Mutagenetix > Incidental Mutation

Incidental Mutation 'R5372:Nup54'

428778

Institutional Source

Beutler Lab

Gene Symbol

Nup54

Ensembl Gene

ENSMUSG00000034826

Gene Name

nucleoporin 54

Synonyms

3110079L04Rik, 54kDa

MMRRC Submission

042948-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.963) question?

Stock #

R5372 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

92563399-92583078 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 92565716 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 406 (I406T)

Ref Sequence

ENSEMBL: ENSMUSP00000046540 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000038514] [ENSMUST00000113083] [ENSMUST00000117108] [ENSMUST00000118106] [ENSMUST00000119587] [ENSMUST00000120193] [ENSMUST00000120416] [ENSMUST00000152041] [ENSMUST00000121096]

AlphaFold

Q8BTS4

Predicted Effect

probably damaging
Transcript: ENSMUST00000038514
AA Change: I406T

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000046540
Gene: ENSMUSG00000034826
AA Change: I406T

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: ENSMUST00000123694

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000129222

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: ENSMUST00000152041

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

Meta Mutation Damage Score

0.6848

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.2%
20x: 95.2%

Validation Efficiency

96% (89/93)

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca4	T	A	3: 121,848,988 (GRCm39)	D108E	probably damaging	Het
Abhd12b	A	G	12: 70,227,800 (GRCm39)	D194G	probably damaging	Het
Adck5	A	G	15: 76,478,707 (GRCm39)		probably benign	Het
Adgrb3	C	T	1: 25,167,940 (GRCm39)	V792I	probably benign	Het
Anxa8	G	A	14: 33,815,868 (GRCm39)	V174M	probably damaging	Het
Apol9b	A	T	15: 77,619,920 (GRCm39)	R239W	probably benign	Het
Arhgap26	A	G	18: 38,775,509 (GRCm39)		noncoding transcript	Het
Atrnl1	A	G	19: 57,743,968 (GRCm39)	Y1190C	probably benign	Het
Brinp3	T	G	1: 146,707,464 (GRCm39)	L376R	probably damaging	Het
Btbd2	A	T	10: 80,484,475 (GRCm39)	M132K	probably damaging	Het
C130073F10Rik	A	T	4: 101,747,684 (GRCm39)	I115K	probably damaging	Het
C1ra	T	A	6: 124,498,584 (GRCm39)	Y426N	probably damaging	Het
Cacna1b	A	T	2: 24,623,971 (GRCm39)	V203E	probably damaging	Het
Catsperg1	T	A	7: 28,910,137 (GRCm39)	D68V	probably benign	Het
Ccdc158	A	C	5: 92,780,419 (GRCm39)	S885A	possibly damaging	Het
Cdc42bpa	T	C	1: 179,892,544 (GRCm39)	V236A	probably damaging	Het
Cdca7	A	T	2: 72,312,793 (GRCm39)	E176D	probably damaging	Het
Cdk17	A	G	10: 93,061,901 (GRCm39)	D211G	probably benign	Het
Clca3a2	A	C	3: 144,503,286 (GRCm39)	M888R	probably benign	Het
Clcn7	T	A	17: 25,376,153 (GRCm39)	M568K	possibly damaging	Het
Clip1	G	T	5: 123,768,303 (GRCm39)	N811K	probably benign	Het
Col12a1	T	A	9: 79,585,648 (GRCm39)	Y1243F	probably damaging	Het
Dctn1	T	A	6: 83,167,192 (GRCm39)	D315E	probably damaging	Het
Dgcr2	T	C	16: 17,690,508 (GRCm39)	T41A	probably benign	Het
Dync2h1	G	A	9: 7,176,962 (GRCm39)		probably benign	Het
Ep300	A	G	15: 81,521,031 (GRCm39)	I1264V	unknown	Het
Fam167b	A	T	4: 129,472,092 (GRCm39)	L26Q	possibly damaging	Het
Fam178b	T	A	1: 36,603,929 (GRCm39)	I457F	possibly damaging	Het
Fgd4	A	T	16: 16,302,155 (GRCm39)	N133K	probably benign	Het
Fndc1	C	G	17: 7,984,042 (GRCm39)	V1295L	unknown	Het
Gad2	A	T	2: 22,580,255 (GRCm39)	D552V	possibly damaging	Het
Hars2	T	C	18: 36,923,534 (GRCm39)	Y361H	possibly damaging	Het
Heca	T	A	10: 17,790,887 (GRCm39)	S390C	probably damaging	Het
Hephl1	G	T	9: 15,009,195 (GRCm39)	Y132*	probably null	Het
Hormad1	T	A	3: 95,483,735 (GRCm39)	D182E	probably damaging	Het
Ifna15	G	A	4: 88,476,338 (GRCm39)	P49S	probably damaging	Het
Khsrp	T	C	17: 57,331,292 (GRCm39)	T429A	possibly damaging	Het
Magi2	A	G	5: 20,907,108 (GRCm39)	Q1094R	possibly damaging	Het
Map3k11	T	A	19: 5,740,990 (GRCm39)	I239K	probably damaging	Het
Mtus2	A	G	5: 148,250,222 (GRCm39)	T1319A	probably damaging	Het
Nxpe2	T	C	9: 48,250,819 (GRCm39)	T43A	possibly damaging	Het
Nynrin	A	G	14: 56,105,948 (GRCm39)	E889G	probably benign	Het
Opa1	A	C	16: 29,404,937 (GRCm39)	H45P	probably benign	Het
Or14c44	T	A	7: 86,062,176 (GRCm39)	I202N	possibly damaging	Het
Or4f60	A	G	2: 111,902,454 (GRCm39)	I158T	probably benign	Het
Or56b2j	A	G	7: 104,353,002 (GRCm39)	D76G	probably benign	Het
Or8a1b	T	C	9: 37,623,234 (GRCm39)	M114V	possibly damaging	Het
Otx1	C	A	11: 21,947,037 (GRCm39)	A91S	probably damaging	Het
Papola	A	G	12: 105,793,309 (GRCm39)	K543R	probably benign	Het
Plcxd3	G	A	15: 4,604,270 (GRCm39)	V293I	probably benign	Het
Polr2g	T	C	19: 8,774,667 (GRCm39)	Y72C	probably damaging	Het
Ppp1r21	A	G	17: 88,858,103 (GRCm39)	K205E	probably benign	Het
Ptpre	A	G	7: 135,255,669 (GRCm39)	K53E	possibly damaging	Het
Rasal3	T	C	17: 32,610,318 (GRCm39)	K990E	probably benign	Het
Rgs3	A	T	4: 62,570,934 (GRCm39)		probably benign	Het
Rhd	A	G	4: 134,611,943 (GRCm39)	T254A	possibly damaging	Het
Rufy4	T	C	1: 74,186,822 (GRCm39)	C537R	probably damaging	Het
Scube3	G	T	17: 28,371,456 (GRCm39)	C57F	probably damaging	Het
Sh2d5	A	G	4: 137,982,010 (GRCm39)	D57G	possibly damaging	Het
Slc12a6	T	A	2: 112,177,705 (GRCm39)	L608*	probably null	Het
Slk	A	T	19: 47,613,832 (GRCm39)	N896I	probably damaging	Het
Smc6	A	G	12: 11,332,431 (GRCm39)	D211G	probably damaging	Het
Sox6	A	T	7: 115,149,386 (GRCm39)	Y371*	probably null	Het
Srcap	G	A	7: 127,156,785 (GRCm39)		probably null	Het
Stard5	T	A	7: 83,282,428 (GRCm39)	D80E	probably damaging	Het
Supv3l1	C	T	10: 62,268,136 (GRCm39)	V570M	probably damaging	Het
Syt7	G	T	19: 10,403,985 (GRCm39)	V180L	probably damaging	Het
Tacc2	T	A	7: 130,224,990 (GRCm39)	H558Q	probably benign	Het
Tas2r120	T	A	6: 132,634,446 (GRCm39)	M176K	possibly damaging	Het
Tmem135	A	T	7: 88,814,382 (GRCm39)		probably null	Het
Trim35	T	C	14: 66,534,715 (GRCm39)	V66A	possibly damaging	Het
Tspan12	A	G	6: 21,772,698 (GRCm39)	S284P	probably benign	Het
Ttll3	A	T	6: 113,378,382 (GRCm39)	K257*	probably null	Het
Uggt1	C	A	1: 36,283,141 (GRCm39)		probably benign	Het
Vmn2r7	T	A	3: 64,623,745 (GRCm39)	I283F	probably damaging	Het
Wdfy2	T	G	14: 63,192,334 (GRCm39)	H363Q	probably damaging	Het
Wdr4	T	A	17: 31,729,554 (GRCm39)	K95N	probably damaging	Het
Zfp141	T	C	7: 42,126,620 (GRCm39)	N91S	possibly damaging	Het
Zfp383	C	T	7: 29,614,695 (GRCm39)	R317*	probably null	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
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
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'- GCTTTAGTACAAGCTAAGCAAACC -3'
(R):5'- AGGCATACATGTAAAGGCGC -3'

Sequencing Primer
(F):5'- CCATGACAGAATTTATTCCTGTGTG -3'
(R):5'- AGTTCTGCAGCATAGACTAGCCTG -3'

Posted On

2016-09-06