Mutagenetix > Incidental Mutation

Incidental Mutation 'R8754:Kdm5d'

664076

Institutional Source

Beutler Lab

Gene Symbol

Kdm5d

Ensembl Gene

ENSMUSG00000056673

Gene Name

lysine demethylase 5D

Synonyms

Smcy, HY, Jarid1d

MMRRC Submission

068620-MU

Accession Numbers

Essential gene?

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

Stock #

R8754 (G1)

Quality Score

221.999

Status

Validated

Chromosome

Chromosomal Location

897566-943813 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 941594 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 1265 (V1265A)

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: V1265A

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

SMART Domains

Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: V1265A

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: 100.0%
3x: 99.9%
10x: 99.3%
20x: 97.5%

Validation Efficiency

100% (67/67)

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	T	C	3: 137,771,798 (GRCm39)	V329A	probably benign	Het
A830018L16Rik	G	T	1: 11,615,472 (GRCm39)	K148N	probably benign	Het
Actn3	A	G	19: 4,913,488 (GRCm39)	F648L	probably damaging	Het
Amotl2	A	G	9: 102,597,358 (GRCm39)	D39G	possibly damaging	Het
Anks1	C	A	17: 28,214,984 (GRCm39)	T477K	possibly damaging	Het
Brix1	A	T	15: 10,476,664 (GRCm39)	S271T	probably benign	Het
Ccdc88b	T	C	19: 6,833,213 (GRCm39)	E278G	probably damaging	Het
Cdc40	C	T	10: 40,717,480 (GRCm39)	D404N	probably damaging	Het
Chrna6	T	C	8: 27,897,229 (GRCm39)	H216R	probably damaging	Het
Col6a3	C	G	1: 90,695,328 (GRCm39)		probably benign	Het
Copa	C	T	1: 171,935,926 (GRCm39)	R423W	probably damaging	Het
Cttnbp2	A	C	6: 18,434,037 (GRCm39)	I607R	possibly damaging	Het
Depdc5	A	T	5: 33,136,881 (GRCm39)	T1384S	probably benign	Het
Dlat	G	T	9: 50,560,967 (GRCm39)	A360E	probably damaging	Het
Dusp26	C	T	8: 31,581,805 (GRCm39)		probably benign	Het
Eif1ad13	T	A	12: 87,762,569 (GRCm39)	N96K	possibly damaging	Het
Fam135a	G	A	1: 24,067,569 (GRCm39)	T1100M	probably benign	Het
Fuca1	T	C	4: 135,652,889 (GRCm39)	L171P	probably damaging	Het
Gpr158	G	A	2: 21,581,693 (GRCm39)	V391I	probably benign	Het
Gtf2h5	C	CA	17: 6,134,833 (GRCm39)		probably null	Het
Heatr1	T	A	13: 12,428,175 (GRCm39)	Y771N	probably damaging	Het
Il17ra	A	G	6: 120,458,417 (GRCm39)	T523A	probably benign	Het
Kcnv1	G	A	15: 44,977,865 (GRCm39)	Q58*	probably null	Het
Kifc3	A	T	8: 95,829,024 (GRCm39)	L726Q	probably damaging	Het
Klk1b21	T	A	7: 43,755,912 (GRCm39)	I247N	probably benign	Het
Kntc1	T	A	5: 123,897,115 (GRCm39)	N159K	probably benign	Het
Krtap4-7	G	T	11: 99,534,667 (GRCm39)	C65*	probably null	Het
Lama2	C	T	10: 26,877,147 (GRCm39)	V2680M	possibly damaging	Het
Lipe	T	A	7: 25,088,007 (GRCm39)	M61L	probably benign	Het
Med17	A	G	9: 15,188,896 (GRCm39)	M123T	possibly damaging	Het
Mrpl37	T	C	4: 106,921,611 (GRCm39)	N206S	probably benign	Het
Muc4	A	T	16: 32,602,356 (GRCm39)	N1390Y		Het
Muc5ac	C	T	7: 141,354,008 (GRCm39)	A869V	possibly damaging	Het
Nckap5l	A	G	15: 99,327,290 (GRCm39)	V133A	probably benign	Het
Nin	A	T	12: 70,077,787 (GRCm39)		probably benign	Het
Nr1h2	C	T	7: 44,200,768 (GRCm39)	A287T	probably damaging	Het
Or8c16	A	T	9: 38,130,865 (GRCm39)	I246L	possibly damaging	Het
Patl1	A	G	19: 11,899,898 (GRCm39)	E230G	probably damaging	Het
Pbxip1	T	C	3: 89,355,235 (GRCm39)	S585P	probably damaging	Het
Pde3b	T	A	7: 114,015,278 (GRCm39)	W165R	possibly damaging	Het
Pdia4	A	C	6: 47,773,464 (GRCm39)	D628E	probably benign	Het
Pigo	T	A	4: 43,024,724 (GRCm39)	H125L	probably benign	Het
Platr25	A	T	13: 62,847,924 (GRCm39)	*313K	probably null	Het
Plxdc1	A	T	11: 97,846,337 (GRCm39)	M169K	possibly damaging	Het
Pxk	T	C	14: 8,151,496 (GRCm38)	I437T	probably damaging	Het
Rlf	T	C	4: 121,004,010 (GRCm39)	T1767A	possibly damaging	Het
Rnf123	T	A	9: 107,948,363 (GRCm39)	D110V	probably damaging	Het
Rnf185	A	T	11: 3,368,052 (GRCm39)	F209I	probably benign	Het
Rpl4	A	T	9: 64,082,242 (GRCm39)	N47I	probably damaging	Het
Rsl1d1	A	T	16: 11,017,512 (GRCm39)	F151L	probably damaging	Het
Sema3d	T	C	5: 12,603,191 (GRCm39)		probably null	Het
Serhl	A	G	15: 82,986,126 (GRCm39)	N80D	probably benign	Het
Sh3tc1	C	A	5: 35,863,802 (GRCm39)	R795L	probably benign	Het
Slc2a12	A	T	10: 22,521,116 (GRCm39)	T7S	probably benign	Het
Snrnp200	A	G	2: 127,068,005 (GRCm39)	Y834C	probably damaging	Het
Ss18	G	C	18: 14,774,016 (GRCm39)	Q258E	probably damaging	Het
Telo2	G	A	17: 25,321,041 (GRCm39)	L725F	probably damaging	Het
Tnxb	A	G	17: 34,934,882 (GRCm39)	E2497G	probably damaging	Het
Tox2	A	G	2: 163,163,360 (GRCm39)	D111G		Het
Trim16	G	A	11: 62,731,763 (GRCm39)	E545K	probably benign	Het
Trpm7	A	G	2: 126,664,623 (GRCm39)	W919R	probably damaging	Het
Ttbk1	G	T	17: 46,756,127 (GRCm39)	S1301*	probably null	Het
Txk	T	C	5: 72,889,122 (GRCm39)	N144S	probably damaging	Het
Ubqln4	T	A	3: 88,473,090 (GRCm39)	V515E	probably benign	Het
Ush2a	C	T	1: 188,581,162 (GRCm39)	R3681*	probably null	Het
Ythdf3	A	T	3: 16,258,138 (GRCm39)	N106I	probably damaging	Het
Zfp367	A	T	13: 64,292,069 (GRCm39)	C187*	probably null	Het
Zfp735	A	G	11: 73,603,000 (GRCm39)	D648G	possibly damaging	Het
Zic1	T	C	9: 91,244,701 (GRCm39)		probably benign	Het
Zik1	A	G	7: 10,223,826 (GRCm39)	S424P	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
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
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'- TGTCATGACTGGTTCCATGG -3'
(R):5'- CTCTGTGAGACAGTCAAAGGC -3'

Sequencing Primer
(F):5'- CATGGACAATGTGTGACTGTACCC -3'
(R):5'- CTGTGAGACAGTCAAAGGCAAAGC -3'

Posted On

2021-03-08