Mutagenetix > Incidental Mutation

Incidental Mutation 'R5914:Gnl3'

461226

Institutional Source

Beutler Lab

Gene Symbol

Gnl3

Ensembl Gene

ENSMUSG00000042354

Gene Name

guanine nucleotide binding protein nucleolar 3

Synonyms

NS, nucleostemin

MMRRC Submission

044111-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5914 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

30734390-30741088 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 30738853 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Aspartic acid at position 65 (E65D)

Ref Sequence

ENSEMBL: ENSMUSP00000153981 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000022476] [ENSMUST00000037739] [ENSMUST00000052239] [ENSMUST00000112094] [ENSMUST00000112095] [ENSMUST00000226740] [ENSMUST00000112098] [ENSMUST00000146325] [ENSMUST00000144009] [ENSMUST00000168584] [ENSMUST00000112106] [ENSMUST00000227467] [ENSMUST00000228341]

AlphaFold

Q8CI11

Predicted Effect

probably benign
Transcript: ENSMUST00000022476

SMART Domains

Protein: ENSMUSP00000022476
Gene: ENSMUSG00000021916

Domain	Start	End	E-Value	Type
transmembrane domain	7	26	N/A	INTRINSIC
Pfam:Glyco_transf_8	67	340	1.7e-69	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000037739
AA Change: E111D

PolyPhen 2 Score 0.078 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000047119
Gene: ENSMUSG00000042354
AA Change: E111D

Domain	Start	End	E-Value	Type
Pfam:GN3L_Grn1	16	90	4.3e-25	PFAM
low complexity region	112	126	N/A	INTRINSIC
SCOP:d1egaa1	130	207	3e-3	SMART
low complexity region	209	220	N/A	INTRINSIC
Pfam:MMR_HSR1	251	362	2.3e-10	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000052239

SMART Domains

Protein: ENSMUSP00000060476
Gene: ENSMUSG00000042323

Domain	Start	End	E-Value	Type
BROMO	43	153	4.97e-35	SMART
BROMO	175	289	5.84e-41	SMART
low complexity region	354	370	N/A	INTRINSIC
BROMO	379	489	1.57e-32	SMART
BROMO	516	627	6.07e-39	SMART
BROMO	651	765	3.01e-43	SMART
BROMO	775	881	2.53e-18	SMART
coiled coil region	907	934	N/A	INTRINSIC
BAH	956	1049	8.64e-22	SMART
low complexity region	1058	1072	N/A	INTRINSIC
BAH	1131	1247	3.02e-35	SMART
low complexity region	1293	1310	N/A	INTRINSIC
HMG	1326	1396	2.87e-13	SMART
low complexity region	1405	1430	N/A	INTRINSIC
low complexity region	1449	1477	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000104024

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000104609

Predicted Effect

probably benign
Transcript: ENSMUST00000112094

SMART Domains

Protein: ENSMUSP00000107723
Gene: ENSMUSG00000042323

Domain	Start	End	E-Value	Type
BROMO	43	153	4.97e-35	SMART
BROMO	175	289	5.84e-41	SMART
low complexity region	322	338	N/A	INTRINSIC
BROMO	347	457	1.57e-32	SMART
BROMO	484	595	6.07e-39	SMART
BROMO	619	733	3.01e-43	SMART
BROMO	743	849	2.53e-18	SMART
coiled coil region	875	902	N/A	INTRINSIC
BAH	924	1042	1.33e-45	SMART
low complexity region	1051	1065	N/A	INTRINSIC
BAH	1124	1240	3.02e-35	SMART
low complexity region	1286	1306	N/A	INTRINSIC
HMG	1346	1416	2.87e-13	SMART
low complexity region	1425	1450	N/A	INTRINSIC
low complexity region	1469	1497	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000112095

SMART Domains

Protein: ENSMUSP00000107724
Gene: ENSMUSG00000042323

Domain	Start	End	E-Value	Type
BROMO	43	153	4.97e-35	SMART
BROMO	175	289	5.84e-41	SMART
low complexity region	354	370	N/A	INTRINSIC
BROMO	379	489	1.57e-32	SMART
BROMO	516	627	6.07e-39	SMART
BROMO	651	765	3.01e-43	SMART
BROMO	775	881	2.53e-18	SMART
coiled coil region	907	934	N/A	INTRINSIC
BAH	956	1074	1.33e-45	SMART
low complexity region	1083	1097	N/A	INTRINSIC
BAH	1156	1272	3.02e-35	SMART
low complexity region	1318	1338	N/A	INTRINSIC
HMG	1378	1448	2.87e-13	SMART
low complexity region	1457	1482	N/A	INTRINSIC
low complexity region	1501	1529	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145497

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000157287

Predicted Effect

probably benign
Transcript: ENSMUST00000226740
AA Change: E111D

PolyPhen 2 Score 0.084 (Sensitivity: 0.93; Specificity: 0.85)

Predicted Effect

probably benign
Transcript: ENSMUST00000112098

SMART Domains

Protein: ENSMUSP00000107727
Gene: ENSMUSG00000042323

Domain	Start	End	E-Value	Type
BROMO	43	153	4.97e-35	SMART
BROMO	175	289	5.84e-41	SMART
low complexity region	354	370	N/A	INTRINSIC
BROMO	379	489	1.57e-32	SMART
BROMO	531	642	6.07e-39	SMART
BROMO	666	780	3.01e-43	SMART
BROMO	790	896	2.53e-18	SMART
coiled coil region	922	949	N/A	INTRINSIC
BAH	971	1089	1.33e-45	SMART
low complexity region	1098	1112	N/A	INTRINSIC
BAH	1171	1287	3.02e-35	SMART
low complexity region	1333	1353	N/A	INTRINSIC
HMG	1393	1463	1.62e-21	SMART
low complexity region	1479	1490	N/A	INTRINSIC
low complexity region	1500	1515	N/A	INTRINSIC
low complexity region	1527	1552	N/A	INTRINSIC
low complexity region	1571	1599	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000146325

SMART Domains

Protein: ENSMUSP00000122805
Gene: ENSMUSG00000042323

Domain	Start	End	E-Value	Type
BROMO	64	174	4.97e-35	SMART
BROMO	196	310	5.84e-41	SMART
low complexity region	343	359	N/A	INTRINSIC
BROMO	368	478	1.57e-32	SMART
BROMO	505	616	6.07e-39	SMART
BROMO	640	754	3.01e-43	SMART
BROMO	764	870	2.53e-18	SMART
coiled coil region	896	923	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000226220

Predicted Effect

probably benign
Transcript: ENSMUST00000144009

SMART Domains

Protein: ENSMUSP00000123518
Gene: ENSMUSG00000042323

Domain	Start	End	E-Value	Type
Blast:BROMO	40	68	8e-14	BLAST
PDB:3IU5\|A	64	84	8e-9	PDB

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000226959

Predicted Effect

probably benign
Transcript: ENSMUST00000226379

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000226348

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000227170

Predicted Effect

probably benign
Transcript: ENSMUST00000168584

SMART Domains

Protein: ENSMUSP00000129323
Gene: ENSMUSG00000021916

Domain	Start	End	E-Value	Type
transmembrane domain	7	26	N/A	INTRINSIC
Pfam:Glyco_transf_8	67	340	8.6e-55	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000112106

SMART Domains

Protein: ENSMUSP00000107734
Gene: ENSMUSG00000042323

Domain	Start	End	E-Value	Type
Blast:BROMO	61	91	6e-16	BLAST
PDB:3IU5\|A	61	91	6e-17	PDB

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000227087

Predicted Effect

probably benign
Transcript: ENSMUST00000227467
AA Change: E99D

PolyPhen 2 Score 0.144 (Sensitivity: 0.92; Specificity: 0.86)

Predicted Effect

possibly damaging
Transcript: ENSMUST00000228341
AA Change: E65D

PolyPhen 2 Score 0.853 (Sensitivity: 0.83; Specificity: 0.93)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000228713

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000228255

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000227389

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000228739

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000228427

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000227869

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000228774

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000227783

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.4%
20x: 95.5%

Validation Efficiency

95% (87/92)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene may interact with p53 and may be involved in tumorigenesis. The encoded protein also appears to be important for stem cell proliferation. This protein is found in both the nucleus and nucleolus. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]
PHENOTYPE: Homozygous disruption of this gene leads to early embryonic loss as blastocysts fail to enter the S phase. MEFs heterozygous for a gene trap allele have reduced proliferative capacity while MEFs heterozygous for a null allele show reduced doubling rates,increased apoptosis and premature senescence. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrb1	G	A	15: 74,410,219 (GRCm39)	R286H	possibly damaging	Het
Ank3	A	T	10: 69,828,774 (GRCm39)		probably benign	Het
Arhgap24	G	A	5: 102,700,025 (GRCm39)		probably null	Het
Arhgef2	T	C	3: 88,543,176 (GRCm39)	Y396H	probably benign	Het
Asap3	G	T	4: 135,968,720 (GRCm39)	G722C	probably benign	Het
Birc2	A	C	9: 7,857,343 (GRCm39)	*377E	probably null	Het
Cdc123	G	T	2: 5,803,174 (GRCm39)	Q282K	possibly damaging	Het
Cdkl4	C	T	17: 80,855,120 (GRCm39)		probably null	Het
Cep97	T	C	16: 55,725,820 (GRCm39)	N689S	probably benign	Het
Cfap97	T	G	8: 46,634,895 (GRCm39)	S407A	probably damaging	Het
Cfh	A	T	1: 140,063,967 (GRCm39)	N436K	probably benign	Het
Chpf2	A	T	5: 24,797,421 (GRCm39)		probably benign	Het
Cnnm2	A	G	19: 46,751,616 (GRCm39)	T469A	probably benign	Het
Col6a3	T	A	1: 90,703,922 (GRCm39)	I2275F	unknown	Het
Ctdspl2	A	T	2: 121,809,414 (GRCm39)	N122Y	probably damaging	Het
Dcaf6	A	T	1: 165,178,724 (GRCm39)	C602S	probably benign	Het
Dda1	T	A	8: 71,927,294 (GRCm39)		probably benign	Het
Dixdc1	T	C	9: 50,609,888 (GRCm39)		probably benign	Het
Dnah2	C	T	11: 69,349,746 (GRCm39)	R2399Q	probably benign	Het
Emilin3	T	A	2: 160,750,990 (GRCm39)	N253I	probably damaging	Het
Epg5	T	A	18: 78,002,847 (GRCm39)		probably null	Het
Fam204a	A	T	19: 60,209,525 (GRCm39)	Y68*	probably null	Het
Fbln5	T	G	12: 101,727,002 (GRCm39)	D329A	possibly damaging	Het
Fkbp15	T	A	4: 62,246,047 (GRCm39)		probably null	Het
Fnbp4	C	G	2: 90,605,137 (GRCm39)		probably benign	Het
Foxn2	C	A	17: 88,770,138 (GRCm39)		probably null	Het
Frem1	T	C	4: 82,920,012 (GRCm39)	D448G	probably damaging	Het
Fzd9	T	C	5: 135,278,199 (GRCm39)	Y562C	probably benign	Het
Gcn1	A	G	5: 115,748,194 (GRCm39)		silent	Het
Gm6003	A	G	7: 32,864,691 (GRCm39)		noncoding transcript	Het
Hax1	GTCATCATCATCATCATC	GTCATCATCATCATCATCATC	3: 89,905,247 (GRCm39)		probably benign	Het
Hk2	C	T	6: 82,713,615 (GRCm39)	R461K	probably benign	Het
Ice1	A	G	13: 70,754,496 (GRCm39)	F530S	possibly damaging	Het
Ing3	T	A	6: 21,968,904 (GRCm39)	S129T	probably benign	Het
Ino80	G	A	2: 119,288,697 (GRCm39)	S3L	probably damaging	Het
Ints2	T	A	11: 86,113,000 (GRCm39)	Q839H	probably benign	Het
Kcnrg	T	C	14: 61,849,280 (GRCm39)	M247T	probably benign	Het
Kpna6	T	C	4: 129,566,485 (GRCm39)		probably benign	Het
Krtap28-13	T	A	1: 83,039,044 (GRCm39)		probably benign	Het
Lgr4	T	A	2: 109,748,617 (GRCm39)	V51E	possibly damaging	Het
Map3k5	A	C	10: 19,980,001 (GRCm39)	E836D	probably benign	Het
Mapk11	T	C	15: 89,030,038 (GRCm39)	I193V	probably benign	Het
Marchf10	A	T	11: 105,276,308 (GRCm39)	V660E	probably damaging	Het
Matn4	T	C	2: 164,235,144 (GRCm39)	E435G	probably damaging	Het
Mre11a	G	T	9: 14,723,232 (GRCm39)	R402M	probably damaging	Het
Msr1	C	T	8: 40,034,868 (GRCm39)	G428R	probably damaging	Het
Ndufv3	C	T	17: 31,750,206 (GRCm39)	R99*	probably null	Het
Nkx6-1	C	T	5: 101,811,847 (GRCm39)	S85N	unknown	Het
Nop2	A	T	6: 125,111,691 (GRCm39)	E141D	probably benign	Het
Or5b3	A	G	19: 13,388,326 (GRCm39)	H131R	probably benign	Het
Or8b1	G	C	9: 38,399,657 (GRCm39)	E111Q	probably damaging	Het
Paox	T	C	7: 139,709,101 (GRCm39)	S205P	probably damaging	Het
Pcdh15	T	C	10: 74,466,768 (GRCm39)	V995A	probably benign	Het
Pdcd1	T	A	1: 93,968,550 (GRCm39)	K161N	probably benign	Het
Pfkfb2	C	A	1: 130,627,832 (GRCm39)	V372L	probably damaging	Het
Phldb1	G	A	9: 44,622,948 (GRCm39)	T19I	probably damaging	Het
Pik3c2g	G	T	6: 139,599,477 (GRCm39)	V198L	probably benign	Het
Pnpla8	T	A	12: 44,342,753 (GRCm39)	L41*	probably null	Het
Postn	C	T	3: 54,281,221 (GRCm39)	Q449*	probably null	Het
Ppp1r3a	C	T	6: 14,718,988 (GRCm39)	S642N	probably benign	Het
Ptpn23	G	A	9: 110,214,511 (GRCm39)		probably benign	Het
Ptprj	T	C	2: 90,283,684 (GRCm39)	N923S	possibly damaging	Het
Rai1	T	C	11: 60,078,630 (GRCm39)	V898A	probably benign	Het
Rasgef1a	A	T	6: 118,057,515 (GRCm39)	Y72F	possibly damaging	Het
Serpinb7	T	C	1: 107,379,580 (GRCm39)	V329A	probably damaging	Het
Slc24a4	T	A	12: 102,201,049 (GRCm39)	I311N	probably damaging	Het
Slc45a1	C	A	4: 150,713,997 (GRCm39)	L749F	possibly damaging	Het
Spon1	G	A	7: 113,630,056 (GRCm39)	D428N	probably damaging	Het
Tcf7l2	G	A	19: 55,886,992 (GRCm39)	E2K	probably benign	Het
Thoc5	A	G	11: 4,870,416 (GRCm39)	M472V	possibly damaging	Het
Tm6sf2	T	C	8: 70,528,213 (GRCm39)	Y121H	probably damaging	Het
Tmc4	T	A	7: 3,675,008 (GRCm39)	D221V	probably benign	Het
Trim30b	A	T	7: 104,006,572 (GRCm39)	S95T	probably damaging	Het
Trip12	T	C	1: 84,741,179 (GRCm39)	E571G	probably damaging	Het
Ttn	T	C	2: 76,781,656 (GRCm39)		probably null	Het
Ubp1	A	T	9: 113,785,807 (GRCm39)	R161W	probably benign	Het
Usp21	G	A	1: 171,109,745 (GRCm39)		probably benign	Het
Vmn1r61	T	A	7: 5,613,529 (GRCm39)	R262W	probably damaging	Het
Vmn2r67	A	T	7: 84,801,044 (GRCm39)	D297E	probably damaging	Het
Vwa5a	T	C	9: 38,653,038 (GRCm39)	L784S	probably benign	Het
Vwc2	G	A	11: 11,104,244 (GRCm39)	V259M	probably damaging	Het
Zeb2	T	C	2: 44,887,064 (GRCm39)	I596M	probably benign	Het
Zgrf1	T	A	3: 127,354,672 (GRCm39)	L97H	probably damaging	Het

Other mutations in Gnl3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00809:Gnl3	APN	14	30,736,146 (GRCm39)	missense	possibly damaging	0.71
IGL00826:Gnl3	APN	14	30,734,753 (GRCm39)	unclassified	probably benign
IGL02323:Gnl3	APN	14	30,739,359 (GRCm39)	missense	probably damaging	1.00
R0277:Gnl3	UTSW	14	30,735,384 (GRCm39)	critical splice donor site	probably null
R0636:Gnl3	UTSW	14	30,739,110 (GRCm39)	missense	probably damaging	1.00
R0727:Gnl3	UTSW	14	30,739,034 (GRCm39)	missense	probably damaging	0.99
R1459:Gnl3	UTSW	14	30,739,803 (GRCm39)	missense	probably damaging	1.00
R1474:Gnl3	UTSW	14	30,738,418 (GRCm39)	splice site	probably benign
R2016:Gnl3	UTSW	14	30,738,326 (GRCm39)	splice site	probably null
R2352:Gnl3	UTSW	14	30,738,783 (GRCm39)	critical splice donor site	probably null
R2517:Gnl3	UTSW	14	30,736,120 (GRCm39)	missense	probably damaging	1.00
R4115:Gnl3	UTSW	14	30,738,813 (GRCm39)	missense	probably damaging	1.00
R4697:Gnl3	UTSW	14	30,739,286 (GRCm39)	missense	probably damaging	0.98
R4853:Gnl3	UTSW	14	30,737,270 (GRCm39)	missense	probably damaging	0.99
R4973:Gnl3	UTSW	14	30,735,462 (GRCm39)	missense	possibly damaging	0.68
R5091:Gnl3	UTSW	14	30,738,803 (GRCm39)	missense	possibly damaging	0.76
R5580:Gnl3	UTSW	14	30,737,242 (GRCm39)	missense	probably benign
R6898:Gnl3	UTSW	14	30,735,136 (GRCm39)	missense	probably benign	0.01
R7292:Gnl3	UTSW	14	30,735,189 (GRCm39)	missense	probably benign
R7372:Gnl3	UTSW	14	30,738,843 (GRCm39)	missense	probably benign	0.06

Predicted Primers

PCR Primer
(F):5'- GAATCCACTGCCCACCCTTTAG -3'
(R):5'- AGTTAGCCCTGGTGATGAGC -3'

Sequencing Primer
(F):5'- GACTCTGACTTCAACAGCGTTCTAAG -3'
(R):5'- CCCTGGTGATGAGCAGTCTAATG -3'

Posted On

2017-02-28