Mutagenetix > Incidental Mutation

Incidental Mutation 'R8213:Kdm5d'

636295

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 #

R8213 (G1)

Quality Score

221.999

Status

Validated

Chromosome

Chromosomal Location

897788-956786 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 941515 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Cysteine to Serine at position 1239 (C1239S)

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: C1239S

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

SMART Domains

Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: C1239S

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: 99.9%
3x: 99.8%
10x: 99.4%
20x: 98.1%

Validation Efficiency

98% (65/66)

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: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A1bg	T	C	15: 60,919,756	Y277C	probably damaging	Het
Acss1	T	A	2: 150,619,710	D651V	possibly damaging	Het
Aktip	G	T	8: 91,124,866	P243H	possibly damaging	Het
Arl11	T	G	14: 61,311,265	S175A	probably benign	Het
Aup1	A	G	6: 83,054,607		probably benign	Het
Avil	A	T	10: 127,008,321	I250F	probably damaging	Het
Btnl6	A	T	17: 34,508,883		probably null	Het
C77080	A	T	4: 129,221,459	V1070D	possibly damaging	Het
Ccdc7b	C	A	8: 129,178,291	Q137K	probably benign	Het
Cdk11b	G	A	4: 155,639,881	E319K	unknown	Het
Chka	A	C	19: 3,885,882	E196A	probably damaging	Het
Depdc5	C	T	5: 32,937,637	R753C	probably damaging	Het
Dhx57	T	A	17: 80,275,156	D340V	possibly damaging	Het
Dicer1	A	T	12: 104,702,693	D1243E	probably benign	Het
Dnajb9	A	T	12: 44,207,133	L164M	probably benign	Het
Dock6	A	G	9: 21,831,444	V785A	possibly damaging	Het
Efcab5	T	C	11: 77,116,071	Y909C	probably damaging	Het
Erp44	A	T	4: 48,208,783	S226T	probably benign	Het
Fgd6	A	T	10: 94,044,052	D256V	probably benign	Het
Fhl5	A	T	4: 25,207,113	Y218*	probably null	Het
Filip1	C	A	9: 79,818,092	A1082S	probably benign	Het
Gm13088	T	A	4: 143,654,185	M423L	probably benign	Het
Gm13128	A	T	4: 144,330,460	D71V	probably benign	Het
Heatr5a	G	A	12: 51,891,443	T1484M	probably damaging	Het
Herc1	G	T	9: 66,450,888	R2417L	probably damaging	Het
Hnrnpr	A	G	4: 136,317,175		probably benign	Het
Igsf5	A	T	16: 96,372,988	I73F	probably damaging	Het
Il17ra	T	C	6: 120,473,034	V91A	probably benign	Het
Inpp5f	A	G	7: 128,679,805	D510G	probably damaging	Het
Kbtbd3	A	G	9: 4,331,269	K548E	probably damaging	Het
Mamdc4	G	A	2: 25,566,356	T709M	probably benign	Het
Mybbp1a	T	A	11: 72,444,721	Y353N	probably damaging	Het
Nepn	A	T	10: 52,391,759	E40D	probably benign	Het
Npat	G	T	9: 53,570,570	E1193*	probably null	Het
Nrde2	G	A	12: 100,131,003	S846L	probably benign	Het
Nup205	T	C	6: 35,225,203	V1290A	probably benign	Het
Olfr1009	T	A	2: 85,721,501	L32Q	probably null	Het
Olfr1424	A	G	19: 12,059,092	V220A	probably benign	Het
Olfr517	C	A	7: 108,868,519	V212L	probably benign	Het
Pde6a	A	T	18: 61,220,696	K31M	possibly damaging	Het
Pms2	C	T	5: 143,914,771	R169C	probably damaging	Het
Polr2g	A	T	19: 8,798,257	L30Q	probably damaging	Het
Prdm15	T	A	16: 97,807,060	H679L	probably damaging	Het
Prl4a1	T	G	13: 28,023,386	Y214*	probably null	Het
Prlr	C	T	15: 10,329,242	T601M	possibly damaging	Het
Psen2	A	C	1: 180,245,691	S22A	probably benign	Het
Ralgapa1	C	A	12: 55,722,914	R764L	probably damaging	Het
Scgb2b11	T	C	7: 32,209,408	E89G	probably damaging	Het
Serpina10	T	C	12: 103,628,277	I228V	probably benign	Het
Serpinb1a	T	A	13: 32,842,999	H320L	probably damaging	Het
Sesn2	C	A	4: 132,498,053	Q267H	possibly damaging	Het
Sgsm1	A	T	5: 113,251,011	W1019R	probably damaging	Het
Sqle	A	G	15: 59,321,302		probably null	Het
Syt14	T	C	1: 192,986,829	M39V	probably benign	Het
Tgm7	A	G	2: 121,101,064	V206A	probably damaging	Het
Thbs4	T	C	13: 92,760,586		probably null	Het
Trpv1	T	C	11: 73,254,251	F721S	probably damaging	Het
Ttll10	A	T	4: 156,036,234	M433K	probably benign	Het
Vmn1r216	T	C	13: 23,099,525	I126T	probably benign	Het
Vmn2r108	G	A	17: 20,470,088	S494F	probably benign	Het
Vwa3b	C	T	1: 37,128,939	A603V	probably benign	Het
Xirp2	T	A	2: 67,476,866	N19K	probably damaging	Het
Zfp397	T	A	18: 23,960,722	N421K	probably damaging	Het
Zscan5b	C	T	7: 6,233,947	P232S	possibly 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
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
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'- TGTCCTCATCGATGAATGCCTC -3'
(R):5'- TCCAGCTGTTTCAACAAAGCAG -3'

Sequencing Primer
(F):5'- TGCAACCTCCATCTGTATATGTGGG -3'
(R):5'- GTCACATCCTCAGAAGCTAGAG -3'

Posted On

2020-07-13