Mutagenetix > Incidental Mutation

Incidental Mutation 'R5876:Kdm5d'

455567

Institutional Source

Beutler Lab

Gene Symbol

Kdm5d

Ensembl Gene

ENSMUSG00000056673

Gene Name

lysine demethylase 5D

Synonyms

Smcy, HY, Jarid1d

Accession Numbers

Essential gene?

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

Stock #

R5876 (G1)

Quality Score

222

Status

Not validated

Chromosome

Chromosomal Location

897566-943813 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 900525 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 190 (Y190C)

Ref Sequence

ENSEMBL: ENSMUSP00000139636 (fasta)

Gene Model

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

AlphaFold

Q62240

Predicted Effect

probably damaging
Transcript: ENSMUST00000055032
AA Change: Y190C

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000061095
Gene: ENSMUSG00000056673
AA Change: Y190C

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 damaging
Transcript: ENSMUST00000186696
AA Change: Y190C

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000140663
Gene: ENSMUSG00000056673
AA Change: Y190C

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 damaging
Transcript: ENSMUST00000186726
AA Change: Y190C

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000140462
Gene: ENSMUSG00000056673
AA Change: Y190C

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

probably damaging
Transcript: ENSMUST00000189069
AA Change: Y190C

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

SMART Domains

Protein: ENSMUSP00000139636
Gene: ENSMUSG00000056673
AA Change: Y190C

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

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 97.9%
20x: 93.6%

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: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700034E13Rik	A	G	18: 52,796,654 (GRCm39)	D64G	possibly damaging	Het
Ano2	T	A	6: 126,016,242 (GRCm39)	M925K	possibly damaging	Het
Arnt2	T	C	7: 83,996,720 (GRCm39)	T69A	probably damaging	Het
Asap2	T	A	12: 21,262,810 (GRCm39)	N229K	possibly damaging	Het
Atp13a3	T	A	16: 30,181,552 (GRCm39)	N23Y	probably benign	Het
Cbr4	G	A	8: 61,943,627 (GRCm39)	G91R	possibly damaging	Het
Cdc27	A	T	11: 104,406,244 (GRCm39)	C624S	probably benign	Het
Cdc42bpg	T	A	19: 6,360,845 (GRCm39)	I201N	probably damaging	Het
Cdh5	A	G	8: 104,869,209 (GRCm39)	Y645C	probably damaging	Het
Celsr2	C	T	3: 108,321,259 (GRCm39)	V518I	probably damaging	Het
Clca4b	T	C	3: 144,617,821 (GRCm39)	T761A	possibly damaging	Het
Cpne4	C	A	9: 104,802,969 (GRCm39)	S204R	probably damaging	Het
Dcaf1	T	C	9: 106,740,849 (GRCm39)	W1279R	probably damaging	Het
Dennd4a	C	T	9: 64,819,037 (GRCm39)	P1731S	probably damaging	Het
Dmxl1	T	A	18: 50,004,051 (GRCm39)	V892D	possibly damaging	Het
Fam131b	A	G	6: 42,298,182 (GRCm39)		probably null	Het
Fam83b	T	A	9: 76,399,132 (GRCm39)	D657V	possibly damaging	Het
Fam83e	T	A	7: 45,371,787 (GRCm39)		probably null	Het
Fbxo4	A	T	15: 4,007,301 (GRCm39)	I121N	probably damaging	Het
Gabrg2	A	G	11: 41,859,647 (GRCm39)	S202P	probably damaging	Het
Grid2	T	A	6: 64,640,146 (GRCm39)	I788N	probably damaging	Het
Grik4	T	A	9: 42,599,319 (GRCm39)	N53Y	probably damaging	Het
Hipk2	A	C	6: 38,707,802 (GRCm39)		probably null	Het
Hps5	T	C	7: 46,438,620 (GRCm39)	T38A	probably damaging	Het
Hs1bp3	A	G	12: 8,391,843 (GRCm39)	D315G	possibly damaging	Het
Kdm4a	C	T	4: 117,996,073 (GRCm39)	M985I	probably damaging	Het
Krt86	T	C	15: 101,374,491 (GRCm39)	S295P	probably damaging	Het
Matr3	T	A	18: 35,720,791 (GRCm39)	D413E	probably benign	Het
Mbd5	T	A	2: 49,164,657 (GRCm39)	F319L	probably damaging	Het
Mcoln1	T	A	8: 3,560,910 (GRCm39)	Y411N	probably damaging	Het
Mpdz	C	A	4: 81,203,711 (GRCm39)	E1863*	probably null	Het
Mrps9	A	G	1: 42,934,538 (GRCm39)	E173G	probably damaging	Het
Or7a42	A	T	10: 78,791,191 (GRCm39)	I51F	probably benign	Het
Osmr	T	C	15: 6,850,528 (GRCm39)	T692A	probably benign	Het
Pkhd1l1	A	T	15: 44,441,984 (GRCm39)	H3641L	possibly damaging	Het
Pml	T	C	9: 58,140,465 (GRCm39)	T421A	possibly damaging	Het
Podxl	A	G	6: 31,505,391 (GRCm39)		probably null	Het
Ppargc1b	C	G	18: 61,442,164 (GRCm39)	D591H	probably damaging	Het
Prkag3	A	G	1: 74,787,975 (GRCm39)		probably benign	Het
Proz	A	G	8: 13,123,448 (GRCm39)	R240G	probably benign	Het
Ptpn13	C	A	5: 103,624,826 (GRCm39)	D43E	probably damaging	Het
Rbm5	T	G	9: 107,637,525 (GRCm39)	K135N	probably damaging	Het
Ska1	G	A	18: 74,330,599 (GRCm39)	T201M	probably damaging	Het
Slc35f5	A	C	1: 125,515,100 (GRCm39)		probably null	Het
Slc9a3	T	C	13: 74,309,842 (GRCm39)	L510P	probably damaging	Het
Speer4a2	T	C	5: 26,289,716 (GRCm39)	E237G	probably damaging	Het
Svil	A	G	18: 5,082,828 (GRCm39)	K1231E	probably damaging	Het
Tanc2	T	C	11: 105,813,439 (GRCm39)	S1628P	possibly damaging	Het
Tm9sf3	T	A	19: 41,229,023 (GRCm39)	D260V	probably damaging	Het
Ttc9	G	T	12: 81,678,396 (GRCm39)	R73L	probably damaging	Het
Vps13b	A	G	15: 35,917,207 (GRCm39)	I3684V	probably damaging	Het
Vps8	T	C	16: 21,280,189 (GRCm39)		probably null	Het
Vwa3b	T	A	1: 37,115,520 (GRCm39)	I328N	probably damaging	Het
Wdr1	C	T	5: 38,687,366 (GRCm39)	V222M	probably benign	Het
Xpnpep1	T	A	19: 52,985,439 (GRCm39)	T530S	probably damaging	Het
Zc3h6	C	T	2: 128,835,197 (GRCm39)	S111F	probably benign	Het
Zfp768	G	A	7: 126,943,718 (GRCm39)	P137S	probably benign	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
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
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'- TAGGTGTTCAAAATGAGTAAGCTGG -3'
(R):5'- AACTAACACTGGCAGCTTATTAGAAGG -3'

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

Posted On

2017-02-10