Mutagenetix > Incidental Mutation

Incidental Mutation 'R1401:Nup54'

160115

Institutional Source

Beutler Lab

Gene Symbol

Nup54

Ensembl Gene

ENSMUSG00000034826

Gene Name

nucleoporin 54

Synonyms

3110079L04Rik, 54kDa

MMRRC Submission

039463-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.963) question?

Stock #

R1401 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

92563399-92583078 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 92576080 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Isoleucine at position 137 (R137I)

Ref Sequence

ENSEMBL: ENSMUSP00000046540 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038514] [ENSMUST00000135112] [ENSMUST00000146470]

AlphaFold

Q8BTS4

Predicted Effect

probably damaging
Transcript: ENSMUST00000038514
AA Change: R137I

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

SMART Domains

Protein: ENSMUSP00000046540
Gene: ENSMUSG00000034826
AA Change: R137I

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

noncoding transcript
Transcript: ENSMUST00000122893

Predicted Effect

probably benign
Transcript: ENSMUST00000130156

SMART Domains

Protein: ENSMUSP00000120937
Gene: ENSMUSG00000034826

Domain	Start	End	E-Value	Type
low complexity region	82	110	N/A	INTRINSIC
low complexity region	112	123	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000135112

SMART Domains

Protein: ENSMUSP00000117237
Gene: ENSMUSG00000034826

Domain	Start	End	E-Value	Type
low complexity region	5	26	N/A	INTRINSIC
internal_repeat_1	34	53	3.34e-6	PROSPERO
internal_repeat_1	49	68	3.34e-6	PROSPERO
low complexity region	69	97	N/A	INTRINSIC
low complexity region	99	110	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000142525

Predicted Effect

probably benign
Transcript: ENSMUST00000146470

SMART Domains

Protein: ENSMUSP00000121171
Gene: ENSMUSG00000034826

Domain	Start	End	E-Value	Type
low complexity region	6	22	N/A	INTRINSIC
low complexity region	46	66	N/A	INTRINSIC
low complexity region	75	97	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000158152

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000201228

Meta Mutation Damage Score

0.4002

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.8%
20x: 91.4%

Validation Efficiency

98% (87/89)

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: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930433I11Rik	A	T	7: 40,642,480 (GRCm39)	T141S	probably benign	Het
Abcg1	T	A	17: 31,333,132 (GRCm39)	I625N	possibly damaging	Het
Adam33	C	A	2: 130,893,391 (GRCm39)		probably benign	Het
Adgrl2	A	T	3: 148,528,617 (GRCm39)	I1185N	probably damaging	Het
Afp	A	T	5: 90,649,486 (GRCm39)		probably benign	Het
Aggf1	A	G	13: 95,501,356 (GRCm39)	V342A	probably benign	Het
Ankrd11	A	T	8: 123,619,789 (GRCm39)	S1333R	probably benign	Het
Arhgef11	C	A	3: 87,640,776 (GRCm39)	S1311*	probably null	Het
Atp6v1g1	T	C	4: 63,466,878 (GRCm39)	Y47H	probably benign	Het
Atp8b4	T	C	2: 126,165,013 (GRCm39)		probably null	Het
Barx2	A	G	9: 31,770,327 (GRCm39)	L67P	probably damaging	Het
Bbs7	G	A	3: 36,627,706 (GRCm39)	P694S	probably benign	Het
Btbd10	A	T	7: 112,946,266 (GRCm39)	V33E	probably benign	Het
C2	T	C	17: 35,091,457 (GRCm39)	T69A	possibly damaging	Het
C8b	T	G	4: 104,641,679 (GRCm39)	L205R	possibly damaging	Het
Cct4	T	G	11: 22,944,333 (GRCm39)	N72K	probably damaging	Het
Cd300lg	C	A	11: 101,944,981 (GRCm39)	P353H	possibly damaging	Het
Cdh20	A	T	1: 104,875,222 (GRCm39)	I335L	possibly damaging	Het
Cfhr2	T	A	1: 139,738,757 (GRCm39)	H268L	probably benign	Het
Chia1	T	A	3: 106,036,255 (GRCm39)	D278E	probably benign	Het
Cntn6	A	G	6: 104,781,359 (GRCm39)	T482A	possibly damaging	Het
Cst13	T	A	2: 148,665,016 (GRCm39)	F4I	probably benign	Het
Ctsc	T	A	7: 87,930,706 (GRCm39)	V95E	probably damaging	Het
Ddhd1	A	T	14: 45,842,508 (GRCm39)		probably null	Het
Dmxl2	A	T	9: 54,322,712 (GRCm39)		probably null	Het
Dnah5	A	C	15: 28,402,059 (GRCm39)	T3407P	probably damaging	Het
Dock1	T	A	7: 134,735,665 (GRCm39)	Y1344*	probably null	Het
Eif4g3	T	C	4: 137,933,395 (GRCm39)	V1740A	probably damaging	Het
Epb41l5	A	G	1: 119,506,634 (GRCm39)		probably benign	Het
Flt4	C	T	11: 49,527,166 (GRCm39)		probably benign	Het
Fnbp1l	C	T	3: 122,339,955 (GRCm39)	R499Q	probably damaging	Het
Gm10033	T	C	8: 69,826,022 (GRCm39)		noncoding transcript	Het
Gm12790	A	G	4: 101,825,396 (GRCm39)	L6P	probably benign	Het
Gramd4	A	G	15: 86,009,397 (GRCm39)	D210G	probably damaging	Het
Hectd3	T	C	4: 116,859,466 (GRCm39)	S697P	possibly damaging	Het
Hsf4	T	C	8: 106,002,235 (GRCm39)	V399A	probably benign	Het
Hyal6	T	A	6: 24,743,434 (GRCm39)	C377S	probably damaging	Het
Myb	C	T	10: 21,028,844 (GRCm39)	V85M	probably damaging	Het
Mypn	A	G	10: 62,988,636 (GRCm39)	V463A	probably damaging	Het
Nav1	T	A	1: 135,388,163 (GRCm39)	I1144L	probably benign	Het
Nckap5	A	G	1: 125,942,398 (GRCm39)		probably benign	Het
Nipbl	A	T	15: 8,401,657 (GRCm39)	S30T	probably damaging	Het
Nmt1	T	C	11: 102,948,307 (GRCm39)	F277S	probably damaging	Het
Nploc4	A	C	11: 120,274,115 (GRCm39)		probably benign	Het
Or52n2b	T	C	7: 104,565,963 (GRCm39)	Y180C	probably damaging	Het
Oxtr	C	T	6: 112,454,138 (GRCm39)	R42Q	probably benign	Het
Pkd1l1	G	T	11: 8,804,487 (GRCm39)	Y1701*	probably null	Het
Plekhg6	T	C	6: 125,340,072 (GRCm39)	T763A	probably damaging	Het
Pmepa1	C	T	2: 173,070,368 (GRCm39)		probably null	Het
Ppfia2	A	G	10: 106,666,518 (GRCm39)	E408G	possibly damaging	Het
Pramel13	G	A	4: 144,121,658 (GRCm39)	T122M	probably benign	Het
Prl8a2	G	A	13: 27,537,979 (GRCm39)	V218I	possibly damaging	Het
Ptpro	T	A	6: 137,420,592 (GRCm39)	V1007D	probably damaging	Het
Rims4	C	T	2: 163,705,849 (GRCm39)	V262M	possibly damaging	Het
Shisal2b	A	T	13: 105,000,113 (GRCm39)	C37S	probably damaging	Het
Slc13a1	A	T	6: 24,118,082 (GRCm39)		probably null	Het
Slc17a8	T	A	10: 89,427,076 (GRCm39)	T342S	probably damaging	Het
Slc30a9	A	G	5: 67,510,005 (GRCm39)	E519G	probably benign	Het
Slc35e1	T	C	8: 73,246,415 (GRCm39)		probably benign	Het
Slc39a5	G	A	10: 128,233,610 (GRCm39)	L296F	probably damaging	Het
Slco6b1	A	C	1: 96,857,610 (GRCm39)		noncoding transcript	Het
Slco6d1	G	A	1: 98,418,341 (GRCm39)	G509D	probably damaging	Het
Spen	A	G	4: 141,199,132 (GRCm39)	V3142A	probably damaging	Het
Spta1	T	A	1: 174,050,250 (GRCm39)	H1763Q	probably damaging	Het
Srcap	T	C	7: 127,159,124 (GRCm39)		probably benign	Het
Stard9	T	C	2: 120,543,328 (GRCm39)		probably benign	Het
Stat4	A	G	1: 52,111,106 (GRCm39)		probably benign	Het
Svbp	T	A	4: 119,053,225 (GRCm39)		probably benign	Het
Tm2d1	A	T	4: 98,258,833 (GRCm39)		probably benign	Het
Trpv1	C	A	11: 73,130,952 (GRCm39)		probably null	Het
Trrap	A	G	5: 144,794,232 (GRCm39)	D3713G	possibly damaging	Het
Ubr1	T	A	2: 120,786,125 (GRCm39)	D165V	probably benign	Het
Utrn	C	A	10: 12,524,897 (GRCm39)	M2195I	probably benign	Het
Vmn1r229	G	A	17: 21,034,904 (GRCm39)	V50I	possibly damaging	Het
Vmn1r44	A	T	6: 89,870,632 (GRCm39)	H126L	probably benign	Het
Vmn2r116	T	C	17: 23,605,570 (GRCm39)		probably benign	Het
Vmn2r27	A	C	6: 124,168,591 (GRCm39)	Y846*	probably null	Het
Vmn2r84	T	A	10: 130,227,859 (GRCm39)	S126C	possibly damaging	Het
Xylb	T	A	9: 119,197,133 (GRCm39)		probably benign	Het
Zfp282	A	T	6: 47,867,108 (GRCm39)	K232*	probably null	Het
Zfp39	C	A	11: 58,781,149 (GRCm39)	V538L	probably benign	Het
Zfp560	T	C	9: 20,263,149 (GRCm39)	N76D	possibly damaging	Het
Zmym4	C	T	4: 126,804,962 (GRCm39)	V433I	probably benign	Het
Zscan5b	A	G	7: 6,233,425 (GRCm39)	E83G	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
R1862:Nup54	UTSW	5	92,567,426 (GRCm39)	missense	possibly damaging	0.75
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'- AGATCACCATGCCAACAGCTTCTTC -3'
(R):5'- TGTTCTGACCTGGCTACAGTCTCG -3'

Sequencing Primer
(F):5'- GTCCTCAGAATCATACACAATTCG -3'
(R):5'- TACAGTCTCGCCCATATGTAAG -3'

Posted On

2014-03-14