Mutagenetix > Incidental Mutation

Incidental Mutation 'R4830:Lemd3'

372749

Institutional Source

Beutler Lab

Gene Symbol

Lemd3

Ensembl Gene

ENSMUSG00000048661

Gene Name

LEM domain containing 3

Synonyms

Man1

MMRRC Submission

042446-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4830 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

120759318-120815237 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 120767853 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 697 (D697G)

Ref Sequence

ENSEMBL: ENSMUSP00000112661 (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

probably damaging
Transcript: ENSMUST00000119093
AA Change: D697G

PolyPhen 2 Score 0.986 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000112661
Gene: ENSMUSG00000048661
AA Change: D697G

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: D675G

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000113103
Gene: ENSMUSG00000048661
AA Change: D675G

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

0.2536

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.5%

Validation Efficiency

97% (71/73)

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcd3	C	A	3: 121,553,933 (GRCm39)	G643V	probably damaging	Het
Adamtsl1	A	G	4: 86,274,619 (GRCm39)	E1225G	probably damaging	Het
Agbl5	G	A	5: 31,048,059 (GRCm39)	R111H	probably damaging	Het
Ankle2	A	C	5: 110,389,879 (GRCm39)	K446Q	probably damaging	Het
Boc	A	C	16: 44,310,520 (GRCm39)	M800R	probably damaging	Het
Ccnt1	A	T	15: 98,441,332 (GRCm39)	N645K	probably damaging	Het
Cd93	G	A	2: 148,285,299 (GRCm39)	Q16*	probably null	Het
Cpsf4l	G	T	11: 113,600,328 (GRCm39)		probably benign	Het
Cuzd1	T	A	7: 130,919,783 (GRCm39)	D111V	probably damaging	Het
Dab2	T	C	15: 6,457,008 (GRCm39)	C232R	probably benign	Het
Dmpk	A	T	7: 18,821,453 (GRCm39)	Y237F	probably damaging	Het
Dnah6	T	A	6: 73,021,745 (GRCm39)	T3526S	possibly damaging	Het
Dock2	T	C	11: 34,223,767 (GRCm39)		probably null	Het
Dsp	G	A	13: 38,376,840 (GRCm39)	V1542I	probably benign	Het
Dst	T	A	1: 34,237,586 (GRCm39)		probably null	Het
Esd	T	C	14: 74,978,600 (GRCm39)	L54S	probably damaging	Het
Exd1	C	T	2: 119,350,807 (GRCm39)	A485T	probably benign	Het
Gm3604	A	T	13: 62,516,857 (GRCm39)	N500K	probably damaging	Het
Grhl2	T	A	15: 37,335,903 (GRCm39)		probably null	Het
Gsto1	C	T	19: 47,852,830 (GRCm39)	R222C	probably benign	Het
Inpp4a	T	A	1: 37,410,861 (GRCm39)	M343K	probably damaging	Het
Itpripl2	T	C	7: 118,090,280 (GRCm39)	Q93R	probably benign	Het
Jakmip2	G	A	18: 43,700,208 (GRCm39)	T450I	probably benign	Het
Kdm6b	A	T	11: 69,294,620 (GRCm39)	I1186N	unknown	Het
Kif1a	T	C	1: 92,948,931 (GRCm39)		probably null	Het
Klhl20	T	C	1: 160,925,946 (GRCm39)	K434R	probably benign	Het
Lipo3	A	G	19: 33,753,987 (GRCm39)	S383P	probably damaging	Het
Ltn1	C	A	16: 87,176,582 (GRCm39)	K1741N	probably damaging	Het
Lvrn	A	T	18: 47,038,418 (GRCm39)	T991S	probably damaging	Het
Macroh2a2	C	T	10: 61,575,132 (GRCm39)	D355N	possibly damaging	Het
Mast3	C	A	8: 71,241,559 (GRCm39)	R151L	possibly damaging	Het
Mplkipl1	C	T	19: 61,164,364 (GRCm39)	G24R	unknown	Het
Muc4	G	C	16: 32,753,919 (GRCm38)	R1265P	probably benign	Het
Myoz1	T	C	14: 20,705,377 (GRCm39)	K14E	probably damaging	Het
Neb	G	T	2: 52,082,532 (GRCm39)	Q5450K	probably damaging	Het
Nedd1	T	A	10: 92,522,120 (GRCm39)	N639I	probably damaging	Het
Nlrp4e	A	T	7: 23,036,165 (GRCm39)	N673Y	probably benign	Het
Nop53	C	T	7: 15,676,129 (GRCm39)	R190Q	probably damaging	Het
Notch4	T	C	17: 34,789,092 (GRCm39)	Y468H	probably damaging	Het
Obscn	T	C	11: 58,958,433 (GRCm39)	T3507A	probably damaging	Het
Opn5	T	C	17: 42,922,187 (GRCm39)	H5R	probably benign	Het
Or4l15	T	C	14: 50,197,681 (GRCm39)	N283D	probably damaging	Het
Patl1	T	C	19: 11,902,515 (GRCm39)	M349T	probably benign	Het
Phactr3	A	G	2: 177,925,811 (GRCm39)	N362S	probably damaging	Het
Pirb	C	T	7: 3,720,602 (GRCm39)	G299S	probably benign	Het
Rapgef5	G	A	12: 117,719,809 (GRCm39)	R579Q	probably damaging	Het
Rgl1	T	C	1: 152,430,081 (GRCm39)	D234G	probably benign	Het
Serpinb3a	C	T	1: 106,976,316 (GRCm39)	E122K	probably benign	Het
Slc22a15	T	C	3: 101,782,919 (GRCm39)		probably benign	Het
Slc25a12	A	T	2: 71,127,149 (GRCm39)	V344E	probably damaging	Het
Slc43a2	T	C	11: 75,434,119 (GRCm39)	L99P	probably damaging	Het
Smim27	G	T	4: 40,269,719 (GRCm39)		probably null	Het
Smtn	A	G	11: 3,470,736 (GRCm39)		probably benign	Het
Szt2	A	T	4: 118,226,445 (GRCm39)	Y3001N	unknown	Het
Tgfbr3	G	T	5: 107,257,585 (GRCm39)	P825T	probably damaging	Het
Tnpo3	T	C	6: 29,568,937 (GRCm39)	T472A	probably benign	Het
Trf	T	A	9: 103,105,114 (GRCm39)	D66V	probably damaging	Het
Vmn1r124	A	G	7: 20,993,624 (GRCm39)	C307R	probably damaging	Het
Vps13b	T	A	15: 35,452,370 (GRCm39)	F656Y	possibly damaging	Het
Zic1	G	T	9: 91,244,584 (GRCm39)	S358R	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
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
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
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'- GCGGCTGTATTAGGGAATCG -3'
(R):5'- CTCCATTATTCCATGAGGCCAG -3'

Sequencing Primer
(F):5'- CTGTATTAGGGAATCGCGGAC -3'
(R):5'- GGGGCACGGGTCACTGTTAG -3'

Posted On

2016-03-01