Mutagenetix > Incidental Mutation

Incidental Mutation 'R6014:Kdm5d'

479949

Institutional Source

Beutler Lab

Gene Symbol

Kdm5d

Ensembl Gene

ENSMUSG00000056673

Gene Name

lysine demethylase 5D

Synonyms

Smcy, HY, Jarid1d

MMRRC Submission

044190-MU

Accession Numbers

Essential gene?

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

Stock #

R6014 (G1)

Quality Score

221.999

Status

Validated

Chromosome

Chromosomal Location

897566-943813 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 921528 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 509 (A509T)

Ref Sequence

ENSEMBL: ENSMUSP00000140663 (fasta)

Gene Model

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

AlphaFold

Q62240

Predicted Effect

probably benign
Transcript: ENSMUST00000055032
AA Change: A509T

PolyPhen 2 Score 0.447 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: A509T

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
AA Change: A509T

PolyPhen 2 Score 0.447 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000140663
Gene: ENSMUSG00000056673
AA Change: A509T

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: ENSMUST00000188910

Predicted Effect

probably benign
Transcript: ENSMUST00000189069

SMART Domains

Protein: ENSMUSP00000139636
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
Blast:ARID	175	298	1e-46	BLAST
PHD	325	371	8.56e-13	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000189626

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.8%
20x: 93.3%

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930568D16Rik	A	T	2: 35,244,881 (GRCm39)	M157K	probably benign	Het
A2ml1	C	T	6: 128,548,948 (GRCm39)	C278Y	probably damaging	Het
Abcc2	A	T	19: 43,815,174 (GRCm39)	Q1187L	probably benign	Het
Adcy9	A	T	16: 4,236,683 (GRCm39)	Y6N	probably damaging	Het
Adh1	T	C	3: 137,992,559 (GRCm39)	I225T	probably benign	Het
Akap11	A	T	14: 78,749,939 (GRCm39)	I816K	probably benign	Het
Ap1b1	T	A	11: 4,969,364 (GRCm39)	M240K	possibly damaging	Het
Apex1	A	T	14: 51,162,982 (GRCm39)	T17S	probably benign	Het
Arhgap21	C	T	2: 20,886,616 (GRCm39)	G26D	probably damaging	Het
Bahcc1	A	G	11: 120,180,615 (GRCm39)	Y2613C	probably benign	Het
Baz1b	C	T	5: 135,246,248 (GRCm39)	R566W	probably damaging	Het
Casp8ap2	A	T	4: 32,641,400 (GRCm39)	Y818F	probably damaging	Het
Col3a1	T	A	1: 45,360,739 (GRCm39)	C56*	probably null	Het
Coro2a	G	A	4: 46,542,261 (GRCm39)	P371S	probably damaging	Het
Cyp2a22	T	A	7: 26,638,605 (GRCm39)		probably null	Het
Dpysl3	T	A	18: 43,494,132 (GRCm39)	I183F	probably damaging	Het
Drc1	A	T	5: 30,502,993 (GRCm39)	N172I	probably damaging	Het
Dst	T	C	1: 34,303,915 (GRCm39)	Y1378H	probably damaging	Het
Dync2i2	C	T	2: 29,921,763 (GRCm39)	A533T	probably benign	Het
Eml2	G	A	7: 18,935,088 (GRCm39)	V432I	probably damaging	Het
Epb41l3	A	T	17: 69,590,955 (GRCm39)	T91S	probably damaging	Het
Exoc4	T	C	6: 33,452,932 (GRCm39)	V474A	probably benign	Het
Fam229b	G	A	10: 38,994,989 (GRCm39)	T56I	probably damaging	Het
Gfm2	A	G	13: 97,288,169 (GRCm39)		probably null	Het
Git2	C	T	5: 114,871,938 (GRCm39)	E152K	probably benign	Het
Golt1b	T	A	6: 142,341,943 (GRCm39)	I109N	probably damaging	Het
Grid2ip	T	A	5: 143,373,578 (GRCm39)	M783K	possibly damaging	Het
Inpp5a	A	G	7: 139,154,898 (GRCm39)	Y339C	probably damaging	Het
Isoc2a	T	C	7: 4,894,625 (GRCm39)	S103P	probably damaging	Het
Itih4	C	A	14: 30,614,586 (GRCm39)	Q483K	probably benign	Het
Kansl2	A	G	15: 98,418,197 (GRCm39)		probably null	Het
Krt13	A	T	11: 100,008,437 (GRCm39)	D433E	unknown	Het
Lat2	C	T	5: 134,632,308 (GRCm39)	V142M	probably damaging	Het
Lemd1	A	C	1: 132,184,463 (GRCm39)	*102S	probably null	Het
Lrfn2	T	C	17: 49,376,934 (GRCm39)	L5P	possibly damaging	Het
Lrrc4c	T	G	2: 97,459,557 (GRCm39)		probably null	Het
Lypla1	T	A	1: 4,878,594 (GRCm39)		probably null	Het
Magi2	G	A	5: 20,816,091 (GRCm39)	G744R	probably damaging	Het
Myh14	T	A	7: 44,274,502 (GRCm39)	E948V	probably null	Het
Myo5a	C	A	9: 75,074,489 (GRCm39)	Y799*	probably null	Het
Nacc1	A	C	8: 85,401,700 (GRCm39)	M371R	possibly damaging	Het
Nlrp5	T	G	7: 23,109,372 (GRCm39)	M106R	probably benign	Het
Oas1h	C	T	5: 121,005,229 (GRCm39)	H226Y	possibly damaging	Het
Obscn	A	C	11: 58,929,690 (GRCm39)	I5175R	probably damaging	Het
Pcdh7	T	A	5: 57,878,497 (GRCm39)	I684N	probably damaging	Het
Pcdhb3	T	A	18: 37,435,706 (GRCm39)	N557K	probably damaging	Het
Pde3b	T	C	7: 114,015,675 (GRCm39)	L297S	probably damaging	Het
Pigv	G	T	4: 133,392,740 (GRCm39)	H143Q	probably benign	Het
Ptk2	T	G	15: 73,176,293 (GRCm39)	Y251S	possibly damaging	Het
Ralgds	A	G	2: 28,433,673 (GRCm39)	N219S	probably damaging	Het
Sardh	C	A	2: 27,087,540 (GRCm39)		probably null	Het
Serpina3b	A	T	12: 104,097,356 (GRCm39)	K212N	possibly damaging	Het
Sh3bp2	A	G	5: 34,716,971 (GRCm39)	N461D	probably benign	Het
Shisa2	A	T	14: 59,867,357 (GRCm39)	Q203L	probably damaging	Het
Shmt1	C	A	11: 60,688,383 (GRCm39)	G255V	probably damaging	Het
Socs1	T	A	16: 10,602,357 (GRCm39)	I127F	possibly damaging	Het
Srcap	A	T	7: 127,137,922 (GRCm39)	T1091S	probably benign	Het
Syt14	A	G	1: 192,613,003 (GRCm39)	I599T	probably damaging	Het
Tep1	A	T	14: 51,084,457 (GRCm39)	N907K	probably benign	Het
Themis2	A	G	4: 132,513,291 (GRCm39)	Y312H	probably benign	Het
Tubgcp5	T	G	7: 55,473,357 (GRCm39)	S812A	probably benign	Het
Ush2a	A	T	1: 188,582,237 (GRCm39)	I3767F	probably damaging	Het
Usp40	T	A	1: 87,907,738 (GRCm39)	E626V	probably damaging	Het
Utrn	T	C	10: 12,566,620 (GRCm39)	R1181G	probably benign	Het
Vmn2r117	T	A	17: 23,698,535 (GRCm39)	I13F	probably damaging	Het
Wdr48	G	T	9: 119,753,775 (GRCm39)	V646F	probably damaging	Het
Wdr64	T	C	1: 175,633,556 (GRCm39)	F936L	possibly 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
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
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'- GTCTGTAGATCTGGCTCATTTTACC -3'
(R):5'- CTCTAAGTGTTCTGCTGCTAGC -3'

Sequencing Primer
(F):5'- GATCTGGCTCATTTTACCTTTCTTAG -3'
(R):5'- GCTGCTAGCGAAGGTACTCCATAC -3'

Posted On

2017-06-26