Mutagenetix > Incidental Mutation

Incidental Mutation 'R6595:Kdm5d'

524903

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

Essential gene?

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

Stock #

R6595 (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 939829 bp (GRCm38)

Zygosity

Homozygous

Amino Acid Change

Serine to Proline at position 994 (S994P)

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: S994P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: S994P

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

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.2%
20x: 94.5%

Validation Efficiency

97% (37/38)

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: 38 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700007G11Rik	A	T	5: 98,801,858	D217V	possibly damaging	Het
Abca15	A	T	7: 120,394,487	Y1310F	probably benign	Het
Ankrd54	A	G	15: 79,057,985	F148L	probably damaging	Het
Bag4	C	T	8: 25,769,500	D224N	probably damaging	Het
Bhlhe40	TG	TGG	6: 108,664,857	254	probably null	Het
Camk2b	A	T	11: 5,992,856	H126Q	probably damaging	Het
Camsap3	G	T	8: 3,604,186	V608L	probably damaging	Het
Camsap3	A	T	8: 3,608,742	M796L	probably damaging	Het
Cdh19	T	C	1: 110,925,787	D308G	probably benign	Het
Cpsf1	T	C	15: 76,602,510	I275M	probably damaging	Het
Cuta	A	G	17: 26,938,882		probably null	Het
Dclk2	A	G	3: 86,792,067		probably benign	Het
Dst	T	G	1: 34,250,680	L784R	probably damaging	Het
Fbn1	T	C	2: 125,342,830	M1681V	possibly damaging	Het
Fbxo9	A	T	9: 78,087,212	D274E	probably damaging	Het
Frem2	T	A	3: 53,549,784	D2049V	probably damaging	Het
Fscn3	T	C	6: 28,430,175	Y115H	probably damaging	Het
Glp2r	G	T	11: 67,764,777	D46E	probably benign	Het
Gm13103	T	C	4: 143,852,756	C304R	probably damaging	Het
Gpat2	G	C	2: 127,431,918	G294R	possibly damaging	Het
Irx5	A	G	8: 92,359,619	Y110C	probably damaging	Het
Klhl2	A	T	8: 64,743,043	C555*	probably null	Het
Krtap4-7	A	T	11: 99,643,734	I101N	unknown	Het
Olfr1308	A	T	2: 111,960,170	V301E	possibly damaging	Het
Olfr60	A	G	7: 140,345,647	L114P	probably damaging	Het
Pcdhb21	T	C	18: 37,515,908	S697P	probably damaging	Het
Rasgrf2	A	T	13: 92,030,853	H237Q	probably damaging	Het
Rnf216	A	T	5: 143,090,657	D157E	probably benign	Het
Rxrg	T	A	1: 167,627,336	F163I	probably damaging	Het
Soat2	T	A	15: 102,160,593	I351N	probably damaging	Het
Srp72	C	T	5: 76,984,200	T242I	probably benign	Het
Svopl	T	C	6: 38,041,067		probably null	Het
Tbc1d2b	G	A	9: 90,226,092	P469S	probably benign	Het
Tbkbp1	G	A	11: 97,138,752		probably benign	Het
Tecta	A	G	9: 42,384,227	V324A	probably damaging	Het
Twnk	T	C	19: 45,010,492	V557A	probably damaging	Het
Vmn2r18	G	A	5: 151,562,424	T535I	probably damaging	Het
Zc3h14	T	A	12: 98,757,026	S85T	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
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'- TGCAATATATAGGTCACCACTGTA -3'
(R):5'- AGCAAAGTAAGAAATGTGATCCTCT -3'

Sequencing Primer
(F):5'- GGTCACCACTGTATCTTACTAAGAC -3'
(R):5'- AGAGTTACTAGCTGTCCTTCCAGAG -3'

Posted On

2018-06-22