Mutagenetix > Incidental Mutation

Incidental Mutation 'R1549:Lime1'

169768

Institutional Source

Beutler Lab

Gene Symbol

Lime1

Ensembl Gene

ENSMUSG00000090077

Gene Name

Lck interacting transmembrane adaptor 1

Synonyms

2810038K19Rik, LIME

MMRRC Submission

039588-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1549 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

181023028-181025421 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 181025169 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 242 (Y242C)

Ref Sequence

ENSEMBL: ENSMUSP00000045010 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029105] [ENSMUST00000029106] [ENSMUST00000048077] [ENSMUST00000108804] [ENSMUST00000108807] [ENSMUST00000116366]

AlphaFold

Q9EQR5

Predicted Effect

probably benign
Transcript: ENSMUST00000029105

SMART Domains

Protein: ENSMUSP00000029105
Gene: ENSMUSG00000027582

Domain	Start	End	E-Value	Type
low complexity region	53	64	N/A	INTRINSIC
low complexity region	116	128	N/A	INTRINSIC
ZnF_C3H1	174	199	5.99e-4	SMART
SCOP:d1g5va_	218	268	2e-3	SMART
low complexity region	270	287	N/A	INTRINSIC
G_patch	311	357	1.34e-9	SMART
low complexity region	379	392	N/A	INTRINSIC
coiled coil region	431	505	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000029106

SMART Domains

Protein: ENSMUSP00000029106
Gene: ENSMUSG00000027583

Domain	Start	End	E-Value	Type
BTB	31	129	2.89e-21	SMART
ZnF_C2H2	418	440	4.72e-2	SMART
ZnF_C2H2	446	468	4.24e-4	SMART
ZnF_C2H2	474	498	1.31e2	SMART
low complexity region	543	557	N/A	INTRINSIC
low complexity region	568	580	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000048077
AA Change: Y242C

PolyPhen 2 Score 0.080 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000045010
Gene: ENSMUSG00000090077
AA Change: Y242C

Domain	Start	End	E-Value	Type
Pfam:LIME1	27	266	5.6e-113	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000108804

SMART Domains

Protein: ENSMUSP00000104432
Gene: ENSMUSG00000090077

Domain	Start	End	E-Value	Type
Pfam:LIME1	27	87	9e-29	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000108807

SMART Domains

Protein: ENSMUSP00000104435
Gene: ENSMUSG00000027582

Domain	Start	End	E-Value	Type
low complexity region	53	64	N/A	INTRINSIC
low complexity region	116	128	N/A	INTRINSIC
ZnF_C3H1	174	199	5.99e-4	SMART
SCOP:d1g5va_	218	268	2e-3	SMART
low complexity region	270	287	N/A	INTRINSIC
G_patch	311	357	1.34e-9	SMART
low complexity region	379	392	N/A	INTRINSIC
coiled coil region	431	505	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000116366

SMART Domains

Protein: ENSMUSP00000112067
Gene: ENSMUSG00000027582

Domain	Start	End	E-Value	Type
low complexity region	53	64	N/A	INTRINSIC
low complexity region	116	128	N/A	INTRINSIC
ZnF_C3H1	174	199	5.99e-4	SMART
SCOP:d1g5va_	218	268	2e-3	SMART
low complexity region	270	287	N/A	INTRINSIC
G_patch	311	357	1.34e-9	SMART
low complexity region	379	392	N/A	INTRINSIC
coiled coil region	431	505	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000126611
AA Change: Y221C

SMART Domains

Protein: ENSMUSP00000119181
Gene: ENSMUSG00000090077
AA Change: Y221C

Domain	Start	End	E-Value	Type
Pfam:LIME1	4	246	9.6e-111	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184328

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151457

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131284

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126733

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176590

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127559

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126862

Predicted Effect

probably benign
Transcript: ENSMUST00000140943

SMART Domains

Protein: ENSMUSP00000117558
Gene: ENSMUSG00000090077

Domain	Start	End	E-Value	Type
Pfam:LIME1	24	189	5.4e-74	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000156258

SMART Domains

Protein: ENSMUSP00000122714
Gene: ENSMUSG00000027582

Domain	Start	End	E-Value	Type
G_patch	1	44	1.18e-5	SMART
low complexity region	66	79	N/A	INTRINSIC
coiled coil region	117	148	N/A	INTRINSIC

Meta Mutation Damage Score

0.3986

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.8%
20x: 90.8%

Validation Efficiency

97% (58/60)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a transmembrane adaptor protein that links the T and B-cell receptor stimulation to downstream signaling pathways via its association with the Src family kinases Lck and Lyn, respectively. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Mar 2015]
PHENOTYPE: Mice homozygous for a targeted null allele exhibit no detectable abnormalities in the development and function of B and T cells. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700006A11Rik	A	T	3: 124,210,441 (GRCm39)	I157K	probably benign	Het
Ank3	A	T	10: 69,837,812 (GRCm39)	N727Y	probably benign	Het
Atg16l1	A	G	1: 87,701,910 (GRCm39)	T251A	probably benign	Het
Bcl11b	T	A	12: 107,883,422 (GRCm39)	I226F	probably damaging	Het
Birc6	A	G	17: 74,969,737 (GRCm39)	H4260R	probably damaging	Het
Camta1	A	G	4: 151,670,920 (GRCm39)	I85T	probably damaging	Het
Cblb	A	G	16: 51,853,373 (GRCm39)		probably benign	Het
Ccnd1	T	G	7: 144,491,073 (GRCm39)	I178L	probably benign	Het
Clcn4	A	G	7: 7,294,681 (GRCm39)	V329A	probably damaging	Het
Col17a1	C	T	19: 47,637,349 (GRCm39)		probably benign	Het
Col7a1	A	G	9: 108,785,034 (GRCm39)	T254A	unknown	Het
Ctif	C	A	18: 75,698,096 (GRCm39)	R188L	probably damaging	Het
Cyp2c69	A	T	19: 39,831,430 (GRCm39)	L461Q	probably benign	Het
Ddc	A	G	11: 11,796,656 (GRCm39)		probably null	Het
Dpp10	T	A	1: 123,269,109 (GRCm39)		probably null	Het
Eef2	CCC	CCCC	10: 81,014,602 (GRCm39)		probably null	Het
Eif2b4	T	C	5: 31,350,265 (GRCm39)	E19G	possibly damaging	Het
Fmnl2	A	G	2: 52,995,549 (GRCm39)	E424G	probably damaging	Het
Galnt14	A	G	17: 73,832,308 (GRCm39)	L269P	possibly damaging	Het
Gm2381	T	A	7: 42,471,825 (GRCm39)	H18L	probably benign	Het
Gpbp1	G	T	13: 111,573,113 (GRCm39)	D326E	probably benign	Het
Gpr162	C	T	6: 124,837,051 (GRCm39)	R331H	probably damaging	Het
Iigp1	G	A	18: 60,522,948 (GRCm39)	G22D	probably benign	Het
Kcns3	T	C	12: 11,142,084 (GRCm39)	H205R	probably damaging	Het
Klk1b26	C	T	7: 43,665,826 (GRCm39)		probably benign	Het
Manba	A	G	3: 135,250,567 (GRCm39)	D398G	probably damaging	Het
Mapk3	A	T	7: 126,362,684 (GRCm39)	K219*	probably null	Het
Mdfic	G	T	6: 15,799,844 (GRCm39)	G324C	probably damaging	Het
Mdga1	G	A	17: 30,056,972 (GRCm39)	H837Y	probably damaging	Het
Nck1	T	A	9: 100,379,925 (GRCm39)	M109L	probably benign	Het
Or1d2	A	G	11: 74,256,076 (GRCm39)	I194V	probably benign	Het
Or2w1b	T	C	13: 21,300,288 (GRCm39)	V142A	probably benign	Het
Pabpc1l	G	T	2: 163,879,091 (GRCm39)	V313F	possibly damaging	Het
Phf3	C	T	1: 30,843,923 (GRCm39)	V1679I	probably benign	Het
Pou4f1	T	C	14: 104,705,076 (GRCm39)	I32V	probably benign	Het
Pspc1	T	G	14: 56,986,398 (GRCm39)	H351P	probably damaging	Het
Ptk7	T	C	17: 46,883,578 (GRCm39)	E829G	probably damaging	Het
Rab23	A	G	1: 33,777,378 (GRCm39)	Y164C	possibly damaging	Het
Slc36a3	A	G	11: 55,033,596 (GRCm39)	W141R	probably damaging	Het
Slc7a14	T	C	3: 31,278,267 (GRCm39)	E446G	possibly damaging	Het
Stim2	G	A	5: 54,262,667 (GRCm39)	R303Q	probably damaging	Het
Tbcd	A	G	11: 121,451,579 (GRCm39)	I550V	probably benign	Het
Tmed3	A	C	9: 89,581,998 (GRCm39)	L155R	probably damaging	Het
Trav16d-dv11	A	G	14: 53,284,799 (GRCm39)		probably benign	Het
Ubap2	C	T	4: 41,199,872 (GRCm39)	A752T	probably benign	Het
Usp16	G	T	16: 87,261,722 (GRCm39)	V113F	probably damaging	Het
Vmn2r12	T	G	5: 109,240,696 (GRCm39)	Y139S	probably benign	Het
Vmn2r5	G	T	3: 64,411,421 (GRCm39)	D382E	probably damaging	Het
Zfp1010	T	C	2: 176,957,378 (GRCm39)	E40G	probably damaging	Het
Zfp217	A	C	2: 169,956,390 (GRCm39)	N869K	probably benign	Het
Zswim2	G	T	2: 83,754,092 (GRCm39)	D189E	probably benign	Het

Other mutations in Lime1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01873:Lime1	APN	2	181,024,667 (GRCm39)	missense	probably benign	0.00
R1782:Lime1	UTSW	2	181,024,849 (GRCm39)	missense	possibly damaging	0.95
R5225:Lime1	UTSW	2	181,024,640 (GRCm39)	missense	probably benign
R7468:Lime1	UTSW	2	181,025,135 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- CGAATATGCCTGCATCCAGAAGCAC -3'
(R):5'- CCTGAAGCAGAAGCCTTGGTACTC -3'

Sequencing Primer
(F):5'- TAAGGTGATCCCAGCTACTCAGG -3'
(R):5'- AGAAGCCTTGGTACTCTTCCTAAC -3'

Posted On

2014-04-13