Mutagenetix > Incidental Mutation

Incidental Mutation 'R4429:Lemd3'

328333

Institutional Source

Beutler Lab

Gene Symbol

Lemd3

Ensembl Gene

ENSMUSG00000048661

Gene Name

LEM domain containing 3

Synonyms

Man1

MMRRC Submission

041699-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4429 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

120759318-120815237 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 120813893 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 447 (T447A)

Ref Sequence

ENSEMBL: ENSMUSP00000113103 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000119093
AA Change: T447A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000112661
Gene: ENSMUSG00000048661
AA Change: T447A

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 benign
Transcript: ENSMUST00000119944
AA Change: T447A

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)

SMART Domains

Protein: ENSMUSP00000113103
Gene: ENSMUSG00000048661
AA Change: T447A

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

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.3%
20x: 95.5%

Validation Efficiency

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: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610040J01Rik	G	T	5: 64,056,182 (GRCm39)		probably benign	Het
Abca5	T	C	11: 110,202,236 (GRCm39)	T390A	probably benign	Het
Ahcyl2	T	G	6: 29,894,874 (GRCm39)	V452G	probably damaging	Het
Ano4	T	A	10: 88,828,804 (GRCm39)	N545I	probably damaging	Het
Bag4	C	T	8: 26,259,516 (GRCm39)	A228T	probably benign	Het
Catip	T	A	1: 74,407,891 (GRCm39)		probably benign	Het
Chrna4	A	G	2: 180,670,413 (GRCm39)	S448P	probably damaging	Het
Cldn8	A	C	16: 88,359,619 (GRCm39)	M102R	probably damaging	Het
Cnpy3	T	A	17: 47,058,070 (GRCm39)	Q111L	probably benign	Het
Dnah8	A	G	17: 30,971,120 (GRCm39)	N2725D	probably damaging	Het
Dock8	T	C	19: 25,042,754 (GRCm39)	V112A	probably benign	Het
Ephb3	G	A	16: 21,033,213 (GRCm39)	E66K	probably damaging	Het
Gm6594	T	A	17: 82,846,923 (GRCm39)	D79E	probably benign	Het
Gtf2e2	T	A	8: 34,242,521 (GRCm39)	Y74*	probably null	Het
Hacd4	A	T	4: 88,353,184 (GRCm39)	F103I	possibly damaging	Het
Hap1	T	C	11: 100,245,098 (GRCm39)	T38A	probably benign	Het
Havcr2	T	A	11: 46,347,387 (GRCm39)	D72E	probably damaging	Het
Iqcg	G	A	16: 32,839,860 (GRCm39)	T362I	probably benign	Het
Lect2	C	T	13: 56,693,538 (GRCm39)		probably null	Het
Lrrc72	T	C	12: 36,258,623 (GRCm39)	N78S	probably damaging	Het
Map3k14	A	G	11: 103,118,410 (GRCm39)	L592P	probably damaging	Het
Meioc	T	C	11: 102,566,546 (GRCm39)	Y721H	probably damaging	Het
Mrps10	T	A	17: 47,689,124 (GRCm39)		probably null	Het
Myo5c	A	G	9: 75,201,283 (GRCm39)	Y1406C	probably damaging	Het
Myo7a	T	C	7: 97,702,395 (GRCm39)	Y2098C	probably damaging	Het
Nol9	C	T	4: 152,125,631 (GRCm39)	T194I	probably damaging	Het
Nox3	G	A	17: 3,733,233 (GRCm39)	T206I	probably benign	Het
Nsd2	T	G	5: 34,000,546 (GRCm39)	M21R	probably damaging	Het
Pcdh9	T	C	14: 94,124,820 (GRCm39)	N327S	probably damaging	Het
Pclo	T	G	5: 14,728,114 (GRCm39)		probably benign	Het
Pparg	T	A	6: 115,416,984 (GRCm39)	M59K	probably benign	Het
Prag1	A	G	8: 36,613,796 (GRCm39)	K1116R	probably damaging	Het
Rhbdf1	C	T	11: 32,163,369 (GRCm39)	E368K	probably benign	Het
Rita1	A	G	5: 120,747,626 (GRCm39)	V224A	probably damaging	Het
Rsph6a	T	A	7: 18,807,988 (GRCm39)	W384R	probably damaging	Het
Scn1a	A	T	2: 66,181,329 (GRCm39)	Y65N	possibly damaging	Het
Serpina5	C	A	12: 104,069,665 (GRCm39)	F292L	probably benign	Het
Sf3b3	A	C	8: 111,552,750 (GRCm39)	L511V	probably benign	Het
Siglecg	C	T	7: 43,067,350 (GRCm39)	P639L	possibly damaging	Het
Slc12a3	A	T	8: 95,069,713 (GRCm39)	I541F	probably damaging	Het
Slco6d1	T	C	1: 98,424,091 (GRCm39)	V581A	possibly damaging	Het
Sptbn2	T	C	19: 4,788,383 (GRCm39)	Y1121H	probably damaging	Het
Sytl5	A	T	X: 9,826,262 (GRCm39)	N412Y	probably damaging	Het
Timm29	G	C	9: 21,504,775 (GRCm39)	A148P	probably damaging	Het
Tmem181a	T	A	17: 6,346,061 (GRCm39)	L185H	probably damaging	Het
Tmem67	T	A	4: 12,051,473 (GRCm39)	N785I	possibly damaging	Het
Trhde	A	T	10: 114,339,028 (GRCm39)	L594Q	probably damaging	Het
Uba6	C	T	5: 86,268,406 (GRCm39)	V941I	probably damaging	Het
Vmn1r174	T	C	7: 23,453,565 (GRCm39)	V77A	probably benign	Het
Zfp661	A	G	2: 127,420,628 (GRCm39)	V57A	probably damaging	Het
Zfp867	C	T	11: 59,355,863 (GRCm39)	D64N	possibly damaging	Het
Zp3r	T	C	1: 130,519,128 (GRCm39)	T294A	possibly 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
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'- TCCTAGGTAAGTCAGTCCCAG -3'
(R):5'- TGGACTCCATTCCTCGATACCG -3'

Sequencing Primer
(F):5'- CTAGGTAAGTCAGTCCCAGTATTAGG -3'
(R):5'- ATTCCTCGATACCGTGCCG -3'

Posted On

2015-07-07