Mutagenetix > Incidental Mutation

Incidental Mutation 'R7835:Kdm5d'

605945

Institutional Source

Beutler Lab

Gene Symbol

Kdm5d

Ensembl Gene

ENSMUSG00000056673

Gene Name

lysine (K)-specific demethylase 5D

Synonyms

Jarid1d, Smcy, HY

MMRRC Submission

Accession Numbers

Is this an essential gene?

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

Stock #

R7835 (G1)

Quality Score

221.999

Status

Validated

Chromosome

Chromosomal Location

897788-956786 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 900558 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 201 (V201A)

Ref Sequence

ENSEMBL: ENSMUSP00000139636 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000055032] [ENSMUST00000186696] [ENSMUST00000186726] [ENSMUST00000189069]

AlphaFold

Q62240

Predicted Effect

probably benign
Transcript: ENSMUST00000055032
AA Change: V201A

PolyPhen 2 Score 0.387 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: V201A

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

noncoding transcript
Transcript: ENSMUST00000185542

Predicted Effect

probably benign
Transcript: ENSMUST00000186696
AA Change: V201A

PolyPhen 2 Score 0.116 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000140663
Gene: ENSMUSG00000056673
AA Change: V201A

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
AA Change: V201A

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000140462
Gene: ENSMUSG00000056673
AA Change: V201A

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: ENSMUST00000188910

Predicted Effect

possibly damaging
Transcript: ENSMUST00000189069
AA Change: V201A

PolyPhen 2 Score 0.635 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000139636
Gene: ENSMUSG00000056673
AA Change: V201A

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
Blast:ARID	175	298	1e-46	BLAST
PHD	325	371	8.56e-13	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000189626

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

98% (48/49)

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: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acan	T	A	7: 79,099,875	S1465T	probably benign	Het
Accsl	T	A	2: 93,865,984	K90*	probably null	Het
Adamts3	A	T	5: 89,700,440	D674E	possibly damaging	Het
Adap2	T	A	11: 80,160,231	V129D	probably benign	Het
Ank3	A	G	10: 69,987,727	D742G		Het
C1ra	G	A	6: 124,517,725	E316K	probably benign	Het
C330021F23Rik	A	G	8: 3,580,452		probably benign	Het
Cachd1	G	T	4: 100,974,153		probably null	Het
Ccne1	G	T	7: 38,102,845	Q133K	probably benign	Het
Cers3	C	T	7: 66,773,639	H111Y	possibly damaging	Het
Chst5	A	T	8: 111,890,602	L129M	probably damaging	Het
Depdc7	A	G	2: 104,728,185	S164P	probably benign	Het
Dnah10	G	A	5: 124,777,234	A1966T	probably damaging	Het
Fam208a	G	T	14: 27,476,643	G1311C	probably damaging	Het
Fcgbp	T	G	7: 28,117,207	S2365A	possibly damaging	Het
Ihh	A	G	1: 74,946,366	V320A	probably damaging	Het
Kif13b	T	A	14: 64,767,452	H1117Q	probably benign	Het
Lcn8	C	A	2: 25,655,296		probably null	Het
Lrp4	T	C	2: 91,495,042	V1404A	possibly damaging	Het
Lrrc61	A	T	6: 48,568,572	T110S	probably benign	Het
Mrpl19	G	A	6: 81,962,126	R232C	probably damaging	Het
Muc5ac	G	C	7: 141,809,303	G2117A	unknown	Het
Mzt1	T	C	14: 99,046,003	T21A	probably benign	Het
Naip6	G	T	13: 100,316,004	A183E	probably benign	Het
Neb	T	C	2: 52,150,577	D6624G	probably benign	Het
Nup85	A	G	11: 115,570,071	D183G	probably benign	Het
Olfm5	A	T	7: 104,154,445	Y195*	probably null	Het
Olfr828	T	A	9: 18,815,809	M162L	probably benign	Het
Piezo2	A	T	18: 63,082,945	F1216I	probably benign	Het
Pkd1l3	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	8: 109,624,195		probably benign	Het
Polr1a	T	C	6: 71,915,142	V135A	probably benign	Het
Ppcdc	A	G	9: 57,420,276	S83P	probably benign	Het
Prss21	A	T	17: 23,869,451	Q130L	possibly damaging	Het
Rdx	T	A	9: 52,065,788	N112K	probably damaging	Het
Rgs22	A	G	15: 36,081,911		probably null	Het
Rps26	C	T	10: 128,626,126	V40I	probably benign	Het
Runx2	A	T	17: 44,608,236	M405K	probably damaging	Het
Serinc2	A	C	4: 130,275,487	C4G	unknown	Het
Sh3rf2	C	A	18: 42,111,170	R266S	probably benign	Het
Slc38a10	A	G	11: 120,116,996	I386T	possibly damaging	Het
Stab2	G	A	10: 86,872,619	P1694L	probably benign	Het
Taf4	G	A	2: 179,932,029	T682M	probably damaging	Het
Tmem102	A	G	11: 69,804,345	V267A	probably damaging	Het
Trim65	A	G	11: 116,130,929	L26P	probably damaging	Het
Vmn1r160	T	A	7: 22,871,954	M244K	possibly damaging	Het
Vmn1r57	A	T	7: 5,221,139	H221L	probably benign	Het
Wdr89	C	A	12: 75,632,899	V194F	probably damaging	Het
Wee1	C	A	7: 110,130,878	Y396*	probably null	Het
Zfp451	A	T	1: 33,772,979	V885D	probably damaging	Het
Zfp981	A	T	4: 146,537,876	Q419H	probably benign	Het
Znfx1	A	G	2: 167,039,827	Y1081H	probably 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
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
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

Predicted Primers

PCR Primer
(F):5'- GTGTTCAAAATGAGTAAGCTGGT -3'
(R):5'- CATTTCCCATTGGTTTCAACTTAGA -3'

Sequencing Primer
(F):5'- AAGCTGGTATTACTTTTGTTTAGCTG -3'
(R):5'- TCCCATTGGTTTCAACTTAGATATTC -3'

Posted On

2019-12-20