Mutagenetix > Incidental Mutation

Incidental Mutation 'R1862:Nup54'

204009

Institutional Source

Beutler Lab

Gene Symbol

Nup54

Ensembl Gene

ENSMUSG00000034826

Gene Name

nucleoporin 54

Synonyms

3110079L04Rik, 54kDa

MMRRC Submission

039885-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.963) question?

Stock #

R1862 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

92563399-92583078 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 92567426 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Leucine at position 375 (I375L)

Ref Sequence

ENSEMBL: ENSMUSP00000046540 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038514] [ENSMUST00000113083] [ENSMUST00000117108] [ENSMUST00000118106] [ENSMUST00000119587] [ENSMUST00000120193] [ENSMUST00000120416] [ENSMUST00000121096]

AlphaFold

Q8BTS4

Predicted Effect

possibly damaging
Transcript: ENSMUST00000038514
AA Change: I375L

PolyPhen 2 Score 0.745 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000046540
Gene: ENSMUSG00000034826
AA Change: I375L

Domain	Start	End	E-Value	Type
low complexity region	5	109	N/A	INTRINSIC
Pfam:Nup54	303	441	4.8e-49	PFAM
PDB:3T98\|C	445	494	2e-26	PDB

Predicted Effect

probably benign
Transcript: ENSMUST00000113083

SMART Domains

Protein: ENSMUSP00000108706
Gene: ENSMUSG00000034842

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
Pfam:ART	29	251	4.4e-65	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000117108

SMART Domains

Protein: ENSMUSP00000113041
Gene: ENSMUSG00000034842

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
Pfam:ART	29	251	1.9e-65	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000118106

SMART Domains

Protein: ENSMUSP00000114083
Gene: ENSMUSG00000034842

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
Pfam:ART	29	251	9e-66	PFAM
low complexity region	298	309	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000119587

SMART Domains

Protein: ENSMUSP00000112648
Gene: ENSMUSG00000034842

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
Pfam:ART	29	251	4e-65	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000120193

SMART Domains

Protein: ENSMUSP00000113074
Gene: ENSMUSG00000034842

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
Pfam:ART	29	251	8.4e-66	PFAM
low complexity region	298	309	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000120416

SMART Domains

Protein: ENSMUSP00000113493
Gene: ENSMUSG00000034842

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
Pfam:ART	29	251	3.1e-65	PFAM
low complexity region	298	309	N/A	INTRINSIC
low complexity region	366	373	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000129222

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123694

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201228

Predicted Effect

probably benign
Transcript: ENSMUST00000126281

SMART Domains

Protein: ENSMUSP00000116110
Gene: ENSMUSG00000034842

Domain	Start	End	E-Value	Type
Pfam:ART	1	190	3e-53	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000121096

SMART Domains

Protein: ENSMUSP00000113510
Gene: ENSMUSG00000034842

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
Pfam:ART	29	251	1.8e-65	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000138003

Coding Region Coverage

1x: 97.5%
3x: 96.8%
10x: 94.9%
20x: 90.5%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The nuclear envelope creates distinct nuclear and cytoplasmic compartments in eukaryotic cells. It consists of two concentric membranes perforated by nuclear pores, large protein complexes that form aqueous channels to regulate the flow of macromolecules between the nucleus and the cytoplasm. These complexes are composed of at least 100 different polypeptide subunits, many of which belong to the nucleoporin family. This gene encodes a member of the phe-gly (FG) repeat-containing nucleoporin subset. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2013]

Allele List at MGI

Other mutations in this stock

Total: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acox2	T	A	14: 8,241,416 (GRCm38)	E565D	probably benign	Het
Adam30	A	T	3: 98,069,429 (GRCm39)	K421*	probably null	Het
Atp6v1b1	A	G	6: 83,726,834 (GRCm39)		probably null	Het
Cacna1a	A	T	8: 85,142,559 (GRCm39)	I96F	possibly damaging	Het
Card10	G	A	15: 78,664,714 (GRCm39)	R747W	probably damaging	Het
Cdh8	T	A	8: 99,917,026 (GRCm39)	D363V	probably damaging	Het
Cecr2	T	C	6: 120,734,902 (GRCm39)	Y685H	probably damaging	Het
Cibar1	C	T	4: 12,155,717 (GRCm39)	V306I	possibly damaging	Het
Cmklr1	T	C	5: 113,752,468 (GRCm39)	T178A	probably damaging	Het
Col16a1	G	A	4: 129,986,575 (GRCm39)		probably null	Het
Col4a1	C	T	8: 11,276,439 (GRCm39)		probably benign	Het
Coro2a	T	A	4: 46,548,797 (GRCm39)	I166F	possibly damaging	Het
Cry2	T	C	2: 92,254,911 (GRCm39)	H148R	probably damaging	Het
Crygd	T	C	1: 65,101,133 (GRCm39)	Y154C	probably benign	Het
Cubn	T	C	2: 13,313,372 (GRCm39)	Y3066C	probably damaging	Het
Defb15	C	T	8: 22,420,002 (GRCm39)	E42K	possibly damaging	Het
Dnah12	A	G	14: 26,418,553 (GRCm39)	D147G	probably benign	Het
Dnah12	A	T	14: 26,430,412 (GRCm39)	Y340F	probably benign	Het
Dot1l	G	T	10: 80,619,373 (GRCm39)	R193L	probably damaging	Het
Dusp29	A	G	14: 21,736,757 (GRCm39)	V115A	probably benign	Het
Esd	A	C	14: 74,979,514 (GRCm39)	Y119S	probably damaging	Het
Esp36	A	G	17: 38,730,330 (GRCm39)		probably benign	Het
Etfbkmt	T	A	6: 149,045,649 (GRCm39)	M1K	probably null	Het
Exph5	A	G	9: 53,287,548 (GRCm39)	H1543R	probably benign	Het
Fbxo16	A	G	14: 65,508,252 (GRCm39)	T23A	probably damaging	Het
Gorasp2	C	A	2: 70,509,808 (GRCm39)	H136Q	probably damaging	Het
Hdc	T	A	2: 126,439,853 (GRCm39)	I367F	probably benign	Het
Hmcn1	C	T	1: 150,514,651 (GRCm39)	V3574M	probably benign	Het
Ilvbl	A	G	10: 78,419,958 (GRCm39)	D592G	probably benign	Het
Inmt	G	A	6: 55,151,868 (GRCm39)	A34V	probably damaging	Het
Ints9	A	C	14: 65,263,862 (GRCm39)	H378P	probably benign	Het
Kcnh7	T	A	2: 62,618,098 (GRCm39)	I464L	possibly damaging	Het
Kcnt2	T	A	1: 140,353,068 (GRCm39)	V259D	probably damaging	Het
Lipo3	A	G	19: 33,762,092 (GRCm39)	F135S	probably damaging	Het
Lrba	T	C	3: 86,680,510 (GRCm39)		probably null	Het
Mapk1	T	A	16: 16,844,293 (GRCm39)	S22T	probably benign	Het
Mbd3l2	T	C	9: 18,356,217 (GRCm39)	S181P	possibly damaging	Het
Mgat5	C	T	1: 127,387,706 (GRCm39)	P554L	probably damaging	Het
Mki67	T	C	7: 135,301,090 (GRCm39)	T1315A	probably benign	Het
Mprip	C	T	11: 59,649,047 (GRCm39)	T917M	possibly damaging	Het
Mroh3	T	A	1: 136,113,726 (GRCm39)	I688F	probably benign	Het
Myo1d	A	T	11: 80,553,874 (GRCm39)	Y536N	probably damaging	Het
Neb	C	T	2: 52,052,199 (GRCm39)		probably null	Het
Noc2l	A	G	4: 156,322,165 (GRCm39)	R161G	probably benign	Het
Nup93	T	C	8: 95,032,730 (GRCm39)	F539L	probably damaging	Het
Or10x1	T	A	1: 174,197,018 (GRCm39)	H178Q	probably damaging	Het
Or2n1e	A	G	17: 38,586,235 (GRCm39)	E191G	probably damaging	Het
Or5p57	A	C	7: 107,665,932 (GRCm39)	Y24*	probably null	Het
Or8b12	T	A	9: 37,658,264 (GRCm39)	M278K	probably benign	Het
Panx1	A	T	9: 14,918,724 (GRCm39)	D378E	probably damaging	Het
Papss1	T	A	3: 131,288,945 (GRCm39)	V170D	possibly damaging	Het
Pcnx1	T	C	12: 81,965,506 (GRCm39)	S558P	probably damaging	Het
Pde3a	G	T	6: 141,433,239 (GRCm39)	A757S	probably damaging	Het
Pde3a	T	A	6: 141,196,079 (GRCm39)	I255N	probably damaging	Het
Pdzph1	A	G	17: 59,229,578 (GRCm39)	Y1027H	probably damaging	Het
Pkhd1	G	T	1: 20,621,244 (GRCm39)	R805S	probably benign	Het
Polr1a	G	A	6: 71,886,187 (GRCm39)	G14D	probably damaging	Het
Prg4	T	A	1: 150,336,420 (GRCm39)	D60V	probably damaging	Het
Ptgr3	T	C	18: 84,113,443 (GRCm39)	V373A	possibly damaging	Het
Ptprc	T	C	1: 138,039,965 (GRCm39)	S311G	probably benign	Het
Rapgefl1	G	A	11: 98,733,035 (GRCm39)	R205K	probably benign	Het
Rcan2	A	T	17: 44,347,980 (GRCm39)		probably null	Het
Rock1	A	G	18: 10,079,207 (GRCm39)	I1087T	probably damaging	Het
Sectm1b	A	G	11: 120,945,768 (GRCm39)	I191T	possibly damaging	Het
Septin4	A	G	11: 87,458,061 (GRCm39)	H145R	possibly damaging	Het
Setd1b	T	C	5: 123,285,676 (GRCm39)	S241P	unknown	Het
Slco1a8	T	C	6: 141,949,149 (GRCm39)	M76V	possibly damaging	Het
Srpk2	T	C	5: 23,729,148 (GRCm39)	K497R	probably benign	Het
Sspo	T	C	6: 48,467,940 (GRCm39)	S4296P	probably damaging	Het
Syne4	T	C	7: 30,016,308 (GRCm39)	V168A	probably benign	Het
Tank	T	C	2: 61,480,256 (GRCm39)	F264S	probably damaging	Het
Ticrr	T	C	7: 79,344,955 (GRCm39)	S1607P	probably damaging	Het
Trim30a	A	G	7: 104,060,405 (GRCm39)	V457A	probably damaging	Het
Trim43b	T	A	9: 88,967,624 (GRCm39)	K336N	probably damaging	Het
Trim47	T	C	11: 115,996,963 (GRCm39)	Q598R	probably damaging	Het
Tspan12	T	C	6: 21,851,022 (GRCm39)	N18S	probably damaging	Het
Ubap2	A	G	4: 41,221,607 (GRCm39)	S231P	probably benign	Het
Vit	A	G	17: 78,930,175 (GRCm39)	D380G	probably damaging	Het
Vmn2r2	T	C	3: 64,041,942 (GRCm39)	N258D	possibly damaging	Het
Vmn2r52	C	T	7: 9,907,333 (GRCm39)	C131Y	possibly damaging	Het
Zfp58	A	T	13: 67,639,307 (GRCm39)	F395I	probably damaging	Het
Zfp940	C	A	7: 29,544,435 (GRCm39)	G491C	probably damaging	Het

Other mutations in Nup54

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00491:Nup54	APN	5	92,565,344 (GRCm39)	missense	probably benign	0.00
IGL01526:Nup54	APN	5	92,565,334 (GRCm39)	missense	probably benign	0.12
IGL01924:Nup54	APN	5	92,572,294 (GRCm39)	missense	probably benign	0.02
IGL02248:Nup54	APN	5	92,576,188 (GRCm39)	splice site	probably null
IGL02253:Nup54	APN	5	92,565,310 (GRCm39)	critical splice donor site	probably null
IGL02508:Nup54	APN	5	92,565,398 (GRCm39)	nonsense	probably null
IGL02721:Nup54	APN	5	92,565,716 (GRCm39)	missense	possibly damaging	0.96
IGL03150:Nup54	APN	5	92,576,023 (GRCm39)	missense	probably damaging	1.00
R0189:Nup54	UTSW	5	92,570,423 (GRCm39)	missense	probably damaging	1.00
R1401:Nup54	UTSW	5	92,576,080 (GRCm39)	missense	probably damaging	1.00
R3938:Nup54	UTSW	5	92,565,388 (GRCm39)	missense	probably damaging	1.00
R4171:Nup54	UTSW	5	92,565,343 (GRCm39)	missense	possibly damaging	0.64
R4574:Nup54	UTSW	5	92,573,641 (GRCm39)	missense	probably benign	0.17
R5372:Nup54	UTSW	5	92,565,716 (GRCm39)	missense	probably damaging	1.00
R6003:Nup54	UTSW	5	92,570,853 (GRCm39)	missense	probably damaging	1.00
R6191:Nup54	UTSW	5	92,572,153 (GRCm39)	missense	probably damaging	0.99
R6197:Nup54	UTSW	5	92,578,663 (GRCm39)	utr 3 prime	probably benign
R7861:Nup54	UTSW	5	92,578,952 (GRCm39)	missense	unknown
R8005:Nup54	UTSW	5	92,576,006 (GRCm39)	missense	probably benign	0.00
R8016:Nup54	UTSW	5	92,582,176 (GRCm39)	missense	unknown
R8439:Nup54	UTSW	5	92,573,605 (GRCm39)	missense	probably benign	0.22
R8709:Nup54	UTSW	5	92,570,267 (GRCm39)	intron	probably benign
R9711:Nup54	UTSW	5	92,582,218 (GRCm39)	missense	unknown
Z1177:Nup54	UTSW	5	92,582,138 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- TACTTTCTGAAACCAGGAATGGG -3'
(R):5'- CTTGGAATTAGGCTTGGACATG -3'

Sequencing Primer
(F):5'- CTGAAACCAGGAATGGGTAATTTTC -3'
(R):5'- ACATGTGGGTGTGCCTATTAAATAG -3'

Posted On

2014-06-23