD	325	371	8.56e-13	SMART
JmjC	467	633	2.52e-63	SMART
low complexity region	675	689	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000186726

SMART Domains

Protein: ENSMUSP00000140462
Gene: ENSMUSG00000056673

Domain	Start	End	E-Value	Type
JmjN	13	54	1.4e-25	SMART
ARID	76	165	3.8e-40	SMART
BRIGHT	80	170	2.3e-40	SMART
Blast:ARID	175	260	1e-41	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000187296

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000189955

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.9%

Validation Efficiency

96% (86/90)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein containing zinc finger domains. A short peptide derived from this protein is a minor histocompatibility antigen which can lead to graft rejection of male donor cells in a female recipient. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

Allele List at MGI

Other mutations in this stock

Total: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8b	G	T	11: 109,845,853 (GRCm39)		probably benign	Het
Acadl	A	T	1: 66,880,805 (GRCm39)	F320L	probably damaging	Het
Acsbg1	T	C	9: 54,530,030 (GRCm39)	D222G	probably benign	Het
Anapc15	A	G	7: 101,547,240 (GRCm39)	T39A	probably benign	Het
Ano3	A	T	2: 110,491,519 (GRCm39)	V919E	probably damaging	Het
Arhgef12	T	C	9: 42,882,286 (GRCm39)		probably null	Het
Atad5	T	A	11: 80,003,658 (GRCm39)	I1091N	probably benign	Het
Atf1	A	T	15: 100,130,708 (GRCm39)	H26L	possibly damaging	Het
Atp10a	T	C	7: 58,434,482 (GRCm39)	M252T	probably benign	Het
Btbd8	C	T	5: 107,658,239 (GRCm39)	T1603I	probably damaging	Het
Cd55	C	T	1: 130,376,109 (GRCm39)	R347H	probably benign	Het
Cdc27	A	C	11: 104,403,853 (GRCm39)		probably null	Het
Cdh9	G	A	15: 16,823,540 (GRCm39)		probably null	Het
Cdk11b	T	C	4: 155,726,969 (GRCm39)		probably benign	Het
Cep70	A	G	9: 99,179,737 (GRCm39)	D567G	probably benign	Het
Cep78	A	T	19: 15,948,334 (GRCm39)	Y382*	probably null	Het
Cgas	G	A	9: 78,343,020 (GRCm39)		probably benign	Het
Col9a2	T	C	4: 120,901,857 (GRCm39)		probably benign	Het
Cyp2d12	G	A	15: 82,443,164 (GRCm39)	D409N	probably benign	Het
Ddx39a	A	G	8: 84,448,398 (GRCm39)	T217A	probably benign	Het
Dennd1b	T	A	1: 139,097,934 (GRCm39)	D733E	probably benign	Het
Dicer1	A	G	12: 104,668,801 (GRCm39)	S1294P	probably damaging	Het
Dnah3	T	C	7: 119,542,795 (GRCm39)	E3539G	probably benign	Het
Dnmbp	A	G	19: 43,840,875 (GRCm39)		probably benign	Het
Dysf	T	C	6: 84,126,739 (GRCm39)	L1332P	probably damaging	Het
F5	A	G	1: 164,010,409 (GRCm39)	D380G	probably damaging	Het
Fam171a1	T	C	2: 3,226,433 (GRCm39)	V522A	probably benign	Het
Fhip1b	A	C	7: 105,038,680 (GRCm39)	C186W	probably damaging	Het
Galr2	C	A	11: 116,172,517 (GRCm39)	A69D	probably damaging	Het
Grk2	T	C	19: 4,340,628 (GRCm39)		probably null	Het
Gtf3c1	A	T	7: 125,262,188 (GRCm39)	Y1119*	probably null	Het
Hgd	A	T	16: 37,409,047 (GRCm39)		probably benign	Het
Ildr2	G	T	1: 166,136,468 (GRCm39)	V436L	probably benign	Het
Intu	G	A	3: 40,629,735 (GRCm39)	C355Y	probably damaging	Het
Irf2bpl	G	T	12: 86,929,870 (GRCm39)	P268T	probably benign	Het
Jarid2	T	C	13: 44,994,358 (GRCm39)		probably null	Het
Jup	A	T	11: 100,263,227 (GRCm39)	M716K	probably benign	Het
Kank1	G	A	19: 25,388,837 (GRCm39)	V809I	probably damaging	Het
Kdm1b	T	A	13: 47,217,720 (GRCm39)		probably benign	Het
Kdm3a	C	T	6: 71,577,739 (GRCm39)	C687Y	probably damaging	Het
Kifap3	T	A	1: 163,693,121 (GRCm39)		probably benign	Het
Macf1	T	A	4: 123,377,453 (GRCm39)	K1400*	probably null	Het
Majin	A	G	19: 6,262,147 (GRCm39)		probably benign	Het
Mctp1	A	G	13: 77,168,940 (GRCm39)	I846V	probably benign	Het
Mrgpra2b	T	A	7: 47,113,875 (GRCm39)	I286F	possibly damaging	Het
Neil3	T	G	8: 54,062,431 (GRCm39)		probably benign	Het
Nox3	G	T	17: 3,745,838 (GRCm39)	N23K	probably damaging	Het
Nt5c3	T	C	6: 56,860,797 (GRCm39)	K219E	probably benign	Het
Or1e29	T	A	11: 73,667,263 (GRCm39)	M297L	probably benign	Het
Or52b4i	T	A	7: 102,191,893 (GRCm39)	I250N	probably damaging	Het
Or5b105	G	A	19: 13,080,642 (GRCm39)	R3C	possibly damaging	Het
Or6b13	A	C	7: 139,782,029 (GRCm39)	F218C	possibly damaging	Het
Or6d13	A	T	6: 116,517,446 (GRCm39)	N11Y	probably damaging	Het
Or8g34	T	C	9: 39,372,889 (GRCm39)	L54P	probably damaging	Het
Pacsin2	A	G	15: 83,263,996 (GRCm39)	V347A	possibly damaging	Het
Pcdhb7	A	T	18: 37,475,857 (GRCm39)	E331V	probably damaging	Het
Pcid2	A	C	8: 13,131,262 (GRCm39)		probably null	Het
Pcsk9	T	C	4: 106,307,274 (GRCm39)	D323G	possibly damaging	Het
Pdhb	T	C	14: 8,169,801 (GRCm38)	E203G	probably damaging	Het
Phlpp2	A	G	8: 110,655,095 (GRCm39)	Y630C	probably benign	Het
Pidd1	C	T	7: 141,019,046 (GRCm39)	A812T	probably damaging	Het
Plau	G	A	14: 20,892,382 (GRCm39)	R389H	probably benign	Het
Plekhg6	G	A	6: 125,341,592 (GRCm39)		probably null	Het
Ppox	T	C	1: 171,105,322 (GRCm39)	Y321C	probably damaging	Het
Pxdn	A	G	12: 30,037,065 (GRCm39)	N281S	possibly damaging	Het
Pycr3	A	T	15: 75,790,237 (GRCm39)	M138K	probably benign	Het
Radil	T	C	5: 142,483,628 (GRCm39)	Y526C	probably damaging	Het
Ranbp3	C	A	17: 57,014,169 (GRCm39)	D233E	probably benign	Het
Rhpn1	A	G	15: 75,583,721 (GRCm39)	Q402R	possibly damaging	Het
Sec23b	T	A	2: 144,410,532 (GRCm39)		probably benign	Het
Sel1l2	A	T	2: 140,082,832 (GRCm39)	L602*	probably null	Het
Sema5b	G	A	16: 35,466,725 (GRCm39)	G209D	probably damaging	Het
Svep1	T	C	4: 58,073,333 (GRCm39)	Y1992C	possibly damaging	Het
Syncrip	T	A	9: 88,338,312 (GRCm39)		probably benign	Het
Synj1	G	T	16: 90,764,242 (GRCm39)	A65E	probably damaging	Het
Taar2	G	A	10: 23,817,393 (GRCm39)	R311H	probably benign	Het
Tecrl	T	C	5: 83,502,610 (GRCm39)		probably benign	Het
Tenm4	G	T	7: 96,427,058 (GRCm39)	G698C	probably damaging	Het
Tmem209	G	A	6: 30,491,181 (GRCm39)	L259F	probably damaging	Het
Tmem247	G	A	17: 87,225,931 (GRCm39)	E124K	possibly damaging	Het
Tnks2	C	A	19: 36,830,221 (GRCm39)	A218E	probably damaging	Het
Tppp	T	A	13: 74,169,430 (GRCm39)	F57I	probably damaging	Het
Trim36	A	G	18: 46,305,592 (GRCm39)	W452R	probably damaging	Het
Vars2	A	T	17: 35,975,476 (GRCm39)	V262E	probably damaging	Het
Vmn2r92	C	T	17: 18,388,219 (GRCm39)	A408V	probably damaging	Het
Zfp516	G	T	18: 82,973,897 (GRCm39)	A32S	probably benign	Het
Zfy2	G	T	Y: 2,107,348 (GRCm39)	L429I	possibly damaging	Het

Other mutations in Kdm5d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0013:Kdm5d	UTSW	Y	941,715 (GRCm39)	missense	probably benign	0.37
R0013:Kdm5d	UTSW	Y	941,715 (GRCm39)	missense	probably benign	0.37
R0486:Kdm5d	UTSW	Y	927,107 (GRCm39)	missense	probably damaging	1.00
R0620:Kdm5d	UTSW	Y	927,330 (GRCm39)	missense	probably damaging	0.98
R0781:Kdm5d	UTSW	Y	910,539 (GRCm39)	missense	probably damaging	1.00
R1015:Kdm5d	UTSW	Y	941,687 (GRCm39)	missense	possibly damaging	0.95
R1110:Kdm5d	UTSW	Y	910,539 (GRCm39)	missense	probably damaging	1.00
R1163:Kdm5d	UTSW	Y	898,029 (GRCm39)	missense	probably benign	0.18
R1203:Kdm5d	UTSW	Y	941,011 (GRCm39)	missense	probably damaging	1.00
R1238:Kdm5d	UTSW	Y	941,282 (GRCm39)	missense	probably damaging	1.00
R1723:Kdm5d	UTSW	Y	927,753 (GRCm39)	missense	probably damaging	1.00
R1842:Kdm5d	UTSW	Y	927,798 (GRCm39)	missense	probably damaging	1.00
R1885:Kdm5d	UTSW	Y	940,781 (GRCm39)	splice site	probably null
R2131:Kdm5d	UTSW	Y	941,483 (GRCm39)	missense	probably benign	0.02
R2571:Kdm5d	UTSW	Y	940,932 (GRCm39)	missense	probably benign	0.11
R2931:Kdm5d	UTSW	Y	942,992 (GRCm39)	missense	probably benign	0.18
R3123:Kdm5d	UTSW	Y	900,558 (GRCm39)	missense	possibly damaging	0.63
R3919:Kdm5d	UTSW	Y	939,914 (GRCm39)	missense	probably damaging	1.00
R4018:Kdm5d	UTSW	Y	910,441 (GRCm39)	splice site	probably benign
R4031:Kdm5d	UTSW	Y	916,910 (GRCm39)	missense	probably damaging	1.00
R4403:Kdm5d	UTSW	Y	899,830 (GRCm39)	missense	probably damaging	1.00
R4571:Kdm5d	UTSW	Y	927,110 (GRCm39)	missense	probably damaging	1.00
R4583:Kdm5d	UTSW	Y	914,134 (GRCm39)	missense	probably damaging	1.00
R4962:Kdm5d	UTSW	Y	940,624 (GRCm39)	missense	probably damaging	1.00
R5105:Kdm5d	UTSW	Y	941,752 (GRCm39)	missense	probably benign	0.00
R5249:Kdm5d	UTSW	Y	916,692 (GRCm39)	missense	probably damaging	1.00
R5367:Kdm5d	UTSW	Y	941,645 (GRCm39)	missense	probably benign	0.05
R5373:Kdm5d	UTSW	Y	927,995 (GRCm39)	missense	probably benign	0.09
R5374:Kdm5d	UTSW	Y	927,995 (GRCm39)	missense	probably benign	0.09
R5876:Kdm5d	UTSW	Y	900,525 (GRCm39)	missense	probably damaging	1.00
R5909:Kdm5d	UTSW	Y	941,306 (GRCm39)	missense	probably benign	0.01
R6014:Kdm5d	UTSW	Y	921,528 (GRCm39)	missense	probably benign	0.45
R6109:Kdm5d	UTSW	Y	921,501 (GRCm39)	missense	probably damaging	1.00
R6251:Kdm5d	UTSW	Y	921,693 (GRCm39)	missense	probably damaging	1.00
R6349:Kdm5d	UTSW	Y	916,847 (GRCm39)	missense	probably damaging	0.99
R6450:Kdm5d	UTSW	Y	927,056 (GRCm39)	missense	probably damaging	1.00
R6595:Kdm5d	UTSW	Y	939,829 (GRCm39)	missense	probably benign
R6628:Kdm5d	UTSW	Y	900,525 (GRCm39)	missense	probably damaging	1.00
R6745:Kdm5d	UTSW	Y	927,112 (GRCm39)	missense	probably benign	0.28
R6867:Kdm5d	UTSW	Y	927,425 (GRCm39)	missense	probably benign
R6963:Kdm5d	UTSW	Y	937,975 (GRCm39)	missense	probably benign	0.01
R7163:Kdm5d	UTSW	Y	899,940 (GRCm39)	missense	probably damaging	1.00
R7374:Kdm5d	UTSW	Y	941,491 (GRCm39)	missense	probably benign	0.41
R7483:Kdm5d	UTSW	Y	914,044 (GRCm39)	missense	possibly damaging	0.50
R7501:Kdm5d	UTSW	Y	941,488 (GRCm39)	missense	probably damaging	1.00
R7815:Kdm5d	UTSW	Y	940,702 (GRCm39)	missense	probably damaging	1.00
R7835:Kdm5d	UTSW	Y	900,558 (GRCm39)	missense	possibly damaging	0.63
R8057:Kdm5d	UTSW	Y	927,355 (GRCm39)	missense	possibly damaging	0.48
R8080:Kdm5d	UTSW	Y	910,742 (GRCm39)	missense	probably benign	0.01
R8130:Kdm5d	UTSW	Y	940,658 (GRCm39)	missense	possibly damaging	0.75
R8213:Kdm5d	UTSW	Y	941,515 (GRCm39)	missense	probably damaging	1.00
R8261:Kdm5d	UTSW	Y	936,929 (GRCm39)	missense	probably damaging	0.99
R8344:Kdm5d	UTSW	Y	942,477 (GRCm39)	missense	probably benign	0.05
R8348:Kdm5d	UTSW	Y	914,056 (GRCm39)	missense	probably benign	0.00
R8445:Kdm5d	UTSW	Y	916,874 (GRCm39)	missense	probably damaging	1.00
R8448:Kdm5d	UTSW	Y	914,056 (GRCm39)	missense	probably benign	0.00
R8754:Kdm5d	UTSW	Y	941,594 (GRCm39)	missense	probably damaging	1.00
R9203:Kdm5d	UTSW	Y	940,981 (GRCm39)	missense	probably damaging	0.99
R9259:Kdm5d	UTSW	Y	942,640 (GRCm39)	missense	possibly damaging	0.84
R9541:Kdm5d	UTSW	Y	910,801 (GRCm39)	missense	probably damaging	1.00
R9668:Kdm5d	UTSW	Y	943,075 (GRCm39)	missense	possibly damaging	0.73

Predicted Primers

PCR Primer
(F):5'- GCACTCTCATGTATCAGTGGTTCTCAG -3'
(R):5'- AGCTGCCAAATGCTGTAGTTCTCATC -3'

Sequencing Primer
(F):5'- gaaagggttacagcattaggaag -3'
(R):5'- CAAATGCTGTAGTTCTCATCTAGGG -3'

Posted On

2013-05-23