Mutagenetix > Incidental Mutations

Incidental Mutation 'R4421:Nsd3'

327102

Institutional Source

Beutler Lab

Gene Symbol

Nsd3

Ensembl Gene

ENSMUSG00000054823

Gene Name

nuclear receptor binding SET domain protein 3

Synonyms

Whsc1l1, WHISTLE

MMRRC Submission

041142-MU

Accession Numbers

Genbank: NM_001081269, NM_001001735.1; MGI: 2142581; Ensemb: ENSMUST00000155861, ENSMUST00000146919, ENSMUST00000142395, ENSMUST00000139966, ENSMUST00000153597, ENSMUST00000084026, ENSMUST0000017135

Is this an essential gene?

Possibly essential (E-score: 0.507) question?

Stock #

R4421 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

25601601-25719667 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 25641272 bp

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 218 (S218T)

Ref Sequence

ENSEMBL: ENSMUSP00000147926 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000084026] [ENSMUST00000136107] [ENSMUST00000139966] [ENSMUST00000142395] [ENSMUST00000143445] [ENSMUST00000146919] [ENSMUST00000155861]

Predicted Effect

probably benign
Transcript: ENSMUST00000084026
AA Change: S218T

PolyPhen 2 Score 0.280 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000081040
Gene: ENSMUSG00000054823
AA Change: S218T

Domain	Start	End	E-Value	Type
low complexity region	128	151	N/A	INTRINSIC
low complexity region	193	225	N/A	INTRINSIC
PWWP	278	341	1.6e-12	SMART
low complexity region	680	701	N/A	INTRINSIC
PHD	713	756	4.49e-7	SMART
PHD	761	808	5.82e-1	SMART
PHD	809	861	3.06e0	SMART
PHD	874	963	1e-4	SMART
PWWP	968	1030	8.62e-18	SMART
AWS	1103	1154	2.61e-17	SMART
SET	1155	1278	2.17e-41	SMART
PostSET	1279	1295	2.63e-3	SMART
low complexity region	1309	1326	N/A	INTRINSIC
PHD	1332	1375	4.32e-9	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000136107
AA Change: S218T

PolyPhen 2 Score 0.957 (Sensitivity: 0.78; Specificity: 0.95)

Predicted Effect

probably benign
Transcript: ENSMUST00000139966
AA Change: S218T

PolyPhen 2 Score 0.280 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000122096
Gene: ENSMUSG00000054823
AA Change: S218T

Domain	Start	End	E-Value	Type
low complexity region	128	151	N/A	INTRINSIC
low complexity region	193	225	N/A	INTRINSIC
PWWP	278	341	1.6e-12	SMART
low complexity region	680	701	N/A	INTRINSIC
PHD	713	756	4.49e-7	SMART
PHD	761	808	5.82e-1	SMART
PHD	809	861	3.06e0	SMART
PHD	874	914	5.24e-8	SMART
PWWP	919	981	8.62e-18	SMART
AWS	1054	1105	2.61e-17	SMART
SET	1106	1229	2.17e-41	SMART
PostSET	1230	1246	2.63e-3	SMART
low complexity region	1260	1277	N/A	INTRINSIC
PHD	1283	1326	4.32e-9	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000142395
AA Change: S218T

PolyPhen 2 Score 0.280 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000117778
Gene: ENSMUSG00000054823
AA Change: S218T

Domain	Start	End	E-Value	Type
low complexity region	128	151	N/A	INTRINSIC
low complexity region	193	225	N/A	INTRINSIC
PWWP	278	341	1.6e-12	SMART
low complexity region	680	701	N/A	INTRINSIC
PHD	713	756	4.49e-7	SMART
PHD	761	808	5.82e-1	SMART
PHD	809	861	3.06e0	SMART
PHD	874	963	1e-4	SMART
PWWP	968	1030	8.62e-18	SMART
AWS	1103	1154	2.61e-17	SMART
SET	1155	1278	2.17e-41	SMART
PostSET	1279	1295	2.63e-3	SMART
low complexity region	1309	1326	N/A	INTRINSIC
PHD	1332	1375	4.32e-9	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000143445
AA Change: S218T

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)

Predicted Effect

probably damaging
Transcript: ENSMUST00000146919
AA Change: S218T

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000115470
Gene: ENSMUSG00000054823
AA Change: S218T

Domain	Start	End	E-Value	Type
low complexity region	128	151	N/A	INTRINSIC
low complexity region	193	225	N/A	INTRINSIC
Pfam:PWWP	278	388	1.6e-25	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000155861
AA Change: S218T

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000117596
Gene: ENSMUSG00000054823
AA Change: S218T

Domain	Start	End	E-Value	Type
low complexity region	128	151	N/A	INTRINSIC
low complexity region	193	225	N/A	INTRINSIC
Pfam:PWWP	278	388	1.6e-25	PFAM

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.4%

Validation Efficiency

MGI Phenotype

FUNCTION: This gene encodes a member of the SET domain family of histone lysine N-methyltransferase proteins. This protein methylates histone H3 at lysine residues 4 and 27, which represses gene transcription. It acts in opposition to the histone demethylase Jmjd1c. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2015]

Allele List at MGI

All alleles(5) : Gene trapped(5)

Other mutations in this stock

Total: 37 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acy1	G	C	9: 106,435,713		probably null	Het
Adgrv1	T	C	13: 81,566,302	E234G	probably damaging	Het
Aga	T	C	8: 53,511,826	S8P	probably benign	Het
C1s2	T	C	6: 124,625,215	D673G	probably benign	Het
Capza3	G	A	6: 140,042,042	M122I	probably benign	Het
Cfap44	T	C	16: 44,422,437	S735P	probably damaging	Het
Cntn3	A	G	6: 102,464,547	F13L	probably damaging	Het
Col6a5	A	T	9: 105,928,473	M1078K	unknown	Het
Colgalt2	A	T	1: 152,485,012	I267F	probably damaging	Het
Cpped1	T	C	16: 11,805,357	*299W	probably null	Het
Cyp3a59	A	G	5: 146,104,903		probably null	Het
Ddx42	T	A	11: 106,231,138	Y160N	probably damaging	Het
Dhx35	A	T	2: 158,806,401	R60W	probably damaging	Het
Gbp10	T	C	5: 105,224,651		probably null	Het
Gtf2i	T	C	5: 134,255,037	T467A	possibly damaging	Het
Hip1r	G	C	5: 123,997,862	G542A	possibly damaging	Het
Hspg2	G	A	4: 137,548,122	A2748T	probably benign	Het
Kcnq3	T	C	15: 65,995,511	Y761C	probably benign	Het
Krt13	T	G	11: 100,118,935	T340P	possibly damaging	Het
Map2k5	A	G	9: 63,164,130	C435R	probably damaging	Het
Ms4a4c	T	A	19: 11,416,375	I53K	probably damaging	Het
Myh15	T	A	16: 49,109,344	F544L	probably damaging	Het
Neurod2	G	T	11: 98,328,200	S46*	probably null	Het
Olfr1184	A	T	2: 88,487,241	N170Y	probably damaging	Het
Olfr706	G	T	7: 106,886,453	D121E	probably damaging	Het
Prrc2c	TTGCTGCTGCTGCTGCTGCTGCTGCTGC	TTGCTGCTGCTGCTGCTGCTGCTGC	1: 162,709,061		probably benign	Het
Prrg3	A	T	X: 71,967,309	S141C	probably damaging	Het
Ranbp17	A	T	11: 33,475,056	D433E	probably benign	Het
Rbm28	T	C	6: 29,154,837	D278G	probably damaging	Het
Sbpl	A	G	17: 23,954,886	L8P	unknown	Het
Spopl	C	T	2: 23,517,945	V241M	probably damaging	Het
Tdrd3	A	G	14: 87,486,283	E311G	probably damaging	Het
Tma16	C	T	8: 66,484,171		probably null	Het
Ubr4	A	G	4: 139,461,856	N3917D	possibly damaging	Het
Vmn2r68	TCC	TC	7: 85,221,550		probably null	Het
Vmn2r72	T	C	7: 85,738,500	N619D	probably damaging	Het
Xab2	C	A	8: 3,614,244		probably null	Het

Other mutations in Nsd3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00435:Nsd3	APN	8	25676712	missense	probably benign	0.40
IGL00718:Nsd3	APN	8	25706534	missense	probably damaging	0.97
IGL00727:Nsd3	APN	8	25641158	missense	probably damaging	1.00
IGL01324:Nsd3	APN	8	25662820	missense	probably damaging	1.00
IGL01614:Nsd3	APN	8	25666079	missense	possibly damaging	0.65
IGL01834:Nsd3	APN	8	25640652	missense	probably damaging	1.00
IGL02066:Nsd3	APN	8	25713488	missense	probably damaging	1.00
IGL02229:Nsd3	APN	8	25710748	missense	probably damaging	0.98
IGL02481:Nsd3	APN	8	25691116	missense	probably damaging	1.00
IGL02686:Nsd3	APN	8	25666070	missense	probably damaging	0.96
IGL03394:Nsd3	APN	8	25675749	splice site	probably benign
Pine	UTSW	8	25679936	missense	possibly damaging	0.87
D3080:Nsd3	UTSW	8	25713545	missense	possibly damaging	0.77
IGL02802:Nsd3	UTSW	8	25640906	missense	probably damaging	1.00
R0136:Nsd3	UTSW	8	25659854	nonsense	probably null
R0195:Nsd3	UTSW	8	25680693	missense	probably damaging	1.00
R0207:Nsd3	UTSW	8	25683257	missense	probably benign	0.02
R0471:Nsd3	UTSW	8	25648434	splice site	probably benign
R0511:Nsd3	UTSW	8	25678716	missense	possibly damaging	0.81
R0524:Nsd3	UTSW	8	25700577	missense	possibly damaging	0.90
R0581:Nsd3	UTSW	8	25710691	missense	probably damaging	1.00
R0589:Nsd3	UTSW	8	25641287	missense	probably damaging	1.00
R0645:Nsd3	UTSW	8	25709069	missense	probably benign	0.08
R0664:Nsd3	UTSW	8	25714240	missense	probably damaging	0.97
R0738:Nsd3	UTSW	8	25678709	splice site	probably null
R1148:Nsd3	UTSW	8	25713380	missense	probably benign	0.09
R1148:Nsd3	UTSW	8	25713380	missense	probably benign	0.09
R1265:Nsd3	UTSW	8	25682562	missense	probably benign
R1298:Nsd3	UTSW	8	25679936	missense	possibly damaging	0.87
R1424:Nsd3	UTSW	8	25700566	missense	probably damaging	1.00
R1493:Nsd3	UTSW	8	25713380	missense	probably benign	0.09
R1528:Nsd3	UTSW	8	25698767	missense	probably damaging	1.00
R2051:Nsd3	UTSW	8	25691089	missense	probably damaging	0.99
R2199:Nsd3	UTSW	8	25666057	missense	probably damaging	0.99
R3414:Nsd3	UTSW	8	25700019	missense	probably damaging	1.00
R3522:Nsd3	UTSW	8	25706614	missense	probably benign
R3623:Nsd3	UTSW	8	25662819	missense	probably damaging	0.98
R3624:Nsd3	UTSW	8	25662819	missense	probably damaging	0.98
R3798:Nsd3	UTSW	8	25698845	missense	probably damaging	1.00
R4345:Nsd3	UTSW	8	25641317	missense	probably benign	0.04
R4370:Nsd3	UTSW	8	25648508	missense	probably benign	0.13
R4583:Nsd3	UTSW	8	25710676	missense	probably benign	0.20
R4664:Nsd3	UTSW	8	25698866	missense	probably damaging	1.00
R4741:Nsd3	UTSW	8	25673366	missense	probably damaging	1.00
R4876:Nsd3	UTSW	8	25691134	missense	possibly damaging	0.94
R4888:Nsd3	UTSW	8	25698911	missense	probably damaging	1.00
R5000:Nsd3	UTSW	8	25682577	missense	probably damaging	1.00
R5132:Nsd3	UTSW	8	25678839	missense	possibly damaging	0.73
R5632:Nsd3	UTSW	8	25679969	missense	probably benign	0.00
R5760:Nsd3	UTSW	8	25659756	missense	probably damaging	1.00
R5778:Nsd3	UTSW	8	25659818	missense	probably damaging	1.00
R5779:Nsd3	UTSW	8	25682669	nonsense	probably null
R5860:Nsd3	UTSW	8	25666091	missense	probably damaging	0.98
R5911:Nsd3	UTSW	8	25666076	missense	probably damaging	1.00
R6168:Nsd3	UTSW	8	25691161	missense	probably null	1.00
R6467:Nsd3	UTSW	8	25640630	missense	probably damaging	1.00
R6490:Nsd3	UTSW	8	25714185	missense	probably damaging	1.00
R6519:Nsd3	UTSW	8	25662939	missense	probably damaging	1.00
R6554:Nsd3	UTSW	8	25662875	missense	probably damaging	0.99
R7038:Nsd3	UTSW	8	25641263	missense	probably damaging	1.00
R7088:Nsd3	UTSW	8	25666034	missense	probably benign	0.40
R7244:Nsd3	UTSW	8	25666039	missense	probably damaging	0.96
R7308:Nsd3	UTSW	8	25640724	missense	probably damaging	1.00
R7678:Nsd3	UTSW	8	25659817	missense	possibly damaging	0.82
R7717:Nsd3	UTSW	8	25682562	missense	probably benign
R8064:Nsd3	UTSW	8	25700670	nonsense	probably null
X0026:Nsd3	UTSW	8	25700593	missense	probably damaging	1.00
Z1088:Nsd3	UTSW	8	25641002	small deletion	probably benign

Predicted Primers

PCR Primer
(F):5'- AGGCTCACCCGAGATTAAAC -3'
(R):5'- AAGCAAGACTCTCGGTGTC -3'

Sequencing Primer
(F):5'- TTCCCTTTGTGGAGACCT -3'
(R):5'- GACTCTCGGTGTCAAAAACG -3'

Posted On

2015-07-07