Mutagenetix > Incidental Mutation

Incidental Mutation 'R1612:Limd1'

176875

Institutional Source

Beutler Lab

Gene Symbol

Limd1

Ensembl Gene

ENSMUSG00000025239

Gene Name

LIM domains containing 1

Synonyms

D9Ertd192e

MMRRC Submission

039649-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.382) question?

Stock #

R1612 (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 123347219 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 620 (Y620C)

Ref Sequence

ENSEMBL: ENSMUSP00000026269 (fasta)

Gene Model

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

AlphaFold

Q9QXD8

Predicted Effect

probably damaging
Transcript: ENSMUST00000026269
AA Change: Y620C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000026269
Gene: ENSMUSG00000025239
AA Change: Y620C

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: ENSMUST00000213278

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000214309

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000216352

Predicted Effect

probably benign
Transcript: ENSMUST00000217639

Meta Mutation Damage Score

0.9604

Coding Region Coverage

1x: 99.2%
3x: 98.4%
10x: 96.6%
20x: 93.6%

Validation Efficiency

97% (69/71)

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: 64 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930579G24Rik	A	G	3: 79,538,451 (GRCm39)	T66A	probably benign	Het
Actb	A	G	5: 142,891,350 (GRCm39)	F31S	probably damaging	Het
Adamts7	T	C	9: 90,070,750 (GRCm39)	S624P	possibly damaging	Het
Adh7	T	C	3: 137,934,642 (GRCm39)	I355T	possibly damaging	Het
Arhgef40	A	G	14: 52,241,538 (GRCm39)	E106G	probably damaging	Het
Brd10	A	G	19: 29,695,245 (GRCm39)	V1483A	possibly damaging	Het
Cabp7	T	C	11: 4,689,198 (GRCm39)	D149G	probably damaging	Het
Cass4	A	T	2: 172,268,998 (GRCm39)	Q362L	possibly damaging	Het
Cd14	G	A	18: 36,858,718 (GRCm39)	Q246*	probably null	Het
Cdr2l	A	C	11: 115,284,232 (GRCm39)	E189D	probably benign	Het
Col6a6	A	G	9: 105,654,748 (GRCm39)	V991A	probably damaging	Het
Coq7	A	G	7: 118,109,134 (GRCm39)	W305R	unknown	Het
Cracr2a	G	T	6: 127,580,892 (GRCm39)	G23*	probably null	Het
Dclk2	C	T	3: 86,712,946 (GRCm39)	R503Q	possibly damaging	Het
Epcam	T	C	17: 87,947,366 (GRCm39)	L40P	possibly damaging	Het
Eps8	G	A	6: 137,477,616 (GRCm39)	P531S	probably benign	Het
Faap100	C	A	11: 120,267,914 (GRCm39)	L286F	probably damaging	Het
Fabp3	C	T	4: 130,206,180 (GRCm39)	T57I	probably benign	Het
Fbn2	A	T	18: 58,194,824 (GRCm39)	C1446S	probably damaging	Het
Fmo3	A	G	1: 162,795,454 (GRCm39)	V127A	probably damaging	Het
Frem3	A	G	8: 81,341,490 (GRCm39)	D1261G	probably damaging	Het
Gabbr1	A	G	17: 37,381,561 (GRCm39)	Y775C	probably damaging	Het
Gbp11	G	T	5: 105,474,462 (GRCm39)	Q405K	possibly damaging	Het
Gdi2	T	A	13: 3,610,051 (GRCm39)	V260E	probably benign	Het
Glp2r	C	T	11: 67,633,033 (GRCm39)	V98M	possibly damaging	Het
Gm13741	T	C	2: 87,486,431 (GRCm39)	Y278C	probably damaging	Het
Gm7732	G	A	17: 21,350,177 (GRCm39)		noncoding transcript	Het
Gnptab	T	A	10: 88,264,344 (GRCm39)		probably null	Het
Hbs1l	T	G	10: 21,234,734 (GRCm39)	F596V	probably damaging	Het
Krt78	A	T	15: 101,860,279 (GRCm39)		probably null	Het
Krt87	A	T	15: 101,386,092 (GRCm39)	L223Q	probably benign	Het
Lcmt2	T	C	2: 120,969,601 (GRCm39)	Y274C	probably damaging	Het
Lvrn	G	T	18: 47,027,770 (GRCm39)	A862S	probably damaging	Het
Map4k2	A	G	19: 6,393,371 (GRCm39)	E206G	probably damaging	Het
Med16	A	G	10: 79,735,079 (GRCm39)	S461P	probably damaging	Het
Mrfap1	C	A	5: 36,953,706 (GRCm39)	A78S	probably damaging	Het
Nav2	T	A	7: 49,220,959 (GRCm39)	N1715K	probably damaging	Het
Ndc1	A	G	4: 107,252,265 (GRCm39)		probably benign	Het
Ngly1	G	T	14: 16,290,867 (GRCm38)	G450*	probably null	Het
Or13c25	T	A	4: 52,911,501 (GRCm39)	M98L	probably benign	Het
Or5k3	T	C	16: 58,969,987 (GRCm39)	M258T	probably benign	Het
Pde3b	T	A	7: 114,118,791 (GRCm39)	Y643*	probably null	Het
Pdilt	T	G	7: 119,086,198 (GRCm39)	N506H	possibly damaging	Het
Pear1	C	T	3: 87,659,160 (GRCm39)		probably null	Het
Pfkp	A	T	13: 6,638,625 (GRCm39)	M582K	probably damaging	Het
Pigl	T	A	11: 62,403,820 (GRCm39)	F251I	probably benign	Het
Plk3	A	G	4: 116,989,004 (GRCm39)	Y252H	probably damaging	Het
Prdx3	A	G	19: 60,862,872 (GRCm39)	S12P	possibly damaging	Het
Prkag2	T	C	5: 25,082,026 (GRCm39)	I96V	probably benign	Het
Pwwp3a	T	A	10: 80,068,889 (GRCm39)		probably benign	Het
Rgs3	G	A	4: 62,544,172 (GRCm39)	V146M	probably damaging	Het
Serpinh1	T	C	7: 98,998,138 (GRCm39)	D164G	probably damaging	Het
Slc35d2	T	C	13: 64,259,324 (GRCm39)		probably benign	Het
Slc6a6	A	G	6: 91,718,008 (GRCm39)	N316D	probably damaging	Het
Snx14	A	T	9: 88,258,958 (GRCm39)	M973K	possibly damaging	Het
Sptan1	C	G	2: 29,893,348 (GRCm39)	R1126G	probably damaging	Het
Stpg3	T	C	2: 25,103,866 (GRCm39)	T157A	probably benign	Het
Tmem39b	A	T	4: 129,580,715 (GRCm39)	M259K	possibly damaging	Het
Tomm40l	A	T	1: 171,049,471 (GRCm39)		probably null	Het
Tsen34	G	T	7: 3,698,395 (GRCm39)	G180W	probably damaging	Het
Ube2l6	C	T	2: 84,636,717 (GRCm39)	R54W	probably damaging	Het
Vdac1	A	T	11: 52,274,897 (GRCm39)	T182S	probably benign	Het
Wdr3	T	C	3: 100,058,515 (GRCm39)		probably benign	Het
Wsb1	T	A	11: 79,139,411 (GRCm39)	Q95L	probably benign	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
R2009:Limd1	UTSW	9	123,308,564 (GRCm39)	missense	probably benign
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'- TCTGACATCCTAGAAGACCACATGGC -3'
(R):5'- TCTTTACCCAGGAGGGAACGACAC -3'

Sequencing Primer
(F):5'- ACTCTCACATCCACTGAATCTGG -3'
(R):5'- TATGTAAGTGACAGTGTAGCCCC -3'

Posted On

2014-04-24