Mutagenetix > Incidental Mutation

Incidental Mutation 'R0486:Kdm5d'

42316

Institutional Source

Beutler Lab

Gene Symbol

Kdm5d

Ensembl Gene

ENSMUSG00000056673

Gene Name

lysine demethylase 5D

Synonyms

Smcy, HY, Jarid1d

MMRRC Submission

038685-MU

Accession Numbers

Essential gene?

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

Stock #

R0486 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

897566-943813 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 927107 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 615 (N615S)

Ref Sequence

ENSEMBL: ENSMUSP00000140663 (fasta)

Gene Model

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

AlphaFold

Q62240

Predicted Effect

probably damaging
Transcript: ENSMUST00000055032
AA Change: N615S

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

SMART Domains

Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: N615S

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 damaging
Transcript: ENSMUST00000186696
AA Change: N615S

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

SMART Domains

Protein: ENSMUSP00000140663
Gene: ENSMUSG00000056673
AA Change: N615S

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

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.1%
20x: 91.9%

Validation Efficiency

98% (65/66)

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: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aco1	T	C	4: 40,177,783 (GRCm39)	L268P	probably damaging	Het
Adam22	A	T	5: 8,380,048 (GRCm39)	H83Q	probably damaging	Het
Anln	T	C	9: 22,264,122 (GRCm39)	D886G	probably benign	Het
Arhgef11	T	A	3: 87,596,159 (GRCm39)		probably null	Het
Ark2c	T	A	18: 77,571,950 (GRCm39)	Q91L	probably damaging	Het
Arl8b	A	T	6: 108,792,287 (GRCm39)	D116V	possibly damaging	Het
BC051665	C	T	13: 60,931,859 (GRCm39)	G180D	probably damaging	Het
Bloc1s2	A	G	19: 44,131,589 (GRCm39)		probably benign	Het
Ccdc185	T	G	1: 182,575,424 (GRCm39)	S422R	possibly damaging	Het
Cd101	T	C	3: 100,915,408 (GRCm39)	K720E	possibly damaging	Het
Cdh23	C	A	10: 60,222,725 (GRCm39)	A1236S	probably damaging	Het
Chd1	G	A	17: 15,954,604 (GRCm39)	A491T	probably damaging	Het
Chdh	T	C	14: 29,754,815 (GRCm39)	V275A	possibly damaging	Het
Cmtm2b	A	T	8: 105,057,047 (GRCm39)	I136F	probably damaging	Het
Cps1	T	C	1: 67,204,551 (GRCm39)	V457A	probably damaging	Het
Cwf19l1	A	G	19: 44,103,129 (GRCm39)	V362A	probably benign	Het
Cyp4f17	T	C	17: 32,743,797 (GRCm39)		probably benign	Het
Cyp4f18	C	A	8: 72,749,861 (GRCm39)	V263L	probably benign	Het
Dclre1a	A	G	19: 56,529,922 (GRCm39)		probably benign	Het
Dpp6	T	C	5: 27,866,640 (GRCm39)	I446T	probably benign	Het
F11r	T	C	1: 171,288,156 (GRCm39)	W61R	probably damaging	Het
Fam120b	C	T	17: 15,646,550 (GRCm39)		probably benign	Het
Fastkd2	T	C	1: 63,791,499 (GRCm39)	V669A	possibly damaging	Het
Foxg1	T	C	12: 49,431,314 (GRCm39)		probably benign	Het
Foxo3	A	G	10: 42,073,477 (GRCm39)	Y347H	probably damaging	Het
G3bp1	T	C	11: 55,389,452 (GRCm39)	F383L	probably damaging	Het
Gbp7	C	A	3: 142,252,078 (GRCm39)		probably benign	Het
Glipr1	T	C	10: 111,832,754 (GRCm39)		probably benign	Het
Gm11555	A	G	11: 99,540,986 (GRCm39)	S8P	unknown	Het
H6pd	G	A	4: 150,067,393 (GRCm39)		probably benign	Het
Haus8	C	T	8: 71,709,182 (GRCm39)	M75I	probably benign	Het
Haus8	C	A	8: 71,709,181 (GRCm39)	G76W	probably damaging	Het
Kcnj13	C	A	1: 87,314,752 (GRCm39)	V157L	probably damaging	Het
Kcnt2	T	A	1: 140,437,218 (GRCm39)	C550*	probably null	Het
Naip2	A	C	13: 100,298,290 (GRCm39)	I582S	probably benign	Het
Ncapd2	G	A	6: 125,160,990 (GRCm39)	R292*	probably null	Het
Ngef	T	A	1: 87,406,848 (GRCm39)	N640I	probably damaging	Het
Nhlrc3	T	C	3: 53,359,858 (GRCm39)	Y335C	probably damaging	Het
Nipbl	A	T	15: 8,368,354 (GRCm39)		probably benign	Het
Nop2	A	G	6: 125,117,636 (GRCm39)	K434R	probably null	Het
Nr4a3	T	C	4: 48,056,525 (GRCm39)		probably benign	Het
Or8b35	A	G	9: 37,903,998 (GRCm39)	N70S	possibly damaging	Het
Piezo2	A	C	18: 63,162,132 (GRCm39)	I2233R	probably damaging	Het
Prag1	A	T	8: 36,613,787 (GRCm39)	E1113V	probably damaging	Het
Prpsap2	A	G	11: 61,631,826 (GRCm39)	I177T	possibly damaging	Het
Psmd1	T	A	1: 86,022,012 (GRCm39)	N611K	probably damaging	Het
Ptpn7	C	T	1: 135,065,096 (GRCm39)	T168I	probably damaging	Het
Pus1	A	T	5: 110,927,596 (GRCm39)	V53E	probably damaging	Het
Rgs22	A	G	15: 36,093,028 (GRCm39)	M415T	probably damaging	Het
Rnf17	C	T	14: 56,751,632 (GRCm39)	T1490M	probably benign	Het
Rnf20	C	A	4: 49,645,907 (GRCm39)	L332I	possibly damaging	Het
Snrnp40	C	G	4: 130,271,836 (GRCm39)		probably null	Het
Spam1	A	T	6: 24,796,394 (GRCm39)	Q115L	probably damaging	Het
Syce1l	A	T	8: 114,381,395 (GRCm39)		probably null	Het
Synj1	T	C	16: 90,735,151 (GRCm39)		probably benign	Het
Tas2r126	A	T	6: 42,412,225 (GRCm39)	I253F	probably benign	Het
Tecpr2	G	A	12: 110,862,803 (GRCm39)	V72I	probably benign	Het
Tfap2a	G	T	13: 40,882,170 (GRCm39)	P45Q	probably damaging	Het
Trip12	C	A	1: 84,738,805 (GRCm39)	G714*	probably null	Het
Wdr31	A	G	4: 62,372,130 (GRCm39)	S330P	probably damaging	Het
Wdr64	T	C	1: 175,622,769 (GRCm39)		probably benign	Het
Yes1	T	A	5: 32,812,926 (GRCm39)	Y343*	probably null	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
R0426:Kdm5d	UTSW	Y	942,437 (GRCm39)	splice site	probably benign
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

Posted On

2013-05-23