Mutagenetix > Incidental Mutation

Incidental Mutation 'R5310:Lmo2'

404760

Institutional Source

Beutler Lab

Gene Symbol

Lmo2

Ensembl Gene

ENSMUSG00000032698

Gene Name

LIM domain only 2

Synonyms

Rbtn2, Rhom-2, Rbtn-2

MMRRC Submission

042893-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5310 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

103788340-103812223 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 103806445 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 108 (I108T)

Ref Sequence

ENSEMBL: ENSMUSP00000106773 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000111139] [ENSMUST00000111140] [ENSMUST00000111143] [ENSMUST00000123437] [ENSMUST00000138815] [ENSMUST00000156813] [ENSMUST00000170926]

AlphaFold

P25801

Predicted Effect

probably benign
Transcript: ENSMUST00000111139

SMART Domains

Protein: ENSMUSP00000106769
Gene: ENSMUSG00000032698

Domain	Start	End	E-Value	Type
low complexity region	22	44	N/A	INTRINSIC
low complexity region	60	73	N/A	INTRINSIC
LIM	91	145	1.71e-13	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000111140
AA Change: I116T

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000106770
Gene: ENSMUSG00000032698
AA Change: I116T

Domain	Start	End	E-Value	Type
low complexity region	22	44	N/A	INTRINSIC
low complexity region	60	73	N/A	INTRINSIC
LIM	99	153	4.03e-10	SMART
LIM	163	217	1.71e-13	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000111143
AA Change: I108T

PolyPhen 2 Score 0.983 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000106773
Gene: ENSMUSG00000032698
AA Change: I108T

Domain	Start	End	E-Value	Type
low complexity region	14	36	N/A	INTRINSIC
low complexity region	52	65	N/A	INTRINSIC
LIM	91	145	4.03e-10	SMART
LIM	155	209	1.71e-13	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000123437
AA Change: I46T

PolyPhen 2 Score 0.967 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000117703
Gene: ENSMUSG00000032698
AA Change: I46T

Domain	Start	End	E-Value	Type
LIM	29	83	4.03e-10	SMART
LIM	93	147	1.71e-13	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000123966

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133210

Predicted Effect

probably damaging
Transcript: ENSMUST00000138815
AA Change: I46T

PolyPhen 2 Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000121927
Gene: ENSMUSG00000032698
AA Change: I46T

Domain	Start	End	E-Value	Type
Pfam:LIM	30	59	2.3e-8	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000156813
AA Change: I46T

PolyPhen 2 Score 0.907 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000122369
Gene: ENSMUSG00000032698
AA Change: I46T

Domain	Start	End	E-Value	Type
LIM	29	83	4.03e-10	SMART
LIM	93	144	1.36e-7	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000170926
AA Change: I46T

PolyPhen 2 Score 0.967 (Sensitivity: 0.77; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000128317
Gene: ENSMUSG00000032698
AA Change: I46T

Domain	Start	End	E-Value	Type
LIM	29	83	4.03e-10	SMART
LIM	93	147	1.71e-13	SMART

Meta Mutation Damage Score

0.1637

Coding Region Coverage

1x: 99.4%
3x: 98.9%
10x: 97.9%
20x: 96.7%

Validation Efficiency

100% (74/74)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] LMO2 encodes a cysteine-rich, two LIM-domain protein that is required for yolk sac erythropoiesis. The LMO2 protein has a central and crucial role in hematopoietic development and is highly conserved. The LMO2 transcription start site is located approximately 25 kb downstream from the 11p13 T-cell translocation cluster (11p13 ttc), where a number T-cell acute lymphoblastic leukemia-specific translocations occur. Alternative splicing results in multiple transcript variants encoding different isoforms.[provided by RefSeq, Nov 2008]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit lack of yolk sac erythropoiesis and die around embryonic day 10.5. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca15	A	T	7: 119,931,839 (GRCm39)	I31L	possibly damaging	Het
Abca17	T	C	17: 24,500,204 (GRCm39)	K1329R	probably benign	Het
Acap2	A	G	16: 30,952,427 (GRCm39)	Y197H	probably benign	Het
Adgrv1	A	G	13: 81,624,809 (GRCm39)	V3720A	possibly damaging	Het
Alms1	T	A	6: 85,592,350 (GRCm39)	S870T	possibly damaging	Het
Anapc4	A	G	5: 53,016,501 (GRCm39)	E493G	probably benign	Het
Ap2a1	A	G	7: 44,555,489 (GRCm39)		probably null	Het
Arhgef38	A	G	3: 132,822,227 (GRCm39)	L179P	probably damaging	Het
Bicral	T	C	17: 47,124,909 (GRCm39)	D630G	possibly damaging	Het
Ccdc97	A	T	7: 25,415,201 (GRCm39)	L154Q	probably damaging	Het
Cd40	T	C	2: 164,905,483 (GRCm39)		probably null	Het
Celsr1	T	A	15: 85,810,423 (GRCm39)	N2155I	possibly damaging	Het
Cemip	A	T	7: 83,641,241 (GRCm39)	L261H	probably damaging	Het
Cep57	G	A	9: 13,730,164 (GRCm39)	H98Y	probably damaging	Het
Chrna7	A	T	7: 62,755,805 (GRCm39)	L247Q	probably damaging	Het
Cyp2c40	T	A	19: 39,766,474 (GRCm39)	M374L	probably damaging	Het
Cyp4f13	T	C	17: 33,144,795 (GRCm39)	D372G	probably damaging	Het
Dazl	C	A	17: 50,588,311 (GRCm39)	S288I	probably damaging	Het
Dnah5	T	C	15: 28,311,474 (GRCm39)	F1818L	probably damaging	Het
Echdc1	T	C	10: 29,210,204 (GRCm39)	V143A	possibly damaging	Het
Eif4enif1	T	A	11: 3,192,687 (GRCm39)	H838Q	probably damaging	Het
Erich3	A	T	3: 154,469,217 (GRCm39)	D1223V	probably damaging	Het
Fbxl2	A	G	9: 113,815,576 (GRCm39)	I229T	possibly damaging	Het
Gfm2	G	A	13: 97,299,659 (GRCm39)	A406T	probably damaging	Het
Ggnbp2	A	G	11: 84,760,794 (GRCm39)	M1T	probably null	Het
Glb1l2	C	T	9: 26,708,162 (GRCm39)		probably benign	Het
Gnl2	A	G	4: 124,946,633 (GRCm39)	K618R	probably benign	Het
Greb1	A	T	12: 16,766,760 (GRCm39)	I346K	probably benign	Het
Greb1l	G	A	18: 10,542,427 (GRCm39)	E1341K	probably damaging	Het
Gtse1	A	G	15: 85,757,993 (GRCm39)	Q533R	probably benign	Het
Hemgn	A	G	4: 46,403,927 (GRCm39)	S23P	possibly damaging	Het
Htr6	G	T	4: 138,788,977 (GRCm39)	H359Q	probably damaging	Het
Ifit1	T	C	19: 34,626,204 (GRCm39)	F447L	probably benign	Het
Kansl1	T	C	11: 104,315,684 (GRCm39)	Y118C	possibly damaging	Het
Khk	G	A	5: 31,084,373 (GRCm39)	V118M	probably benign	Het
Klra17	T	A	6: 129,845,671 (GRCm39)	K181M	probably damaging	Het
Lbh	T	C	17: 73,228,287 (GRCm39)		probably null	Het
Maco1	T	C	4: 134,564,330 (GRCm39)		probably benign	Het
Mgat5	T	A	1: 127,315,251 (GRCm39)		probably null	Het
Mink1	T	C	11: 70,498,169 (GRCm39)	V525A	probably benign	Het
Myo10	C	A	15: 25,778,164 (GRCm39)		probably null	Het
Nlrp2	T	C	7: 5,328,007 (GRCm39)	N682S	probably benign	Het
Nr2e3	G	A	9: 59,856,617 (GRCm39)		probably benign	Het
Or5p5	T	C	7: 107,414,171 (GRCm39)	C129R	probably damaging	Het
Or6b2b	T	C	1: 92,418,758 (GRCm39)	T240A	probably damaging	Het
Pabpc4l	T	C	3: 46,401,276 (GRCm39)	T123A	probably benign	Het
Pfas	G	A	11: 68,878,847 (GRCm39)	S1319F	probably damaging	Het
Phf3	T	C	1: 30,842,887 (GRCm39)	K2024R	probably damaging	Het
Pld4	G	A	12: 112,735,046 (GRCm39)	C501Y	probably damaging	Het
Psg16	C	T	7: 16,824,560 (GRCm39)	R115W	probably damaging	Het
Rab3gap1	G	A	1: 127,870,110 (GRCm39)		probably null	Het
Rimkla	C	A	4: 119,335,049 (GRCm39)	K111N	probably damaging	Het
Rrm2b	T	C	15: 37,927,571 (GRCm39)	E113G	probably damaging	Het
Rspry1	C	T	8: 95,349,813 (GRCm39)	T67I	probably benign	Het
Skint6	C	A	4: 113,041,965 (GRCm39)	E292*	probably null	Het
Skint8	C	A	4: 111,807,390 (GRCm39)	L359M	probably damaging	Het
Slc13a1	A	G	6: 24,134,373 (GRCm39)	M170T	probably benign	Het
Slc15a5	T	C	6: 138,050,034 (GRCm39)	N127S	probably benign	Het
Slc39a10	G	A	1: 46,875,285 (GRCm39)	H6Y	probably damaging	Het
Spata31e2	A	C	1: 26,724,169 (GRCm39)	V337G	probably benign	Het
Sugct	A	T	13: 17,427,145 (GRCm39)	C338*	probably null	Het
Tbk1	A	T	10: 121,391,956 (GRCm39)	M486K	probably benign	Het
Terf1	A	T	1: 15,875,909 (GRCm39)	E3V	probably damaging	Het
Thoc5	T	A	11: 4,860,648 (GRCm39)	Y246N	probably damaging	Het
Tmem167b	G	A	3: 108,469,415 (GRCm39)		probably benign	Het
Tmtc1	T	A	6: 148,256,910 (GRCm39)		probably benign	Het
Zfp322a	A	T	13: 23,541,532 (GRCm39)	M70K	possibly damaging	Het
Zfp979	A	T	4: 147,698,375 (GRCm39)	H111Q	possibly damaging	Het

Other mutations in Lmo2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02631:Lmo2	APN	2	103,811,432 (GRCm39)	missense	probably benign	0.21
R1983:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R2013:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R2014:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R2131:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R2132:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R2133:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R2233:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R2235:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R2510:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R3038:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R3813:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R4058:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R4059:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R4448:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R4450:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R4544:Lmo2	UTSW	2	103,806,382 (GRCm39)	missense	probably damaging	1.00
R4805:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R4808:Lmo2	UTSW	2	103,811,407 (GRCm39)	missense	probably damaging	0.99
R4975:Lmo2	UTSW	2	103,806,488 (GRCm39)	nonsense	probably null
R5823:Lmo2	UTSW	2	103,811,417 (GRCm39)	missense	probably damaging	1.00
R6267:Lmo2	UTSW	2	103,800,946 (GRCm39)	missense	possibly damaging	0.86
R6296:Lmo2	UTSW	2	103,800,946 (GRCm39)	missense	possibly damaging	0.86
R6949:Lmo2	UTSW	2	103,801,018 (GRCm39)	start codon destroyed	probably null	0.53
R8051:Lmo2	UTSW	2	103,801,045 (GRCm39)	missense	possibly damaging	0.95
R8719:Lmo2	UTSW	2	103,811,264 (GRCm39)	missense	probably damaging	0.98
R8746:Lmo2	UTSW	2	103,806,384 (GRCm39)	missense	possibly damaging	0.85

Predicted Primers

PCR Primer
(F):5'- GAATTTGGGCGTCCTTTCTC -3'
(R):5'- GAGACTATGTATCCAACCCCGG -3'

Sequencing Primer
(F):5'- TGTAGTGAGGTTCCCCATAGAAC -3'
(R):5'- GACTATGTATCCAACCCCGGATGTG -3'

Posted On

2016-07-22