Mutagenetix > Incidental Mutation

Incidental Mutation 'R1842:Kdm5d'

205863

Institutional Source

Beutler Lab

Gene Symbol

Kdm5d

Ensembl Gene

ENSMUSG00000056673

Gene Name

lysine demethylase 5D

Synonyms

Smcy, HY, Jarid1d

MMRRC Submission

039867-MU

Accession Numbers

Essential gene?

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

Stock #

R1842 (G1)

Quality Score

222

Status

Not validated

Chromosome

Chromosomal Location

897566-943813 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 927798 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Leucine at position 716 (S716L)

Ref Sequence

ENSEMBL: ENSMUSP00000061095 (fasta)

Gene Model

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

AlphaFold

Q62240

Predicted Effect

probably damaging
Transcript: ENSMUST00000055032
AA Change: S716L

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

SMART Domains

Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: S716L

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

Coding Region Coverage

1x: 97.4%
3x: 96.7%
10x: 94.8%
20x: 90.8%

Validation Efficiency

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
Abca6	G	T	11: 110,087,865 (GRCm39)	N1087K	probably benign	Het
Abcc3	G	A	11: 94,250,438 (GRCm39)	T921I	probably benign	Het
Abr	T	A	11: 76,399,812 (GRCm39)	I4F	probably damaging	Het
Adcy10	T	A	1: 165,330,812 (GRCm39)	V25D	probably damaging	Het
Ahnak	T	A	19: 8,983,231 (GRCm39)	M1505K	probably damaging	Het
Alms1-ps2	T	C	6: 85,773,231 (GRCm39)		noncoding transcript	Het
Apob	C	G	12: 8,061,559 (GRCm39)	T3347S	probably damaging	Het
Arhgap27	C	A	11: 103,230,822 (GRCm39)	G11W	probably damaging	Het
Ccdc110	A	T	8: 46,393,605 (GRCm39)	I106F	probably damaging	Het
Ccdc28b	T	A	4: 129,514,806 (GRCm39)	D101V	probably damaging	Het
Ccdc30	T	C	4: 119,188,324 (GRCm39)	E566G	probably benign	Het
Cenpm	T	C	15: 82,123,565 (GRCm39)	S111G	probably benign	Het
Cep55	A	G	19: 38,046,348 (GRCm39)	I34V	probably benign	Het
Dcdc2a	T	C	13: 25,291,585 (GRCm39)	L190S	probably damaging	Het
Dhh	T	C	15: 98,792,441 (GRCm39)		probably null	Het
Dst	A	G	1: 34,203,200 (GRCm39)	N703S	probably null	Het
E030025P04Rik	G	A	11: 109,030,396 (GRCm39)	L164F	unknown	Het
Efcab5	A	G	11: 77,025,701 (GRCm39)	V538A	probably benign	Het
Egflam	A	G	15: 7,333,422 (GRCm39)	S177P	probably benign	Het
Ehbp1l1	A	T	19: 5,775,958 (GRCm39)	C31S	probably damaging	Het
Eif2d	C	A	1: 131,098,797 (GRCm39)	Q532K	probably damaging	Het
Elf3	T	C	1: 135,184,531 (GRCm39)	D175G	possibly damaging	Het
F5	T	C	1: 164,012,129 (GRCm39)	V449A	probably damaging	Het
Fam110a	A	T	2: 151,811,954 (GRCm39)	I272N	probably damaging	Het
Fbxo34	A	G	14: 47,768,464 (GRCm39)	D608G	probably damaging	Het
Flrt2	T	C	12: 95,746,058 (GRCm39)	L132P	probably damaging	Het
Frg2f1	A	T	4: 119,388,277 (GRCm39)	V74D	possibly damaging	Het
Gad1	G	T	2: 70,404,597 (GRCm39)	E162D	probably benign	Het
Glb1l	A	G	1: 75,177,104 (GRCm39)	V444A	probably damaging	Het
Gm10770	G	A	2: 150,021,076 (GRCm39)	T147I	probably damaging	Het
Gm43302	T	C	5: 105,425,602 (GRCm39)	I276V	probably benign	Het
Greb1	T	C	12: 16,746,244 (GRCm39)	H1314R	probably damaging	Het
Hapln2	A	G	3: 87,931,308 (GRCm39)	V69A	probably damaging	Het
Hcn1	T	C	13: 118,112,544 (GRCm39)	I836T	probably damaging	Het
Hspa5	A	G	2: 34,665,815 (GRCm39)	D553G	probably damaging	Het
Iqgap1	A	T	7: 80,410,631 (GRCm39)	I194N	probably damaging	Het
Kansl3	A	G	1: 36,390,825 (GRCm39)	V304A	probably damaging	Het
Klra6	T	C	6: 129,999,573 (GRCm39)	T132A	probably benign	Het
Krt26	CTAGTA	CTA	11: 99,224,352 (GRCm39)		probably benign	Het
Lrp1	A	G	10: 127,409,337 (GRCm39)	I1594T	possibly damaging	Het
Lrp2bp	A	G	8: 46,464,152 (GRCm39)	D15G	probably benign	Het
Map4k1	T	C	7: 28,686,588 (GRCm39)	L170P	probably damaging	Het
Mast3	A	G	8: 71,233,037 (GRCm39)	F1108L	possibly damaging	Het
Mettl5	G	T	2: 69,715,686 (GRCm39)	L6I	unknown	Het
Mfsd14a	A	T	3: 116,426,057 (GRCm39)	F447I	possibly damaging	Het
Mrc2	A	G	11: 105,228,546 (GRCm39)	I642V	probably damaging	Het
Necap1	A	G	6: 122,851,547 (GRCm39)	Y7C	probably damaging	Het
Nsd1	G	A	13: 55,394,258 (GRCm39)	E723K	probably damaging	Het
Nsun3	A	T	16: 62,596,755 (GRCm39)	L121H	probably damaging	Het
Nsun6	A	T	2: 15,014,288 (GRCm39)	M284K	probably damaging	Het
Nutf2	T	C	8: 106,603,242 (GRCm39)		probably null	Het
Odad2	A	T	18: 7,223,551 (GRCm39)	D497E	probably benign	Het
Or1j20	A	T	2: 36,759,601 (GRCm39)	N8Y	probably damaging	Het
Or5d38	A	T	2: 87,954,471 (GRCm39)	M286K	probably damaging	Het
Pacs1	T	C	19: 5,205,912 (GRCm39)	E288G	probably damaging	Het
Peg10	A	T	6: 4,756,381 (GRCm39)		probably benign	Het
Rab38	G	A	7: 88,099,730 (GRCm39)	E82K	possibly damaging	Het
Rgsl1	T	A	1: 153,675,543 (GRCm39)	E206V	probably damaging	Het
Saxo5	T	A	8: 3,533,668 (GRCm39)	F295L	possibly damaging	Het
Scube3	G	A	17: 28,384,063 (GRCm39)	V521I	probably damaging	Het
Sgpp1	C	T	12: 75,762,982 (GRCm39)	V400M	probably damaging	Het
Slc18b1	T	C	10: 23,681,891 (GRCm39)	S152P	possibly damaging	Het
Slit1	A	T	19: 41,709,477 (GRCm39)		probably null	Het
Spata31d1e	T	C	13: 59,890,320 (GRCm39)	Y82C	probably damaging	Het
Spta1	A	G	1: 174,023,513 (GRCm39)	K640R	probably benign	Het
Svil	A	G	18: 5,062,373 (GRCm39)	T898A	probably damaging	Het
Timm44	A	G	8: 4,310,510 (GRCm39)		probably null	Het
Tomm40	A	G	7: 19,447,650 (GRCm39)	S127P	probably benign	Het
Vmn2r23	T	A	6: 123,706,649 (GRCm39)	V493D	possibly damaging	Het
Yeats2	T	C	16: 19,989,988 (GRCm39)	V288A	probably damaging	Het
Zfhx4	C	T	3: 5,466,558 (GRCm39)	R2239W	probably damaging	Het
Zscan2	A	C	7: 80,525,301 (GRCm39)	K341Q	probably 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
R0426:Kdm5d	UTSW	Y	942,437 (GRCm39)	splice site	probably benign
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
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'- AGCTATCCTTACAAGCTTAAGCC -3'
(R):5'- AGCAGGCAGTTCATCCAATG -3'

Sequencing Primer
(F):5'- CCACAGCAGGGCTCAGTATTG -3'
(R):5'- CCAATGTGTACCTGTACCTAGAGG -3'

Posted On

2014-06-23