Mutagenetix > Incidental Mutations

Incidental Mutation 'R4529:Lin54'

333026

Institutional Source

Beutler Lab

Gene Symbol

Lin54

Ensembl Gene

ENSMUSG00000035310

Gene Name

lin-54 homolog (C. elegans)

Synonyms

MMRRC Submission

041592-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.950) question?

Stock #

R4529 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

100441918-100500639 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 100446560 bp

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 582 (T582I)

Ref Sequence

ENSEMBL: ENSMUSP00000121902 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000046154] [ENSMUST00000123572] [ENSMUST00000137750] [ENSMUST00000139234] [ENSMUST00000144030] [ENSMUST00000149714] [ENSMUST00000152387] [ENSMUST00000154921]

Predicted Effect

probably benign
Transcript: ENSMUST00000046154
AA Change: T671I

PolyPhen 2 Score 0.441 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000041374
Gene: ENSMUSG00000035310
AA Change: T671I

Domain	Start	End	E-Value	Type
low complexity region	364	382	N/A	INTRINSIC
low complexity region	404	419	N/A	INTRINSIC
CXC	520	560	3.06e-15	SMART
CXC	594	635	1.84e-18	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000123572
AA Change: T671I

PolyPhen 2 Score 0.441 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000123425
Gene: ENSMUSG00000035310
AA Change: T671I

Domain	Start	End	E-Value	Type
low complexity region	364	382	N/A	INTRINSIC
low complexity region	404	419	N/A	INTRINSIC
CXC	520	560	3.06e-15	SMART
CXC	594	635	1.84e-18	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000137750
AA Change: T450I

PolyPhen 2 Score 0.605 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000120644
Gene: ENSMUSG00000035310
AA Change: T450I

Domain	Start	End	E-Value	Type
low complexity region	143	161	N/A	INTRINSIC
low complexity region	183	198	N/A	INTRINSIC
CXC	299	339	3.06e-15	SMART
CXC	373	414	1.84e-18	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000139234

SMART Domains

Protein: ENSMUSP00000119322
Gene: ENSMUSG00000035310

Domain	Start	End	E-Value	Type
low complexity region	218	229	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000144030

Predicted Effect

possibly damaging
Transcript: ENSMUST00000149714
AA Change: T450I

PolyPhen 2 Score 0.605 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000123544
Gene: ENSMUSG00000035310
AA Change: T450I

Domain	Start	End	E-Value	Type
low complexity region	143	161	N/A	INTRINSIC
low complexity region	183	198	N/A	INTRINSIC
CXC	299	339	3.06e-15	SMART
CXC	373	414	1.84e-18	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000152387
AA Change: T582I

PolyPhen 2 Score 0.908 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000121902
Gene: ENSMUSG00000035310
AA Change: T582I

Domain	Start	End	E-Value	Type
low complexity region	218	231	N/A	INTRINSIC
low complexity region	275	293	N/A	INTRINSIC
low complexity region	315	330	N/A	INTRINSIC
CXC	431	471	3.06e-15	SMART
CXC	505	546	1.84e-18	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000154921
AA Change: T450I

PolyPhen 2 Score 0.605 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000121137
Gene: ENSMUSG00000035310
AA Change: T450I

Domain	Start	End	E-Value	Type
low complexity region	143	161	N/A	INTRINSIC
low complexity region	183	198	N/A	INTRINSIC
CXC	299	339	3.06e-15	SMART
CXC	373	414	1.84e-18	SMART

Meta Mutation Damage Score

0.0888

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.2%
20x: 95.0%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] LIN54 is a component of the LIN, or DREAM, complex, an essential regulator of cell cycle genes (Schmit et al., 2009 [PubMed 19725879]).[supplied by OMIM, Dec 2010]

Allele List at MGI

Other mutations in this stock

Total: 40 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgre1	A	G	17: 57,420,519	Y483C	possibly damaging	Het
Akap9	T	A	5: 4,043,948	F2157I	probably damaging	Het
Aldh1a3	T	C	7: 66,401,994	N404D	probably benign	Het
Ankrd2	A	T	19: 42,043,801	I231F	probably benign	Het
Apba1	A	G	19: 23,936,535	N641D	probably damaging	Het
C1qbp	T	C	11: 70,978,724	T178A	probably benign	Het
Chtf18	T	C	17: 25,720,618	Y64C	probably damaging	Het
Cyp1a1	A	G	9: 57,701,679	H281R	probably benign	Het
Ehmt2	A	G	17: 34,913,731	I1235V	probably damaging	Het
Fam122c	G	A	X: 53,293,499	R94H	possibly damaging	Het
Fcamr	A	G	1: 130,804,576	H44R	probably damaging	Het
Gm12185	T	C	11: 48,907,920	Y582C	probably damaging	Het
Gm12185	T	C	11: 48,908,094	N524S	possibly damaging	Het
Gm5460	A	C	14: 34,045,812	D459A	probably damaging	Het
H2-Q6	C	T	17: 35,425,844	T203I	probably null	Het
Inmt	T	C	6: 55,171,027	M206V	probably benign	Het
Khdc3	T	C	9: 73,104,019	S360P	possibly damaging	Het
Ltbp1	T	G	17: 75,151,360	V312G	probably benign	Het
Nlrp9a	T	C	7: 26,571,407	L899P	probably damaging	Het
Olfr786	T	C	10: 129,437,418	V202A	probably benign	Het
Orc4	G	A	2: 48,937,489	P31S	probably benign	Het
Pappa	A	G	4: 65,231,182	I920V	probably benign	Het
Parp1	T	A	1: 180,591,312	V679E	probably damaging	Het
Pla2g4f	C	T	2: 120,300,619	R785Q	probably damaging	Het
Plbd1	T	A	6: 136,651,825	I82F	probably benign	Het
Plekhm3	A	G	1: 64,937,825	V162A	probably benign	Het
Plin4	A	G	17: 56,104,274	L919P	probably damaging	Het
Plxna4	C	T	6: 32,496,896		probably null	Het
Pou3f3	C	A	1: 42,698,554	T470K	probably benign	Het
Prss38	T	C	11: 59,373,499	Y214C	probably damaging	Het
Retreg1	T	A	15: 25,968,514	Y109N	probably damaging	Het
Slco1c1	A	G	6: 141,555,181	Y413C	probably damaging	Het
Stk32a	T	C	18: 43,242,979	C38R	possibly damaging	Het
Themis	T	C	10: 28,782,335	F453L	possibly damaging	Het
Tmem38a	C	T	8: 72,572,161	P20S	possibly damaging	Het
Tubgcp3	G	T	8: 12,663,932	L62I	probably damaging	Het
Ubqlnl	C	T	7: 104,149,718	V191M	probably benign	Het
Xpo7	G	A	14: 70,668,748	T986M	probably damaging	Het
Zfp51	C	T	17: 21,464,736	L538F	probably damaging	Het
Zfy1	A	G	Y: 726,511	L418S	possibly damaging	Het

Other mutations in Lin54

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01286:Lin54	APN	5	100485607	missense	probably benign	0.03
IGL01356:Lin54	APN	5	100454017	missense	probably damaging	0.98
IGL02931:Lin54	APN	5	100480321	missense	possibly damaging	0.93
IGL03089:Lin54	APN	5	100450993	missense	probably damaging	1.00
IGL03095:Lin54	APN	5	100454478	missense	probably damaging	0.99
IGL03202:Lin54	APN	5	100475814	missense	possibly damaging	0.92
R0505:Lin54	UTSW	5	100452293	missense	probably damaging	0.98
R1138:Lin54	UTSW	5	100444134	missense	probably damaging	0.98
R1540:Lin54	UTSW	5	100480250	missense	probably damaging	0.99
R1719:Lin54	UTSW	5	100485249	missense	possibly damaging	0.91
R1991:Lin54	UTSW	5	100485801	critical splice donor site	probably null
R2698:Lin54	UTSW	5	100480250	missense	probably damaging	0.99
R3738:Lin54	UTSW	5	100459806	splice site	probably benign
R4238:Lin54	UTSW	5	100475744	missense	possibly damaging	0.45
R4424:Lin54	UTSW	5	100446560	missense	probably damaging	0.98
R4530:Lin54	UTSW	5	100446560	missense	possibly damaging	0.91
R4531:Lin54	UTSW	5	100446560	missense	possibly damaging	0.91
R4532:Lin54	UTSW	5	100446560	missense	possibly damaging	0.91
R4533:Lin54	UTSW	5	100485403	missense	possibly damaging	0.79
R4665:Lin54	UTSW	5	100453084	missense	possibly damaging	0.92
R4784:Lin54	UTSW	5	100459738	missense	probably damaging	0.99
R4785:Lin54	UTSW	5	100459738	missense	probably damaging	0.99
R5252:Lin54	UTSW	5	100480204	missense	probably benign
R5265:Lin54	UTSW	5	100485519	missense	probably damaging	1.00
R6545:Lin54	UTSW	5	100485137	splice site	probably null
R7150:Lin54	UTSW	5	100485300	missense	possibly damaging	0.74
R7544:Lin54	UTSW	5	100485270	missense	possibly damaging	0.84
R8165:Lin54	UTSW	5	100454499	missense	probably benign	0.11
X0025:Lin54	UTSW	5	100454443	missense	probably benign	0.11
X0026:Lin54	UTSW	5	100450999	missense	probably damaging	0.97

Predicted Primers

PCR Primer
(F):5'- ACTTTGTGGCTCAGTCTGGC -3'
(R):5'- TCTGTTGAGGAATCTACTTACTGTG -3'

Sequencing Primer
(F):5'- CTGGGAATTAAACTCAGGACCTTCG -3'
(R):5'- TCTGCTTTTGATTTGGAAACTTTTC -3'

Posted On

2015-08-18