Mutagenetix > Incidental Mutation

Incidental Mutation 'R8130:Kdm5d'

631996

Institutional Source

Beutler Lab

Gene Symbol

Kdm5d

Ensembl Gene

ENSMUSG00000056673

Gene Name

lysine demethylase 5D

Synonyms

Smcy, HY, Jarid1d

MMRRC Submission

067559-MU

Accession Numbers

Essential gene?

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

Stock #

R8130 (G1)

Quality Score

221.999

Status

Validated

Chromosome

Chromosomal Location

897566-943813 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 940658 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 1056 (D1056E)

Ref Sequence

ENSEMBL: ENSMUSP00000061095 (fasta)

Gene Model

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

AlphaFold

Q62240

Predicted Effect

possibly damaging
Transcript: ENSMUST00000055032
AA Change: D1056E

PolyPhen 2 Score 0.748 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: D1056E

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

Coding Region Coverage

1x: 99.8%
3x: 99.7%
10x: 99.1%
20x: 97.3%

Validation Efficiency

96% (52/54)

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: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700123K08Rik	T	C	5: 138,561,271 (GRCm39)	I130M	probably damaging	Het
4921539E11Rik	T	C	4: 103,092,895 (GRCm39)	D142G	probably damaging	Het
Abcb10	C	T	8: 124,691,757 (GRCm39)	A403T		Het
Arfgef2	T	A	2: 166,678,170 (GRCm39)	S218T	possibly damaging	Het
Armc8	C	T	9: 99,433,600 (GRCm39)	V40I	probably benign	Het
Caps2	A	T	10: 112,018,381 (GRCm39)	D177V	probably benign	Het
Cdh8	A	T	8: 99,757,676 (GRCm39)	F641I	probably damaging	Het
Cemip	T	C	7: 83,596,384 (GRCm39)	S1127G	probably benign	Het
Cmtm1	C	A	8: 105,036,088 (GRCm39)	Q180H	unknown	Het
Col15a1	C	T	4: 47,312,196 (GRCm39)	T1337I	probably damaging	Het
Col18a1	A	T	10: 76,910,284 (GRCm39)	M555K	probably benign	Het
Ctrb1	A	G	8: 112,415,823 (GRCm39)	F89L	possibly damaging	Het
Disp1	T	C	1: 182,917,199 (GRCm39)	T76A	probably benign	Het
Dpep1	T	C	8: 123,926,965 (GRCm39)	V263A	probably damaging	Het
Dysf	G	A	6: 84,114,358 (GRCm39)	E1216K	probably damaging	Het
F830016B08Rik	A	G	18: 60,433,052 (GRCm39)	Y45C	probably benign	Het
Fam186a	CGG	CG	15: 99,841,914 (GRCm39)		probably null	Het
Gcm1	T	A	9: 77,971,816 (GRCm39)	D252E	probably benign	Het
Gm11559	A	G	11: 99,755,416 (GRCm39)	T22A	unknown	Het
Gm4847	C	T	1: 166,465,917 (GRCm39)	R224Q	probably damaging	Het
Hypk	A	G	2: 121,286,859 (GRCm39)		probably benign	Het
I830077J02Rik	C	T	3: 105,834,233 (GRCm39)	C64Y	possibly damaging	Het
Igkv4-86	T	C	6: 68,887,650 (GRCm39)	I30V	probably benign	Het
Il17ra	A	G	6: 120,455,416 (GRCm39)	I342V	probably benign	Het
Kcnip3	C	T	2: 127,352,828 (GRCm39)	A64T	possibly damaging	Het
Kif19b	C	T	5: 140,460,716 (GRCm39)	R461C	probably damaging	Het
Krtap19-2	C	T	16: 88,670,903 (GRCm39)	G81R	unknown	Het
Ldlrad1	G	A	4: 107,066,688 (GRCm39)	A8T	probably benign	Het
Lpin1	A	T	12: 16,629,965 (GRCm39)	I69N		Het
Matcap1	G	A	8: 106,012,145 (GRCm39)	R101W	probably benign	Het
Mki67	C	T	7: 135,299,293 (GRCm39)	D1914N	probably damaging	Het
Mmrn1	A	T	6: 60,937,707 (GRCm39)	Q235L	probably damaging	Het
Mndal	T	A	1: 173,699,111 (GRCm39)	K185*	probably null	Het
Muc6	T	C	7: 141,233,354 (GRCm39)	T802A	probably damaging	Het
Necab1	A	T	4: 15,005,073 (GRCm39)	F130L	probably damaging	Het
Nemf	A	T	12: 69,402,826 (GRCm39)	M70K	possibly damaging	Het
Nploc4	A	G	11: 120,280,240 (GRCm39)	I436T	possibly damaging	Het
Obscn	C	A	11: 59,015,439 (GRCm39)	R1011M	probably damaging	Het
Or4k44	A	T	2: 111,367,825 (GRCm39)	F270I	probably damaging	Het
Or5aq1b	T	C	2: 86,901,570 (GRCm39)	K303E	probably benign	Het
Or8k24	T	A	2: 86,215,911 (GRCm39)	M284L	probably benign	Het
Ormdl1	T	A	1: 53,338,139 (GRCm39)	M1K	probably null	Het
Pramel34	A	T	5: 93,784,597 (GRCm39)	L289Q	probably damaging	Het
Psmb3	A	G	11: 97,594,723 (GRCm39)	D38G	probably benign	Het
Psme4	T	A	11: 30,792,026 (GRCm39)	L1171Q	probably damaging	Het
Repin1	G	T	6: 48,574,279 (GRCm39)	E403*	probably null	Het
Slc22a18	G	A	7: 143,052,911 (GRCm39)	V379I	probably damaging	Het
Speg	T	A	1: 75,392,240 (GRCm39)	F1632L	probably damaging	Het
Taok1	G	A	11: 77,470,659 (GRCm39)	R49C	possibly damaging	Het
Ttll6	T	C	11: 96,047,425 (GRCm39)	S675P	probably benign	Het
Usp8	A	T	2: 126,559,918 (GRCm39)		probably benign	Het
Vmn2r81	T	A	10: 79,110,538 (GRCm39)	N550K	possibly damaging	Het
Zfp119a	A	T	17: 56,172,971 (GRCm39)	C291S	probably damaging	Het
Zfp329	C	A	7: 12,544,313 (GRCm39)	G404C	probably damaging	Het
Zfp934	C	A	13: 62,667,985 (GRCm39)		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
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
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'- TTGATTCTGAGTCAGCAAAAGGAAG -3'
(R):5'- CACTTATGTGCTCAGGGTCAG -3'

Sequencing Primer
(F):5'- CTGAGTCAGCAAAAGGAAGAATTTTG -3'
(R):5'- TGCTCAGGGTCAGGCACAG -3'

Posted On

2020-06-30