Mutagenetix > Incidental Mutation

Incidental Mutation 'R4407:Lemd3'

327720

Institutional Source

Beutler Lab

Gene Symbol

Lemd3

Ensembl Gene

ENSMUSG00000048661

Gene Name

LEM domain containing 3

Synonyms

Man1

MMRRC Submission

041689-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4407 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

120759318-120815237 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 120761335 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 907 (L907Q)

Ref Sequence

ENSEMBL: ENSMUSP00000113103 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000118291

Predicted Effect

possibly damaging
Transcript: ENSMUST00000119093
AA Change: L929Q

PolyPhen 2 Score 0.885 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000112661
Gene: ENSMUSG00000048661
AA Change: L929Q

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

possibly damaging
Transcript: ENSMUST00000119944
AA Change: L907Q

PolyPhen 2 Score 0.932 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000113103
Gene: ENSMUSG00000048661
AA Change: L907Q

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

Meta Mutation Damage Score

0.1795

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.3%

Validation Efficiency

100% (61/61)

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: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A830035A12Rik	T	C	11: 107,422,881 (GRCm39)		noncoding transcript	Het
Bbs10	A	G	10: 111,135,720 (GRCm39)	T278A	probably benign	Het
Bcl6b	A	G	11: 70,116,929 (GRCm39)	L450P	probably damaging	Het
Braf	T	G	6: 39,592,654 (GRCm39)	K674Q	probably damaging	Het
Cep112	C	T	11: 108,410,027 (GRCm39)	T481I	possibly damaging	Het
Cep135	T	A	5: 76,772,514 (GRCm39)	M633K	probably benign	Het
Cpped1	T	C	16: 11,623,285 (GRCm39)	Y278C	probably damaging	Het
Depdc5	T	A	5: 33,061,878 (GRCm39)		probably null	Het
Dolpp1	C	T	2: 30,286,464 (GRCm39)	A128V	possibly damaging	Het
E2f5	T	A	3: 14,668,823 (GRCm39)	D238E	probably benign	Het
Fat4	A	T	3: 39,012,689 (GRCm39)	D2328V	probably benign	Het
Fbln1	T	A	15: 85,115,757 (GRCm39)		probably null	Het
Fkbp3	T	C	12: 65,116,778 (GRCm39)	T53A	probably damaging	Het
Flg2	G	T	3: 93,122,176 (GRCm39)	G1449C	unknown	Het
G530012D18Rik	G	C	1: 85,504,923 (GRCm39)		probably benign	Het
Glyctk	A	T	9: 106,034,307 (GRCm39)		probably benign	Het
Gm6430	T	C	1: 96,953,297 (GRCm39)		noncoding transcript	Het
Golga1	C	A	2: 38,909,653 (GRCm39)		probably null	Het
Gucy2g	A	T	19: 55,226,269 (GRCm39)	F216I	probably benign	Het
L3mbtl3	A	G	10: 26,189,782 (GRCm39)	V494A	unknown	Het
Lama2	AATCAGACAGGAG	A	10: 27,088,124 (GRCm39)		probably benign	Het
Lrp2	A	T	2: 69,332,861 (GRCm39)	V1552D	probably damaging	Het
Map3k12	T	C	15: 102,413,837 (GRCm39)	T45A	probably damaging	Het
Mycbp2	A	T	14: 103,524,664 (GRCm39)	D665E	probably damaging	Het
Myof	A	G	19: 37,911,426 (GRCm39)	S1502P	probably damaging	Het
Or4p7	A	T	2: 88,222,427 (GRCm39)	M279L	probably benign	Het
Pcdhac2	G	T	18: 37,277,499 (GRCm39)	V160L	probably benign	Het
Pcnt	T	C	10: 76,210,704 (GRCm39)	E2473G	possibly damaging	Het
Pitpnm2	T	A	5: 124,290,678 (GRCm39)	I3L	possibly damaging	Het
Prkd3	C	A	17: 79,290,987 (GRCm39)	W176L	probably damaging	Het
Prpf39	C	T	12: 65,103,040 (GRCm39)	A438V	probably damaging	Het
Rpgrip1	T	A	14: 52,384,856 (GRCm39)	F655I	probably damaging	Het
Rrp12	T	C	19: 41,880,990 (GRCm39)	Y147C	probably damaging	Het
Sec23b	A	T	2: 144,416,638 (GRCm39)	N429Y	possibly damaging	Het
Slc2a10	T	A	2: 165,356,684 (GRCm39)	S115T	probably damaging	Het
Spg11	A	C	2: 121,905,813 (GRCm39)	D1277E	probably benign	Het
Sspo	A	G	6: 48,437,454 (GRCm39)	D1279G	probably damaging	Het
St18	T	C	1: 6,898,061 (GRCm39)	I621T	probably benign	Het
Tbc1d31	T	A	15: 57,783,438 (GRCm39)	D112E	possibly damaging	Het
Tdpoz6	C	A	3: 93,599,419 (GRCm39)	V317L	probably benign	Het
Tgm4	A	T	9: 122,885,595 (GRCm39)	D379V	probably damaging	Het
Thyn1	A	T	9: 26,914,893 (GRCm39)	D15V	possibly damaging	Het
Timd6	A	G	11: 46,468,207 (GRCm39)	T94A	probably damaging	Het
Tm4sf19	T	C	16: 32,226,712 (GRCm39)	V167A	possibly damaging	Het
Trim38	A	C	13: 23,975,474 (GRCm39)	Q471P	probably benign	Het
Trmt1	T	A	8: 85,424,384 (GRCm39)		probably benign	Het
Ubqlnl	C	T	7: 103,798,925 (GRCm39)	V191M	probably benign	Het
Usp9y	T	C	Y: 1,336,375 (GRCm39)	I1500V	probably benign	Het
Vgll4	C	T	6: 114,867,573 (GRCm39)		probably null	Het
Vmn1r173	T	A	7: 23,402,441 (GRCm39)	N225K	probably damaging	Het
Vmn2r22	C	T	6: 123,614,913 (GRCm39)	G226R	probably damaging	Het
Wnk3	C	A	X: 150,016,209 (GRCm39)	P555Q	probably benign	Het
Yes1	T	G	5: 32,797,929 (GRCm39)	Y83D	possibly damaging	Het
Zdhhc15	G	A	X: 103,604,294 (GRCm39)	R322*	probably null	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
R1954:Lemd3	UTSW	10	120,814,845 (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
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'- ATTTGCAGAACTCTCAAACAGC -3'
(R):5'- AGCATTGCATGGCTCTTGG -3'

Sequencing Primer
(F):5'- GAACTCTCAAACAGCTGTCTTCAG -3'
(R):5'- TGACTCTTACAAAGATTTGGGAAGG -3'

Posted On

2015-07-07