Mutagenetix > Incidental Mutation

Incidental Mutation 'R9274:Lemd3'

703171

Institutional Source

Beutler Lab

Gene Symbol

Lemd3

Ensembl Gene

ENSMUSG00000048661

Gene Name

LEM domain containing 3

Synonyms

Man1

MMRRC Submission

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R9274 (G1)

Quality Score

115.008

Status

Validated

Chromosome

Chromosomal Location

120759318-120815237 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 120814717 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Valine at position 172 (A172V)

Ref Sequence

ENSEMBL: ENSMUSP00000113103 (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: A172V

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000112661
Gene: ENSMUSG00000048661
AA Change: A172V

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: A172V

PolyPhen 2 Score 0.922 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000113103
Gene: ENSMUSG00000048661
AA Change: A172V

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

100% (65/65)

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: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actc1	A	T	2: 113,879,752 (GRCm39)	S236T	probably benign	Het
Adam30	A	G	3: 98,069,267 (GRCm39)	T239A	probably benign	Het
Aoc1l2	T	C	6: 48,907,341 (GRCm39)	F114L	possibly damaging	Het
Ascl2	G	A	7: 142,521,753 (GRCm39)	R232C	probably damaging	Het
Atp10a	C	A	7: 58,478,369 (GRCm39)	Q1471K	probably benign	Het
Avl9	T	A	6: 56,720,346 (GRCm39)	D461E	probably damaging	Het
Baiap3	T	A	17: 25,463,354 (GRCm39)	Y983F	probably damaging	Het
C1rl	A	G	6: 124,485,483 (GRCm39)	S285G	probably benign	Het
Cacna1i	G	A	15: 80,254,354 (GRCm39)	V772M	probably damaging	Het
Ccser2	T	A	14: 36,660,737 (GRCm39)	D472V	possibly damaging	Het
Cd244a	T	G	1: 171,401,928 (GRCm39)	V218G	probably benign	Het
Cdhr1	T	C	14: 36,802,564 (GRCm39)	K633R	probably benign	Het
Col14a1	A	G	15: 55,381,671 (GRCm39)	Q1748R	probably damaging	Het
Col6a3	T	A	1: 90,707,020 (GRCm39)	Y2638F	unknown	Het
Crnkl1	A	T	2: 145,765,836 (GRCm39)	F411L	probably damaging	Het
Crp	T	A	1: 172,526,072 (GRCm39)	F52L	possibly damaging	Het
Dnah12	A	G	14: 26,537,374 (GRCm39)	N2208D	probably benign	Het
Exd2	T	C	12: 80,539,674 (GRCm39)		probably null	Het
F13a1	A	T	13: 37,052,761 (GRCm39)	I726N	probably damaging	Het
Fmo6	G	A	1: 162,747,921 (GRCm39)	T381I	probably benign	Het
Gdpd5	T	C	7: 99,107,989 (GRCm39)	L522P	probably damaging	Het
Gm12790	T	A	4: 101,824,743 (GRCm39)	D175V	possibly damaging	Het
Gm3543	T	C	14: 41,802,125 (GRCm39)	R120G	probably damaging	Het
Gpatch2	T	A	1: 186,963,029 (GRCm39)	D273E	probably damaging	Het
Hlcs	A	G	16: 94,088,785 (GRCm39)	S66P	possibly damaging	Het
Hmcn1	T	C	1: 150,506,046 (GRCm39)	T3827A	probably benign	Het
Ism2	G	A	12: 87,331,827 (GRCm39)	Q237*	probably null	Het
Jph2	G	A	2: 163,239,547 (GRCm39)		probably benign	Het
Kcnb2	A	G	1: 15,781,723 (GRCm39)	Q865R	probably benign	Het
Kcnh6	C	G	11: 105,924,860 (GRCm39)	H941Q	possibly damaging	Het
Kcnk9	A	G	15: 72,384,224 (GRCm39)	V318A	unknown	Het
Lifr	G	T	15: 7,217,591 (GRCm39)	A840S	probably damaging	Het
Lnpep	T	C	17: 17,758,837 (GRCm39)	T836A	probably benign	Het
Mapk13	A	G	17: 28,988,490 (GRCm39)	Y36C	probably damaging	Het
Mdm2	G	A	10: 117,541,081 (GRCm39)		probably benign	Het
Msmb	T	C	14: 31,870,130 (GRCm39)	M34T	probably benign	Het
Myo5a	A	G	9: 75,097,279 (GRCm39)	N1319S	possibly damaging	Het
Myot	T	A	18: 44,479,265 (GRCm39)	V334E	probably damaging	Het
Nalcn	A	G	14: 123,753,068 (GRCm39)	I306T	probably damaging	Het
Nicn1	C	T	9: 108,171,708 (GRCm39)	R163C	possibly damaging	Het
Nphp4	T	C	4: 152,640,056 (GRCm39)	Y981H	probably benign	Het
Nphs2	G	A	1: 156,144,416 (GRCm39)	R140Q	probably damaging	Het
Nsa2	C	T	13: 97,272,170 (GRCm39)	R17H	probably benign	Het
Nup98	C	A	7: 101,788,037 (GRCm39)	R1011L	probably benign	Het
Obox6	T	C	7: 15,567,766 (GRCm39)	H227R	possibly damaging	Het
Or10ak14	G	A	4: 118,610,883 (GRCm39)	A286V	probably benign	Het
Or1j14	T	C	2: 36,417,559 (GRCm39)	I45T	probably damaging	Het
Or4c1	A	C	2: 89,133,513 (GRCm39)	L141R	probably damaging	Het
P2rx2	C	T	5: 110,489,709 (GRCm39)	G202D	probably damaging	Het
Pcdh12	A	G	18: 38,415,950 (GRCm39)	W392R	probably damaging	Het
Plxna2	G	A	1: 194,471,136 (GRCm39)	G969D	probably damaging	Het
Prg4	T	C	1: 150,331,924 (GRCm39)	T250A	possibly damaging	Het
Rad54l	G	T	4: 115,967,667 (GRCm39)	P205Q	probably damaging	Het
Ralgapb	A	G	2: 158,278,539 (GRCm39)	I334M	probably damaging	Het
Ric3	C	T	7: 108,647,212 (GRCm39)	D204N	probably damaging	Het
Rnf10	A	T	5: 115,385,322 (GRCm39)	Y557*	probably null	Het
Ruvbl1	A	G	6: 88,474,334 (GRCm39)	I446V	probably benign	Het
Serinc3	A	T	2: 163,468,371 (GRCm39)	V361D	probably damaging	Het
Slc4a1	C	A	11: 102,242,047 (GRCm39)	V864L	probably benign	Het
Slf1	C	A	13: 77,191,669 (GRCm39)	*1055L	probably null	Het
Stk25	T	C	1: 93,552,806 (GRCm39)	S328G	probably benign	Het
Stpg1	T	C	4: 135,252,782 (GRCm39)	F178L	possibly damaging	Het
Tmem25	C	T	9: 44,706,336 (GRCm39)	R345H	probably benign	Het
Tssk1	A	T	16: 17,712,724 (GRCm39)	I170L	probably benign	Het
Tubg1	A	G	11: 101,017,241 (GRCm39)		probably benign	Het
Uchl3	A	G	14: 101,903,240 (GRCm39)	D33G	probably damaging	Het
Vmn1r152	A	T	7: 22,223,056 (GRCm39)	H222L	probably benign	Het
Zfp975	C	T	7: 42,312,299 (GRCm39)	V105I	probably benign	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
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

Predicted Primers

PCR Primer
(F):5'- TTTAATACCTGTCTGGCCGGG -3'
(R):5'- CCGTCTACCTCAAGAAGCTG -3'

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

Posted On

2022-03-25