Mutagenetix > Incidental Mutation

Incidental Mutation 'R0013:Kdm5d'

32675

Institutional Source

Beutler Lab

Gene Symbol

Kdm5d

Ensembl Gene

ENSMUSG00000056673

Gene Name

lysine (K)-specific demethylase 5D

Synonyms

Jarid1d, Smcy, HY

MMRRC Submission

038308-MU

Accession Numbers

Essential gene?

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

Stock #

R0013 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

897788-956786 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 941715 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Asparagine at position 1305 (K1305N)

Ref Sequence

ENSEMBL: ENSMUSP00000061095 (fasta)

Gene Model

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

AlphaFold

Q62240

Predicted Effect

probably benign
Transcript: ENSMUST00000055032
AA Change: K1305N

PolyPhen 2 Score 0.366 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: K1305N

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

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.8%

Validation Efficiency

94% (79/84)

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2610028H24Rik	A	G	10: 76,457,512	M156V	probably benign	Het
Adnp2	A	T	18: 80,129,745	V483D	probably damaging	Het
Aff1	G	T	5: 103,828,484	E491*	probably null	Het
Agl	A	T	3: 116,776,608	C911*	probably null	Het
Akt2	A	G	7: 27,636,058	D284G	probably damaging	Het
Alox15	A	G	11: 70,349,635	M240T	possibly damaging	Het
Antxr2	A	G	5: 97,979,985	V229A	probably damaging	Het
Arap2	G	A	5: 62,683,484	L680F	probably damaging	Het
Btaf1	A	G	19: 36,958,373	T188A	probably benign	Het
Btnl6	G	A	17: 34,515,531	Q86*	probably null	Het
C2cd3	T	A	7: 100,416,062	L685H	probably damaging	Het
Cdh23	T	C	10: 60,413,173	T878A	possibly damaging	Het
Clec4b2	T	C	6: 123,202,149	Y137H	probably damaging	Het
Dchs1	T	A	7: 105,755,836	T2500S	possibly damaging	Het
Def6	A	G	17: 28,217,092	Y75C	probably damaging	Het
Dhx33	A	T	11: 70,993,635	F448L	probably damaging	Het
Dner	C	T	1: 84,494,893		probably benign	Het
Dnmbp	G	A	19: 43,902,231	P366S	probably benign	Het
Eif4g3	T	C	4: 138,175,848	C1160R	possibly damaging	Het
Elmod1	G	A	9: 53,912,901		probably benign	Het
Faah	C	A	4: 116,004,391	L305F	probably damaging	Het
Fam71b	A	G	11: 46,406,804	T312A	unknown	Het
Flt1	A	G	5: 147,571,014		probably benign	Het
Fyco1	A	T	9: 123,822,406	N1196K	probably benign	Het
Galnt18	T	C	7: 111,554,457	N320S	probably damaging	Het
Glp2r	C	A	11: 67,709,712	G437V	possibly damaging	Het
Gm4884	T	C	7: 41,044,292	S562P	probably damaging	Het
Gm9936	A	G	5: 114,857,347		probably benign	Het
Gpn2	C	A	4: 133,584,792	P112T	probably damaging	Het
Grm4	A	G	17: 27,431,575	Y816H	probably benign	Het
Helz2	A	T	2: 181,240,959	S14T	probably benign	Het
Htt	T	C	5: 34,820,104	L778P	probably benign	Het
Il11ra1	T	C	4: 41,765,060	S129P	probably damaging	Het
Ints11	T	C	4: 155,887,168	F315S	probably damaging	Het
Itga11	A	T	9: 62,776,613	N1059Y	possibly damaging	Het
Jak3	A	G	8: 71,684,327	S716G	probably damaging	Het
Kcns1	G	T	2: 164,168,643	D65E	probably benign	Het
Kif26a	G	T	12: 112,177,880	V1523L	probably benign	Het
Mboat7	A	G	7: 3,683,822	S340P	probably damaging	Het
Mctp2	T	C	7: 72,229,408	I234V	probably benign	Het
Mex3c	G	A	18: 73,590,551	A572T	probably benign	Het
Mpp3	C	A	11: 102,005,425	R424L	probably benign	Het
Mroh4	T	A	15: 74,608,237		probably benign	Het
Myo9a	A	T	9: 59,860,206		probably benign	Het
Myog	T	A	1: 134,290,235	H60Q	probably damaging	Het
Nlrp9a	T	A	7: 26,571,225		probably null	Het
Notch1	A	G	2: 26,473,818	V868A	possibly damaging	Het
Olfr352	A	G	2: 36,870,160	N198S	probably damaging	Het
Olfr59	T	A	11: 74,289,051	I135N	possibly damaging	Het
Olfr73	T	C	2: 88,034,266	Y291C	possibly damaging	Het
Olfr980	A	T	9: 40,006,355	I198N	probably damaging	Het
Pink1	T	C	4: 138,317,401	T342A	probably benign	Het
Plb1	T	A	5: 32,349,615		probably benign	Het
Plec	T	C	15: 76,178,246	D2524G	probably damaging	Het
Plekhg4	G	T	8: 105,375,396	E6*	probably null	Het
Polq	T	C	16: 37,061,839	F1455S	possibly damaging	Het
Ppm1e	A	G	11: 87,249,058		probably benign	Het
Prkaca	G	A	8: 83,988,303	M119I	possibly damaging	Het
Prss46	G	T	9: 110,850,055	S108I	probably damaging	Het
Ptma	C	T	1: 86,529,776		probably benign	Het
Rab11fip4	C	T	11: 79,689,653	T437M	probably benign	Het
Rngtt	T	A	4: 33,379,409	M437K	probably benign	Het
Rrn3	T	A	16: 13,813,113	D604E	possibly damaging	Het
Scn4a	A	G	11: 106,348,405		probably benign	Het
Sis	A	G	3: 72,910,476	L1468P	possibly damaging	Het
Slit3	A	G	11: 35,707,918	M1450V	probably benign	Het
Smg5	T	C	3: 88,349,233	S269P	probably benign	Het
Sntg1	T	C	1: 8,463,462	T323A	probably damaging	Het
Son	C	T	16: 91,651,662	T37I	probably damaging	Het
Stk17b	T	C	1: 53,764,132	I41M	probably benign	Het
Tgm5	T	A	2: 121,076,882	Y120F	probably damaging	Het
Tppp	A	G	13: 74,021,360	K73R	possibly damaging	Het
Ttn	C	A	2: 76,739,158	K27130N	probably damaging	Het
Ttn	C	T	2: 76,907,752	V4148I	probably benign	Het
Uba7	A	T	9: 107,978,249	Y375F	probably damaging	Het
Ugcg	T	C	4: 59,213,931	L171P	possibly damaging	Het
Vsig2	T	C	9: 37,542,576		probably benign	Het
Zcchc11	T	A	4: 108,530,955		probably benign	Het
Zfp839	T	A	12: 110,868,386	S692T	possibly damaging	Het

Other mutations in Kdm5d

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
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
R0620:Kdm5d	UTSW	Y	927330	missense	probably damaging	0.98
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
R9541:Kdm5d	UTSW	Y	910801	missense	probably damaging	1.00
R9668:Kdm5d	UTSW	Y	943075	missense	possibly damaging	0.73

Predicted Primers

PCR Primer
(F):5'- CCTGGAGACCATCTTGTCATTGCTG -3'
(R):5'- TTGCTTACTCCCCACAGAGAGCAC -3'

Sequencing Primer
(F):5'- TGCTGGTAGGACTACAGAGACTG -3'
(R):5'- caaccttcctaatgctgtaacc -3'

Posted On

2013-05-09