Mutagenetix > Incidental Mutation

Incidental Mutation 'R1954:Lemd3'

268143

Institutional Source

Beutler Lab

Gene Symbol

Lemd3

Ensembl Gene

ENSMUSG00000048661

Gene Name

LEM domain containing 3

Synonyms

Man1

MMRRC Submission

039968-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1954 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

120759318-120815237 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 120814845 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 129 (S129R)

Ref Sequence

ENSEMBL: ENSMUSP00000112661 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000119093] [ENSMUST00000119944]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000119093
AA Change: S129R

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000112661
Gene: ENSMUSG00000048661
AA Change: S129R

Domain	Start	End	E-Value	Type
LEM	8	51	1.01e-20	SMART
low complexity region	66	87	N/A	INTRINSIC
low complexity region	106	129	N/A	INTRINSIC
low complexity region	150	161	N/A	INTRINSIC
low complexity region	169	176	N/A	INTRINSIC
low complexity region	195	229	N/A	INTRINSIC
low complexity region	258	272	N/A	INTRINSIC
low complexity region	346	355	N/A	INTRINSIC
low complexity region	366	384	N/A	INTRINSIC
low complexity region	418	429	N/A	INTRINSIC
low complexity region	451	462	N/A	INTRINSIC
transmembrane domain	480	502	N/A	INTRINSIC
Pfam:MSC	526	779	8.9e-25	PFAM
PDB:4OZ1\|B	812	919	2e-23	PDB
SCOP:d1jmta_	813	894	6e-7	SMART
Blast:RRM	814	893	4e-49	BLAST

Predicted Effect

probably damaging
Transcript: ENSMUST00000119944
AA Change: S129R

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000113103
Gene: ENSMUSG00000048661
AA Change: S129R

Domain	Start	End	E-Value	Type
LEM	8	51	1.01e-20	SMART
low complexity region	66	87	N/A	INTRINSIC
low complexity region	106	129	N/A	INTRINSIC
low complexity region	150	161	N/A	INTRINSIC
low complexity region	169	176	N/A	INTRINSIC
low complexity region	195	229	N/A	INTRINSIC
low complexity region	258	272	N/A	INTRINSIC
low complexity region	346	355	N/A	INTRINSIC
low complexity region	366	384	N/A	INTRINSIC
low complexity region	418	429	N/A	INTRINSIC
low complexity region	451	462	N/A	INTRINSIC
transmembrane domain	480	502	N/A	INTRINSIC
Pfam:MSC	518	758	5.7e-57	PFAM
PDB:4OZ1\|B	790	897	2e-23	PDB
SCOP:d1jmta_	791	872	5e-7	SMART
Blast:RRM	792	871	4e-49	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175289

Meta Mutation Damage Score

0.0629

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 94.0%

Validation Efficiency

97% (101/104)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This locus encodes a LEM domain-containing protein. The encoded protein functions to antagonize transforming growth factor-beta signaling at the inner nuclear membrane. Two transcript variants encoding different isoforms have been found for this gene. Mutations in this gene have been associated with osteopoikilosis, Buschke-Ollendorff syndrome and melorheostosis.[provided by RefSeq, Nov 2009]
PHENOTYPE: Homozygous mutation of this gene results in embryonic lethality at midgestation, defects in vascular remodeling and increased apoptosis in embryos, particularly in mesenchymal tissues. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts15	T	A	9: 30,822,004 (GRCm39)	M478L	probably benign	Het
Akap8l	T	A	17: 32,555,710 (GRCm39)	Y123F	possibly damaging	Het
Anapc4	T	G	5: 53,003,967 (GRCm39)		probably benign	Het
Arap3	A	G	18: 38,115,055 (GRCm39)	V987A	probably damaging	Het
Atp2b4	T	A	1: 133,667,730 (GRCm39)	T105S	probably damaging	Het
Atp6v0d1	A	G	8: 106,292,525 (GRCm39)	L7P	probably damaging	Het
Atp6v1b2	T	C	8: 69,558,555 (GRCm39)	V341A	possibly damaging	Het
Baz2b	C	A	2: 59,799,087 (GRCm39)	A346S	probably benign	Het
Brpf3	G	A	17: 29,025,533 (GRCm39)	S202N	probably benign	Het
Btnl4	T	C	17: 34,691,904 (GRCm39)	K233E	possibly damaging	Het
Capn7	A	G	14: 31,082,107 (GRCm39)	T438A	probably damaging	Het
Cars2	A	T	8: 11,600,286 (GRCm39)	Y68N	probably damaging	Het
Cbx2	G	T	11: 118,919,166 (GRCm39)	G244W	probably damaging	Het
Ccr4	A	T	9: 114,321,753 (GRCm39)	V104D	probably damaging	Het
Cdc5l	T	C	17: 45,737,442 (GRCm39)		probably null	Het
Cep170	A	T	1: 176,583,950 (GRCm39)	C810S	probably benign	Het
Cfap299	A	T	5: 98,714,612 (GRCm39)		probably benign	Het
Clp1	T	C	2: 84,554,395 (GRCm39)	D258G	probably damaging	Het
Clstn3	T	C	6: 124,436,257 (GRCm39)	E164G	possibly damaging	Het
Col28a1	T	C	6: 7,998,516 (GRCm39)	E1131G	probably damaging	Het
Cps1	A	G	1: 67,234,355 (GRCm39)	D914G	possibly damaging	Het
Ctnnal1	C	T	4: 56,817,242 (GRCm39)		probably benign	Het
Cyp2c38	A	G	19: 39,393,131 (GRCm39)	L312P	probably damaging	Het
Cytip	T	C	2: 58,038,265 (GRCm39)	N99D	possibly damaging	Het
Dennd4a	A	T	9: 64,759,749 (GRCm39)	T285S	probably benign	Het
Dhx8	A	G	11: 101,644,105 (GRCm39)	S842G	probably damaging	Het
Disp1	A	T	1: 182,870,107 (GRCm39)	M771K	probably damaging	Het
Dnah17	A	G	11: 117,915,557 (GRCm39)	I4326T	probably damaging	Het
Efcab7	T	C	4: 99,757,887 (GRCm39)	F345L	probably damaging	Het
Erc1	G	T	6: 119,774,266 (GRCm39)	Q230K	probably damaging	Het
Ern1	A	T	11: 106,312,800 (GRCm39)		probably benign	Het
Espl1	T	C	15: 102,206,823 (GRCm39)	Y96H	probably damaging	Het
Fam135a	A	T	1: 24,068,683 (GRCm39)	L533I	probably damaging	Het
Fat2	G	A	11: 55,201,910 (GRCm39)	T388I	probably benign	Het
Galnt1	T	G	18: 24,404,831 (GRCm39)		probably benign	Het
Glmn	A	G	5: 107,720,243 (GRCm39)	F212S	probably damaging	Het
Gm3604	A	T	13: 62,517,025 (GRCm39)	N444K	probably damaging	Het
Gvin-ps5	A	C	7: 105,928,888 (GRCm39)	D336E	probably damaging	Het
H1f2	T	C	13: 23,923,385 (GRCm39)	V185A	unknown	Het
H1f3	A	G	13: 23,739,690 (GRCm39)		probably benign	Het
H2-M10.3	T	C	17: 36,678,390 (GRCm39)	D145G	probably damaging	Het
Hic2	T	A	16: 17,076,857 (GRCm39)	L562Q	probably damaging	Het
Hip1r	G	T	5: 124,139,907 (GRCm39)	E1003D	probably damaging	Het
Hsfy2	C	T	1: 56,676,342 (GRCm39)	C65Y	probably benign	Het
Inpp1	T	C	1: 52,833,788 (GRCm39)	T103A	probably damaging	Het
Ints5	T	C	19: 8,872,260 (GRCm39)	V73A	probably damaging	Het
Iqch	A	T	9: 63,455,298 (GRCm39)	D166E	probably benign	Het
Klhdc3	A	T	17: 46,988,901 (GRCm39)	N96K	probably damaging	Het
Klk1b8	C	T	7: 43,603,272 (GRCm39)		probably benign	Het
Klrb1	T	C	6: 128,700,036 (GRCm39)		probably null	Het
Krt71	C	A	15: 101,643,901 (GRCm39)	G446*	probably null	Het
Lars1	G	A	18: 42,343,115 (GRCm39)	R1101C	probably damaging	Het
Lrp1b	A	G	2: 40,748,453 (GRCm39)	L3015P	probably damaging	Het
Mdga2	T	C	12: 66,533,482 (GRCm39)		probably benign	Het
Mlst8	A	T	17: 24,696,195 (GRCm39)	I178N	probably damaging	Het
Mon2	A	T	10: 122,874,388 (GRCm39)	I320N	probably damaging	Het
Morc2b	T	C	17: 33,356,464 (GRCm39)	Y436C	probably damaging	Het
Moxd1	T	A	10: 24,155,781 (GRCm39)	M295K	probably benign	Het
Mrps5	T	A	2: 127,438,817 (GRCm39)		probably null	Het
Mtor	C	A	4: 148,552,730 (GRCm39)	S744R	probably damaging	Het
Myo3a	T	A	2: 22,246,037 (GRCm39)	D61E	probably damaging	Het
Nars1	C	T	18: 64,633,635 (GRCm39)	R545Q	probably damaging	Het
Ncoa6	A	G	2: 155,248,741 (GRCm39)	V1521A	possibly damaging	Het
Ndor1	T	C	2: 25,145,305 (GRCm39)	E20G	possibly damaging	Het
Nipsnap3b	T	C	4: 53,017,213 (GRCm39)		probably benign	Het
Notch3	G	T	17: 32,385,652 (GRCm39)	A39E	probably benign	Het
Or1j16	A	G	2: 36,530,227 (GRCm39)	M59V	possibly damaging	Het
Or2a14	T	C	6: 43,130,911 (GRCm39)	I224T	possibly damaging	Het
Or6z3	G	T	7: 6,464,144 (GRCm39)	W212L	probably benign	Het
Otud3	T	C	4: 138,625,343 (GRCm39)	K237R	possibly damaging	Het
Papola	T	A	12: 105,794,532 (GRCm39)		probably null	Het
Parl	T	A	16: 20,121,077 (GRCm39)	M1L	possibly damaging	Het
Parp14	G	T	16: 35,678,671 (GRCm39)	N432K	probably benign	Het
Patz1	T	G	11: 3,241,088 (GRCm39)	S159A	probably damaging	Het
Prpf6	T	G	2: 181,273,870 (GRCm39)	M338R	probably benign	Het
Psd3	A	G	8: 68,149,727 (GRCm39)	L343P	probably damaging	Het
Ptpn23	A	T	9: 110,215,393 (GRCm39)	N1422K	probably damaging	Het
Rab19	A	T	6: 39,361,016 (GRCm39)	T55S	probably benign	Het
Sh3yl1	A	G	12: 30,972,332 (GRCm39)	K34E	possibly damaging	Het
Skint8	T	A	4: 111,807,278 (GRCm39)	F321L	possibly damaging	Het
Slc25a46	A	T	18: 31,733,294 (GRCm39)		probably null	Het
Slc26a3	T	C	12: 31,500,815 (GRCm39)	L184S	probably damaging	Het
Slc39a10	A	T	1: 46,874,334 (GRCm39)	S323T	possibly damaging	Het
Sorbs2	G	T	8: 46,198,775 (GRCm39)	R20L	probably benign	Het
Stk32a	A	T	18: 43,345,090 (GRCm39)	D13V	probably benign	Het
Tab2	T	C	10: 7,795,094 (GRCm39)	T463A	probably damaging	Het
Tenm2	T	A	11: 35,938,374 (GRCm39)	N1433I	possibly damaging	Het
Tmem200c	A	T	17: 69,147,956 (GRCm39)	I180F	probably damaging	Het
Tmem232	G	T	17: 65,791,482 (GRCm39)	H129N	probably benign	Het
Tmem242	T	C	17: 5,489,854 (GRCm39)	T47A	possibly damaging	Het
Ube2d1	A	T	10: 71,120,953 (GRCm39)	M1K	probably null	Het
Ube2frt	A	G	12: 36,140,595 (GRCm39)		probably benign	Het
Uckl1	T	C	2: 181,212,320 (GRCm39)	Q332R	probably benign	Het
Unc5b	T	C	10: 60,605,044 (GRCm39)		probably benign	Het
Vmn2r114	T	C	17: 23,530,086 (GRCm39)	Y107C	probably benign	Het
Vmn2r82	A	T	10: 79,231,890 (GRCm39)	S630C	probably damaging	Het
Wdr25	T	A	12: 108,864,467 (GRCm39)	V204E	probably damaging	Het
Xab2	T	A	8: 3,666,094 (GRCm39)	D227V	probably damaging	Het
Zfp286	A	G	11: 62,674,534 (GRCm39)	S104P	possibly damaging	Het
Zfp345	T	C	2: 150,316,741 (GRCm39)	D22G	probably damaging	Het

Other mutations in Lemd3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01488:Lemd3	APN	10	120,769,304 (GRCm39)	nonsense	probably null
IGL01733:Lemd3	APN	10	120,769,568 (GRCm39)	nonsense	probably null
IGL02127:Lemd3	APN	10	120,761,933 (GRCm39)	missense	possibly damaging	0.58
IGL02171:Lemd3	APN	10	120,769,527 (GRCm39)	splice site	probably benign
Culebra	UTSW	10	120,769,538 (GRCm39)	missense	probably damaging	1.00
R2044_Lemd3_698	UTSW	10	120,769,347 (GRCm39)	missense	probably damaging	1.00
R0037:Lemd3	UTSW	10	120,761,361 (GRCm39)	missense	possibly damaging	0.95
R0309:Lemd3	UTSW	10	120,773,015 (GRCm39)	missense	possibly damaging	0.71
R0829:Lemd3	UTSW	10	120,814,988 (GRCm39)	missense	probably benign
R1171:Lemd3	UTSW	10	120,785,246 (GRCm39)	missense	possibly damaging	0.90
R1382:Lemd3	UTSW	10	120,767,641 (GRCm39)	missense	probably damaging	0.99
R2044:Lemd3	UTSW	10	120,769,347 (GRCm39)	missense	probably damaging	1.00
R2197:Lemd3	UTSW	10	120,814,432 (GRCm39)	small deletion	probably benign
R3118:Lemd3	UTSW	10	120,783,156 (GRCm39)	missense	probably benign	0.00
R3697:Lemd3	UTSW	10	120,814,432 (GRCm39)	small deletion	probably benign
R3729:Lemd3	UTSW	10	120,763,920 (GRCm39)	missense	probably damaging	1.00
R4407:Lemd3	UTSW	10	120,761,335 (GRCm39)	missense	possibly damaging	0.93
R4429:Lemd3	UTSW	10	120,813,893 (GRCm39)	missense	probably benign	0.00
R4830:Lemd3	UTSW	10	120,767,853 (GRCm39)	missense	probably damaging	0.99
R5316:Lemd3	UTSW	10	120,788,161 (GRCm39)	critical splice acceptor site	probably null
R5355:Lemd3	UTSW	10	120,769,538 (GRCm39)	missense	probably damaging	1.00
R5404:Lemd3	UTSW	10	120,767,863 (GRCm39)	nonsense	probably null
R6754:Lemd3	UTSW	10	120,769,565 (GRCm39)	missense	probably damaging	1.00
R7007:Lemd3	UTSW	10	120,788,137 (GRCm39)	missense	probably benign	0.28
R7213:Lemd3	UTSW	10	120,814,145 (GRCm39)	nonsense	probably null
R7699:Lemd3	UTSW	10	120,813,995 (GRCm39)	missense	probably damaging	0.99
R7700:Lemd3	UTSW	10	120,813,995 (GRCm39)	missense	probably damaging	0.99
R7781:Lemd3	UTSW	10	120,761,678 (GRCm39)	missense	probably damaging	1.00
R8681:Lemd3	UTSW	10	120,767,728 (GRCm39)	missense	possibly damaging	0.80
R9031:Lemd3	UTSW	10	120,767,878 (GRCm39)	missense	possibly damaging	0.94
R9274:Lemd3	UTSW	10	120,814,717 (GRCm39)	missense	possibly damaging	0.92

Predicted Primers

PCR Primer
(F):5'- TTTAATACCTGTCTGGCCGG -3'
(R):5'- CGTCTACCTCAAGAAGCTGAAG -3'

Sequencing Primer
(F):5'- TCCTCCGAGTCCGAGTAGTG -3'
(R):5'- CTGAAGAAGCTTCGCGAGG -3'

Posted On

2015-02-19