Mutagenetix > Incidental Mutations

Incidental Mutation 'R0620:Kdm5d'

58642

Institutional Source

Beutler Lab

Gene Symbol

Kdm5d

Ensembl Gene

ENSMUSG00000056673

Gene Name

lysine (K)-specific demethylase 5D

Synonyms

Jarid1d, Smcy, HY

MMRRC Submission

038809-MU

Accession Numbers

Is this an essential gene?

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

Stock #

R0620 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

897788-956786 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 927330 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 650 (M650K)

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: M650K

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: M650K

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: M650K

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000140663
Gene: ENSMUSG00000056673
AA Change: M650K

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: 99.4%
3x: 99.0%
10x: 97.8%
20x: 96.1%

Validation Efficiency

100% (74/74)

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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2810474O19Rik	A	T	6: 149,328,375	Q973L	probably damaging	Het
Adamts9	T	C	6: 92,858,113	T679A	possibly damaging	Het
Ahr	T	C	12: 35,508,194	T276A	probably benign	Het
Akap9	A	T	5: 4,064,136	Q3138H	probably damaging	Het
Armt1	T	A	10: 4,432,689	F7I	probably benign	Het
B3galt2	A	G	1: 143,646,140	R5G	probably damaging	Het
Bod1l	T	C	5: 41,801,233	N2750S	probably benign	Het
Cadps2	T	A	6: 23,583,396	E365V	probably damaging	Het
Cd200r3	T	A	16: 44,957,717		probably null	Het
Cst7	T	A	2: 150,575,886		probably benign	Het
Defb30	A	T	14: 63,049,763		probably benign	Het
Dido1	C	T	2: 180,659,851	G2087S	probably benign	Het
Dio2	A	G	12: 90,738,071	Y72H	probably benign	Het
Dnah11	C	T	12: 117,987,469	E3035K	probably damaging	Het
Dnajb13	T	C	7: 100,503,249	K287E	possibly damaging	Het
Dnajc11	G	A	4: 151,973,628	V244I	possibly damaging	Het
Ect2	C	T	3: 27,139,652	A226T	probably damaging	Het
Ercc8	G	A	13: 108,174,061		probably null	Het
Fam120b	T	A	17: 15,402,927	M389K	probably benign	Het
Fam151a	A	G	4: 106,747,931	M497V	probably benign	Het
Fam186b	C	A	15: 99,280,128	G439V	probably benign	Het
Fank1	A	G	7: 133,876,765	Y185C	probably damaging	Het
Gart	T	C	16: 91,630,602		probably benign	Het
Glb1l	T	C	1: 75,199,720	Y572C	probably damaging	Het
Gm11563	C	T	11: 99,658,437	A164T	unknown	Het
Gnb4	C	T	3: 32,591,207	V112I	probably benign	Het
Gsdmc3	T	A	15: 63,859,693	D330V	probably damaging	Het
H2-DMa	C	T	17: 34,137,960	T144M	probably damaging	Het
Haus6	A	T	4: 86,583,514	F707I	possibly damaging	Het
Hmcn1	T	A	1: 150,594,016	T4971S	probably benign	Het
Ints6	A	T	14: 62,696,759	F766L	probably benign	Het
Kif21b	T	C	1: 136,159,428	F881S	possibly damaging	Het
Klrk1	C	A	6: 129,614,635	Q176H	possibly damaging	Het
Ky	T	C	9: 102,537,621	V244A	probably benign	Het
Mia2	T	A	12: 59,154,419	L191M	possibly damaging	Het
Miga2	T	A	2: 30,381,744		probably benign	Het
Mtss1l	C	T	8: 110,737,948	P322S	probably damaging	Het
Nalcn	A	G	14: 123,299,141		probably benign	Het
Ncbp3	T	A	11: 73,049,845		probably benign	Het
Nprl3	G	A	11: 32,234,876	L378F	probably damaging	Het
Ntrk2	A	T	13: 58,846,821	M184L	probably benign	Het
Olfr311	T	G	11: 58,841,443	C110G	probably damaging	Het
Olfr738	G	T	14: 50,413,697	C51F	probably benign	Het
Osbpl9	T	C	4: 109,083,128	E287G	probably damaging	Het
Parva	T	C	7: 112,576,411	F250L	probably damaging	Het
Pcdhb11	C	T	18: 37,421,811	Q65*	probably null	Het
Phtf1	A	G	3: 103,993,765	T377A	probably damaging	Het
Pkp4	G	A	2: 59,322,643	V612I	possibly damaging	Het
Plscr2	C	A	9: 92,287,654	S52R	probably benign	Het
Pnisr	C	T	4: 21,874,092		probably benign	Het
Pole2	A	C	12: 69,209,879	S291A	probably damaging	Het
Ppp2r5d	A	G	17: 46,684,018	F586L	probably benign	Het
Prrx1	G	A	1: 163,257,816	R182C	probably damaging	Het
Ptprs	A	G	17: 56,429,103	I110T	possibly damaging	Het
Rasgrf2	G	A	13: 91,919,817		probably benign	Het
Riox2	T	C	16: 59,491,892	V464A	probably benign	Het
Robo2	A	G	16: 73,967,802	V646A	possibly damaging	Het
Ros1	T	A	10: 52,118,348	I1279F	probably damaging	Het
Siglec1	G	A	2: 131,074,268	T1254M	probably benign	Het
Snx7	T	C	3: 117,846,675	N62D	probably damaging	Het
Sp100	G	A	1: 85,659,867		probably null	Het
Stil	A	T	4: 115,007,159	I86L	possibly damaging	Het
Tbc1d16	T	A	11: 119,209,038	D170V	probably benign	Het
Tmem2	T	A	19: 21,817,971	S743T	probably benign	Het
Trappc13	G	A	13: 104,161,081	T105M	probably damaging	Het
Trhr	T	A	15: 44,229,500	S378T	probably benign	Het
Ttc7b	T	C	12: 100,500,073		probably null	Het
Vegfc	A	T	8: 54,157,139	Y110F	probably benign	Het
Vmn1r184	C	A	7: 26,267,177	P116H	possibly damaging	Het
Vmn2r5	A	T	3: 64,503,814	C444*	probably null	Het
Zfp341	A	G	2: 154,634,273	E460G	possibly damaging	Het
Zfp819	T	A	7: 43,616,444	V41E	probably benign	Het

Other mutations in Kdm5d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0013:Kdm5d	UTSW	Y	941715	missense	probably benign	0.37
R0013:Kdm5d	UTSW	Y	941715	missense	probably benign	0.37
R0426:Kdm5d	UTSW	Y	942437	splice site	probably benign
R0486:Kdm5d	UTSW	Y	927107	missense	probably damaging	1.00
R0781:Kdm5d	UTSW	Y	910539	missense	probably damaging	1.00
R1015:Kdm5d	UTSW	Y	941687	missense	possibly damaging	0.95
R1110:Kdm5d	UTSW	Y	910539	missense	probably damaging	1.00
R1163:Kdm5d	UTSW	Y	898029	missense	probably benign	0.18
R1203:Kdm5d	UTSW	Y	941011	missense	probably damaging	1.00
R1238:Kdm5d	UTSW	Y	941282	missense	probably damaging	1.00
R1723:Kdm5d	UTSW	Y	927753	missense	probably damaging	1.00
R1842:Kdm5d	UTSW	Y	927798	missense	probably damaging	1.00
R1885:Kdm5d	UTSW	Y	940781	splice site	probably null
R2131:Kdm5d	UTSW	Y	941483	missense	probably benign	0.02
R2571:Kdm5d	UTSW	Y	940932	missense	probably benign	0.11
R2931:Kdm5d	UTSW	Y	942992	missense	probably benign	0.18
R3123:Kdm5d	UTSW	Y	900558	missense	possibly damaging	0.63
R3919:Kdm5d	UTSW	Y	939914	missense	probably damaging	1.00
R4018:Kdm5d	UTSW	Y	910441	splice site	probably benign
R4031:Kdm5d	UTSW	Y	916910	missense	probably damaging	1.00
R4403:Kdm5d	UTSW	Y	899830	missense	probably damaging	1.00
R4571:Kdm5d	UTSW	Y	927110	missense	probably damaging	1.00
R4583:Kdm5d	UTSW	Y	914134	missense	probably damaging	1.00
R4962:Kdm5d	UTSW	Y	940624	missense	probably damaging	1.00
R5105:Kdm5d	UTSW	Y	941752	missense	probably benign	0.00
R5249:Kdm5d	UTSW	Y	916692	missense	probably damaging	1.00
R5367:Kdm5d	UTSW	Y	941645	missense	probably benign	0.05
R5373:Kdm5d	UTSW	Y	927995	missense	probably benign	0.09
R5374:Kdm5d	UTSW	Y	927995	missense	probably benign	0.09
R5876:Kdm5d	UTSW	Y	900525	missense	probably damaging	1.00
R5909:Kdm5d	UTSW	Y	941306	missense	probably benign	0.01
R6014:Kdm5d	UTSW	Y	921528	missense	probably benign	0.45
R6109:Kdm5d	UTSW	Y	921501	missense	probably damaging	1.00
R6251:Kdm5d	UTSW	Y	921693	missense	probably damaging	1.00
R6349:Kdm5d	UTSW	Y	916847	missense	probably damaging	0.99
R6450:Kdm5d	UTSW	Y	927056	missense	probably damaging	1.00
R6595:Kdm5d	UTSW	Y	939829	missense	probably benign
R6628:Kdm5d	UTSW	Y	900525	missense	probably damaging	1.00
R6745:Kdm5d	UTSW	Y	927112	missense	probably benign	0.28
R6867:Kdm5d	UTSW	Y	927425	missense	probably benign
R6963:Kdm5d	UTSW	Y	937975	missense	probably benign	0.01
R7163:Kdm5d	UTSW	Y	899940	missense	probably damaging	1.00
R7374:Kdm5d	UTSW	Y	941491	missense	probably benign	0.41
R7483:Kdm5d	UTSW	Y	914044	missense	possibly damaging	0.50
R7501:Kdm5d	UTSW	Y	941488	missense	probably damaging	1.00
R7815:Kdm5d	UTSW	Y	940702	missense	probably damaging	1.00
R7835:Kdm5d	UTSW	Y	900558	missense	possibly damaging	0.63
R8057:Kdm5d	UTSW	Y	927355	missense	possibly damaging	0.48
R8080:Kdm5d	UTSW	Y	910742	missense	probably benign	0.01
R8130:Kdm5d	UTSW	Y	940658	missense	possibly damaging	0.75
R8213:Kdm5d	UTSW	Y	941515	missense	probably damaging	1.00
R8261:Kdm5d	UTSW	Y	936929	missense	probably damaging	0.99
R8344:Kdm5d	UTSW	Y	942477	missense	probably benign	0.05
R8348:Kdm5d	UTSW	Y	914056	missense	probably benign	0.00
R8445:Kdm5d	UTSW	Y	916874	missense	probably damaging	1.00
R8448:Kdm5d	UTSW	Y	914056	missense	probably benign	0.00
R8754:Kdm5d	UTSW	Y	941594	missense	probably damaging	1.00
R9203:Kdm5d	UTSW	Y	940981	missense	probably damaging	0.99
R9259:Kdm5d	UTSW	Y	942640	missense	possibly damaging	0.84

Predicted Primers

PCR Primer
(F):5'- CGTGCTTACCACAGTGGCTTTAACC -3'
(R):5'- ACTAGGAGCAGTGTTCTGGACACC -3'

Sequencing Primer
(F):5'- CAAGGCTATAACTTTGCTGAGGC -3'
(R):5'- AATACTGAGCCCTGCTGTG -3'

Posted On

2013-07-11