Mutagenetix > Incidental Mutation

Incidental Mutation 'R5225:Lime1'

402539

Institutional Source

Beutler Lab

Gene Symbol

Lime1

Ensembl Gene

ENSMUSG00000090077

Gene Name

Lck interacting transmembrane adaptor 1

Synonyms

2810038K19Rik, LIME

MMRRC Submission

042798-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5225 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

181023028-181025421 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 181024640 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 98 (M98K)

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: M98K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000045010
Gene: ENSMUSG00000090077
AA Change: M98K

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: M77K

SMART Domains

Protein: ENSMUSP00000119181
Gene: ENSMUSG00000090077
AA Change: M77K

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126733

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131284

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184328

Predicted Effect

unknown
Transcript: ENSMUST00000140943
AA Change: M99K

SMART Domains

Protein: ENSMUSP00000117558
Gene: ENSMUSG00000090077
AA Change: M99K

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000127559

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151457

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126862

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176590

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

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.1%
20x: 95.0%

Validation Efficiency

100% (70/70)

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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700010I14Rik	C	T	17: 9,226,839 (GRCm39)	R465*	probably null	Het
Abcg3	A	T	5: 105,114,649 (GRCm39)	D289E	probably damaging	Het
Ablim2	G	T	5: 36,024,115 (GRCm39)		probably null	Het
Acp1	A	T	12: 30,955,078 (GRCm39)	V36D	probably benign	Het
Adgrb1	T	A	15: 74,449,348 (GRCm39)		probably benign	Het
Akap6	G	A	12: 52,933,329 (GRCm39)	V274I	probably damaging	Het
Arhgap39	T	C	15: 76,609,715 (GRCm39)		probably benign	Het
Bmp1	G	A	14: 70,717,605 (GRCm39)	R789W	probably damaging	Het
Catspere2	A	T	1: 177,976,474 (GRCm39)		probably benign	Het
Cfhr2	T	A	1: 139,749,520 (GRCm39)	Y154F	possibly damaging	Het
Cilp2	T	C	8: 70,336,015 (GRCm39)	Y358C	probably damaging	Het
Cyp1a2	T	A	9: 57,584,516 (GRCm39)	K513*	probably null	Het
Dennd4a	G	T	9: 64,796,210 (GRCm39)	K745N	possibly damaging	Het
Dlg1	T	A	16: 31,655,085 (GRCm39)	S542T	probably benign	Het
Dmbt1	A	T	7: 130,696,465 (GRCm39)	I893F	possibly damaging	Het
Dnhd1	A	T	7: 105,353,130 (GRCm39)	E2761V	possibly damaging	Het
F11	T	C	8: 45,708,341 (GRCm39)	T40A	probably benign	Het
Fam227a	T	C	15: 79,520,936 (GRCm39)	D296G	possibly damaging	Het
Fance	C	T	17: 28,534,589 (GRCm39)		probably benign	Het
Gaa	A	G	11: 119,167,669 (GRCm39)	D149G	probably damaging	Het
Gapt	A	G	13: 110,490,522 (GRCm39)	M47T	possibly damaging	Het
Gm1110	T	C	9: 26,813,774 (GRCm39)	N202D	probably damaging	Het
Gm7535	T	C	17: 18,131,809 (GRCm39)		probably benign	Het
Gm973	T	A	1: 59,601,859 (GRCm39)	M491K	probably benign	Het
Gmnc	A	G	16: 26,782,695 (GRCm39)	V27A	probably benign	Het
Kif27	T	C	13: 58,440,915 (GRCm39)	T1167A	possibly damaging	Het
Klrg1	T	A	6: 122,248,331 (GRCm39)	*189C	probably null	Het
Lrp1	C	A	10: 127,391,965 (GRCm39)	A2867S	probably benign	Het
Lrrd1	G	A	5: 3,908,735 (GRCm39)	S669N	probably benign	Het
Mmel1	A	G	4: 154,976,456 (GRCm39)	N520S	probably damaging	Het
Mrpl48	A	C	7: 100,198,535 (GRCm39)	L206V	probably damaging	Het
Nagpa	C	T	16: 5,021,596 (GRCm39)	A52T	probably benign	Het
Or1o3	A	G	17: 37,573,919 (GRCm39)	V212A	probably benign	Het
Or4c3	T	G	2: 89,851,528 (GRCm39)	D294A	probably benign	Het
Orai2	A	G	5: 136,190,355 (GRCm39)	S71P	probably damaging	Het
Pcbp1	A	T	6: 86,502,209 (GRCm39)	I230N	probably damaging	Het
Pcdh15	T	C	10: 74,138,986 (GRCm39)	L349P	probably damaging	Het
Pcdhb16	T	C	18: 37,613,011 (GRCm39)	V657A	probably benign	Het
Prdm15	G	T	16: 97,609,875 (GRCm39)	H590N	probably damaging	Het
Psg18	T	C	7: 18,079,874 (GRCm39)	I442M	probably damaging	Het
Pygm	C	A	19: 6,439,494 (GRCm39)	D279E	probably benign	Het
Rrn3	T	A	16: 13,610,798 (GRCm39)		probably null	Het
Sass6	T	C	3: 116,407,702 (GRCm39)	S273P	possibly damaging	Het
Schip1	A	G	3: 68,402,270 (GRCm39)	M116V	probably benign	Het
Sdc3	G	A	4: 130,546,087 (GRCm39)	V55I	unknown	Het
Serpinb8	T	A	1: 107,525,201 (GRCm39)	M1K	probably null	Het
Slc24a5	T	C	2: 124,927,739 (GRCm39)	I346T	probably damaging	Het
Slc35f3	T	A	8: 127,117,846 (GRCm39)	I335N	probably damaging	Het
Snapc2	T	A	8: 4,305,299 (GRCm39)	V147E	probably damaging	Het
Snx2	T	C	18: 53,322,784 (GRCm39)	S56P	possibly damaging	Het
Sptbn5	A	G	2: 119,915,812 (GRCm39)		probably benign	Het
Stk19	A	T	17: 35,040,400 (GRCm39)		probably benign	Het
Sulf1	A	G	1: 12,911,702 (GRCm39)	E692G	probably benign	Het
Tet1	C	T	10: 62,674,450 (GRCm39)	V1209I	probably damaging	Het
Tln1	T	C	4: 43,539,406 (GRCm39)	T1639A	probably benign	Het
Tmem135	G	T	7: 88,845,335 (GRCm39)	Y165*	probably null	Het
Tmprss6	T	C	15: 78,336,707 (GRCm39)	T398A	probably damaging	Het
Ube4a	C	T	9: 44,851,258 (GRCm39)		probably null	Het
Vmn1r227	T	C	17: 20,955,499 (GRCm39)		noncoding transcript	Het
Wdhd1	T	C	14: 47,488,273 (GRCm39)	S745G	probably benign	Het
Xylt1	A	G	7: 117,191,263 (GRCm39)	H353R	probably damaging	Het
Zfp788	A	G	7: 41,298,980 (GRCm39)	T539A	probably benign	Het
Zfp866	A	T	8: 70,218,091 (GRCm39)	F510I	possibly damaging	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
R1549:Lime1	UTSW	2	181,025,169 (GRCm39)	missense	probably benign	0.08
R1782:Lime1	UTSW	2	181,024,849 (GRCm39)	missense	possibly damaging	0.95
R7468:Lime1	UTSW	2	181,025,135 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- ACACCAGACTGCATGAGCTG -3'
(R):5'- GCCTGGCACAACTAATGGTCAG -3'

Sequencing Primer
(F):5'- ATGAGCTGCACCGAGGC -3'
(R):5'- CAACTAATGGTCAGCTGTGTTCCAG -3'

Posted On

2016-07-22