Mutagenetix > Incidental Mutation

Incidental Mutation 'R7374:Kdm5d'

572302

Institutional Source

Beutler Lab

Gene Symbol

Kdm5d

Ensembl Gene

ENSMUSG00000056673

Gene Name

lysine demethylase 5D

Synonyms

Smcy, HY, Jarid1d

MMRRC Submission

045457-MU

Accession Numbers

Essential gene?

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

Stock #

R7374 (G1)

Quality Score

221.999

Status

Not validated

Chromosome

Chromosomal Location

897566-943813 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 941491 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tryptophan to Arginine at position 1231 (W1231R)

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: W1231R

PolyPhen 2 Score 0.415 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: W1231R

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: 100.0%
10x: 99.8%
20x: 99.2%

Validation Efficiency

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: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	C	T	11: 9,242,136 (GRCm39)	T1333I	possibly damaging	Het
Abcd4	A	T	12: 84,653,017 (GRCm39)	L395*	probably null	Het
Cdh23	G	A	10: 60,153,679 (GRCm39)	R2304W	probably damaging	Het
Ckap2l	T	C	2: 129,126,883 (GRCm39)	T432A	probably damaging	Het
Cplane1	T	A	15: 8,276,731 (GRCm39)	W2792R	unknown	Het
Cyp2c68	T	C	19: 39,727,648 (GRCm39)		probably null	Het
Ddx51	C	A	5: 110,804,998 (GRCm39)	T580K	probably damaging	Het
Fbxo44	T	A	4: 148,241,094 (GRCm39)	D112V	probably benign	Het
Ffar2	T	C	7: 30,519,465 (GRCm39)	N25S	probably damaging	Het
Gas6	A	T	8: 13,524,802 (GRCm39)	V330D	probably damaging	Het
Gfpt1	A	G	6: 87,027,959 (GRCm39)	T22A	probably benign	Het
Gm3371	A	G	14: 44,641,240 (GRCm39)	V108A		Het
Gm8257	T	C	14: 44,887,740 (GRCm39)	E215G	probably benign	Het
Gria1	T	A	11: 57,080,634 (GRCm39)	S206T	probably benign	Het
Gria2	T	C	3: 80,648,383 (GRCm39)	T118A	probably benign	Het
Hfe	T	G	13: 23,890,030 (GRCm39)	T248P	probably damaging	Het
Ltbp2	C	T	12: 84,876,949 (GRCm39)	D419N	probably damaging	Het
Mei1	G	A	15: 81,980,109 (GRCm39)	A232T		Het
Mgam	G	A	6: 40,734,373 (GRCm39)	E1473K	possibly damaging	Het
Mtbp	A	C	15: 55,426,355 (GRCm39)	E99A	possibly damaging	Het
Muc5b	A	T	7: 141,416,863 (GRCm39)	T3270S	probably benign	Het
Myl2	A	G	5: 122,239,726 (GRCm39)	Y28C		Het
Nrxn1	A	G	17: 90,896,097 (GRCm39)		probably null	Het
Ntn4	A	G	10: 93,518,434 (GRCm39)	H247R	probably benign	Het
Numa1	T	C	7: 101,658,335 (GRCm39)	V1568A	probably benign	Het
Nyap1	C	T	5: 137,733,791 (GRCm39)	G414D	probably damaging	Het
Or5p68	A	G	7: 107,946,095 (GRCm39)	F31S	probably damaging	Het
Or8k25	C	A	2: 86,244,196 (GRCm39)	A67S	probably benign	Het
Pdgfrb	G	A	18: 61,204,780 (GRCm39)	V547I	possibly damaging	Het
Pom121l12	A	T	11: 14,549,962 (GRCm39)	M223L	probably benign	Het
Prps1l1	T	C	12: 35,035,424 (GRCm39)	S180P	possibly damaging	Het
Ptprf	A	G	4: 118,114,689 (GRCm39)	S189P	probably damaging	Het
Radil	G	A	5: 142,471,235 (GRCm39)	R1014W	probably damaging	Het
Rfx5	C	T	3: 94,866,053 (GRCm39)	P451S	unknown	Het
Rhbdl2	G	C	4: 123,711,658 (GRCm39)	V132L	probably benign	Het
Slc15a2	G	T	16: 36,572,207 (GRCm39)	T719K	probably benign	Het
Slc9a9	A	G	9: 94,937,542 (GRCm39)	T465A	possibly damaging	Het
Son	AGAACCCCCAGCCGCAGGAGCCGAACCCCCAGCCGCAGGAGCCGAACCCCCAGCCGCAGGAGCCGAACCCCCAGCCG	AGAACCCCCAGCCGCAGGAGCCGAACCCCCAGCCGCAGGAGCCGAACCCCCAGCCG	16: 91,457,222 (GRCm39)		probably benign	Het
Sv2a	A	T	3: 96,095,525 (GRCm39)	Y306F	probably benign	Het
Sv2c	A	T	13: 96,125,644 (GRCm39)	H364Q	probably damaging	Het
Tmem181a	T	A	17: 6,354,533 (GRCm39)	L401Q	possibly damaging	Het
Trav9d-4	A	G	14: 53,221,300 (GRCm39)	Y98C	probably damaging	Het
Trim33	T	A	3: 103,217,639 (GRCm39)	C195S	probably damaging	Het
Uroc1	T	C	6: 90,315,815 (GRCm39)	Y191H	probably damaging	Het
Usp9y	T	C	Y: 1,381,305 (GRCm39)	I839V	probably benign	Het
Vmn1r52	A	T	6: 90,156,118 (GRCm39)	I141F	probably benign	Het
Vmn1r59	T	C	7: 5,457,160 (GRCm39)	H200R	probably damaging	Het
Vmn2r68	A	T	7: 84,881,607 (GRCm39)	M491K	possibly damaging	Het
Vmn2r74	T	C	7: 85,606,630 (GRCm39)	I239V	probably benign	Het
Wrn	A	C	8: 33,758,939 (GRCm39)	C1006W	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
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
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'- GTCCTCATCGATGAATGCCTC -3'
(R):5'- TTCCAGCTGTTTCAACAAAGC -3'

Sequencing Primer
(F):5'- CTCATCGATGAATGCCTCTGCAAC -3'
(R):5'- TCCTCAGAAGCTAGAGCCTG -3'

Posted On

2019-09-13