Mutagenetix > Incidental Mutation

Incidental Mutation 'R2009:Limd1'

219373

Institutional Source

Beutler Lab

Gene Symbol

Limd1

Ensembl Gene

ENSMUSG00000025239

Gene Name

LIM domains containing 1

Synonyms

D9Ertd192e

MMRRC Submission

040018-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.340) question?

Stock #

R2009 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

123307771-123350617 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 123308564 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Glycine at position 88 (S88G)

Ref Sequence

ENSEMBL: ENSMUSP00000026269 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000026269]

AlphaFold

Q9QXD8

Predicted Effect

probably benign
Transcript: ENSMUST00000026269
AA Change: S88G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000026269
Gene: ENSMUSG00000025239
AA Change: S88G

Domain	Start	End	E-Value	Type
low complexity region	57	67	N/A	INTRINSIC
low complexity region	238	252	N/A	INTRINSIC
LIM	463	516	2.17e-15	SMART
LIM	528	580	9.6e-17	SMART
LIM	588	649	2.26e-13	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000216352

Predicted Effect

probably benign
Transcript: ENSMUST00000217639

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.3%
20x: 95.1%

Validation Efficiency

100% (47/47)

MGI Phenotype

PHENOTYPE: Mice homozygous for a knock-out allele exhibit normal basal bone osteoclast numbers and bone density but are resistant to physiological and pathologic osteoclastogenic stimuli. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 44 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts15	T	A	9: 30,833,433 (GRCm39)	D34V	probably benign	Het
Adgrf1	A	T	17: 43,632,112 (GRCm39)	R884*	probably null	Het
Adgrg7	T	C	16: 56,582,236 (GRCm39)	T301A	probably benign	Het
Arhgef17	A	G	7: 100,530,988 (GRCm39)	I1366T	probably damaging	Het
C1s2	A	T	6: 124,612,048 (GRCm39)	L112H	probably damaging	Het
C2cd6	A	T	1: 59,042,391 (GRCm39)		noncoding transcript	Het
Cfap74	G	A	4: 155,504,724 (GRCm39)	R103H	possibly damaging	Het
Col7a1	A	T	9: 108,797,943 (GRCm39)		probably null	Het
Dmp1	A	G	5: 104,360,706 (GRCm39)	S461G	probably damaging	Het
Eif4g2	A	T	7: 110,673,405 (GRCm39)	D753E	probably benign	Het
Espl1	A	G	15: 102,221,424 (GRCm39)	I944V	probably damaging	Het
Etv4	T	C	11: 101,665,063 (GRCm39)	D130G	probably damaging	Het
Gabbr2	A	T	4: 46,734,119 (GRCm39)	I533N	probably damaging	Het
Gne	T	C	4: 44,055,273 (GRCm39)	E234G	probably benign	Het
Itga6	C	A	2: 71,647,025 (GRCm39)	N78K	probably benign	Het
Lap3	C	T	5: 45,650,899 (GRCm39)	T33M	probably benign	Het
Lrp1	G	T	10: 127,380,385 (GRCm39)	T3922K	probably damaging	Het
Map4k3	A	G	17: 80,971,517 (GRCm39)		probably benign	Het
Mib1	T	C	18: 10,812,118 (GRCm39)	L263S	probably damaging	Het
Ncor1	T	C	11: 62,216,427 (GRCm39)	S1474G	probably benign	Het
Nkapl	A	C	13: 21,651,607 (GRCm39)	S335R	probably damaging	Het
Nrg3	A	G	14: 38,092,771 (GRCm39)	S605P	probably damaging	Het
Or10x4	G	T	1: 174,218,995 (GRCm39)	R120L	possibly damaging	Het
Or52b3	A	G	7: 102,204,151 (GRCm39)	Y220C	probably damaging	Het
Patj	G	A	4: 98,344,406 (GRCm39)	D577N	probably damaging	Het
Pfpl	A	C	19: 12,407,319 (GRCm39)	K523N	possibly damaging	Het
Pik3c2a	A	C	7: 115,963,738 (GRCm39)	L924R	probably damaging	Het
Pkd2l1	C	A	19: 44,144,403 (GRCm39)	R278L	probably benign	Het
Prss2	A	T	6: 41,500,910 (GRCm39)	I108F	probably damaging	Het
Rnase2b	A	G	14: 51,400,347 (GRCm39)	T143A	possibly damaging	Het
Sgk1	C	T	10: 21,872,500 (GRCm39)	R171W	probably damaging	Het
Sphk2	A	T	7: 45,360,437 (GRCm39)	H522Q	probably damaging	Het
Szt2	A	G	4: 118,235,261 (GRCm39)		probably null	Het
Tmem88	C	A	11: 69,288,602 (GRCm39)	A106S	probably damaging	Het
Trappc14	C	A	5: 138,259,191 (GRCm39)	C434F	probably damaging	Het
Trim39	A	G	17: 36,574,646 (GRCm39)	L252S	possibly damaging	Het
Trim60	T	A	8: 65,453,975 (GRCm39)	E91D	probably damaging	Het
Trpm5	A	G	7: 142,641,475 (GRCm39)	I145T	possibly damaging	Het
Vmn2r107	A	T	17: 20,595,729 (GRCm39)	M761L	probably benign	Het
Wdr4	G	A	17: 31,719,584 (GRCm39)		probably benign	Het
Wfs1	A	T	5: 37,125,653 (GRCm39)	S413T	probably damaging	Het
Wnt2	A	T	6: 18,030,208 (GRCm39)	W27R	probably damaging	Het
Zc3h3	A	T	15: 75,651,158 (GRCm39)	H687Q	probably damaging	Het
Zfp750	G	A	11: 121,403,951 (GRCm39)	P308L	possibly damaging	Het

Other mutations in Limd1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00953:Limd1	APN	9	123,308,948 (GRCm39)	missense	probably benign	0.31
IGL00972:Limd1	APN	9	123,309,141 (GRCm39)	missense	probably benign	0.06
IGL01815:Limd1	APN	9	123,308,801 (GRCm39)	missense	probably benign	0.01
IGL02598:Limd1	APN	9	123,309,236 (GRCm39)	missense	probably benign
IGL02598:Limd1	APN	9	123,345,933 (GRCm39)	missense	probably benign	0.11
IGL02633:Limd1	APN	9	123,308,987 (GRCm39)	unclassified	probably benign
IGL02999:Limd1	APN	9	123,345,864 (GRCm39)	missense	probably damaging	1.00
R0314:Limd1	UTSW	9	123,345,892 (GRCm39)	missense	probably benign	0.04
R1612:Limd1	UTSW	9	123,347,219 (GRCm39)	missense	probably damaging	1.00
R2299:Limd1	UTSW	9	123,345,942 (GRCm39)	nonsense	probably null
R3791:Limd1	UTSW	9	123,309,439 (GRCm39)	missense	possibly damaging	0.92
R4453:Limd1	UTSW	9	123,309,359 (GRCm39)	missense	possibly damaging	0.52
R5979:Limd1	UTSW	9	123,308,479 (GRCm39)	missense	possibly damaging	0.96
R7493:Limd1	UTSW	9	123,308,748 (GRCm39)	missense	probably benign	0.00
R8101:Limd1	UTSW	9	123,329,216 (GRCm39)	nonsense	probably null
R8332:Limd1	UTSW	9	123,308,319 (GRCm39)	missense	probably damaging	1.00
R9060:Limd1	UTSW	9	123,309,514 (GRCm39)	missense	probably benign	0.08
R9679:Limd1	UTSW	9	123,308,457 (GRCm39)	missense	probably damaging	1.00
R9681:Limd1	UTSW	9	123,345,903 (GRCm39)	missense	possibly damaging	0.48
R9726:Limd1	UTSW	9	123,308,984 (GRCm39)	missense	probably benign	0.00
X0028:Limd1	UTSW	9	123,345,927 (GRCm39)	missense	probably damaging	0.99
Z1177:Limd1	UTSW	9	123,309,086 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- ACATGTATGAGGCCTCCAAGG -3'
(R):5'- AAGCAGGTCTCTGGGAACTC -3'

Sequencing Primer
(F):5'- AAGGATGGGCTCTTCCGG -3'
(R):5'- TGGGAACTCACAGGCCC -3'

Posted On

2014-08-25