Mutagenetix > Incidental Mutation

Incidental Mutation 'R9060:Limd1'

688935

Institutional Source

Beutler Lab

Gene Symbol

Limd1

Ensembl Gene

ENSMUSG00000025239

Gene Name

LIM domains containing 1

Synonyms

D9Ertd192e

MMRRC Submission

068886-MU

Accession Numbers

Essential gene?

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

Stock #

R9060 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

123307771-123350617 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 123309514 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 404 (S404R)

Ref Sequence

ENSEMBL: ENSMUSP00000026269 (fasta)

Gene Model

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

AlphaFold

Q9QXD8

Predicted Effect

probably benign
Transcript: ENSMUST00000026269
AA Change: S404R

PolyPhen 2 Score 0.078 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000026269
Gene: ENSMUSG00000025239
AA Change: S404R

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

probably benign
Transcript: ENSMUST00000217639

Meta Mutation Damage Score

0.0846

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

98% (54/55)

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: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acat3	A	C	17: 13,145,293 (GRCm39)	V295G		Het
Agfg1	T	C	1: 82,872,254 (GRCm39)	V529A	possibly damaging	Het
Ap1g2	G	A	14: 55,337,887 (GRCm39)	P667L	probably benign	Het
Arhgap29	T	A	3: 121,783,973 (GRCm39)	S176T	probably damaging	Het
Casq2	A	G	3: 102,052,619 (GRCm39)	D377G	unknown	Het
Ccdc14	T	C	16: 34,517,486 (GRCm39)	L104P	probably benign	Het
Cep104	T	C	4: 154,074,281 (GRCm39)	I511T	probably damaging	Het
Cgn	A	G	3: 94,687,165 (GRCm39)	Y46H	probably damaging	Het
Cilp	T	C	9: 65,186,302 (GRCm39)	V799A	probably benign	Het
Col6a1	A	G	10: 76,557,711 (GRCm39)	V175A	probably benign	Het
Dclk1	C	A	3: 55,163,575 (GRCm39)	D222E	probably benign	Het
Dnah10	G	T	5: 124,905,141 (GRCm39)	C4058F	probably damaging	Het
Dnai4	A	T	4: 102,947,750 (GRCm39)	D175E	probably benign	Het
Elmod3	A	T	6: 72,543,790 (GRCm39)	Y334N	probably damaging	Het
Enah	C	A	1: 181,749,817 (GRCm39)	A341S	probably damaging	Het
Eomes	T	C	9: 118,311,364 (GRCm39)	*396Q	probably null	Het
Epb41l1	T	A	2: 156,345,679 (GRCm39)	Y227*	probably null	Het
Epha5	A	T	5: 84,218,977 (GRCm39)	D765E	probably benign	Het
Fat3	T	C	9: 15,910,782 (GRCm39)	N1740S	possibly damaging	Het
Fhip2a	C	T	19: 57,361,450 (GRCm39)	H125Y	probably damaging	Het
Galnt9	G	A	5: 110,737,710 (GRCm39)	R222H	possibly damaging	Het
Gm19410	A	G	8: 36,269,480 (GRCm39)	D1105G	probably damaging	Het
Hoxa13	T	A	6: 52,236,897 (GRCm39)	Y121F	probably damaging	Het
Hps4	G	A	5: 112,525,905 (GRCm39)	S642N	possibly damaging	Het
Jag1	T	G	2: 136,931,204 (GRCm39)	T643P	probably damaging	Het
Micall2	A	T	5: 139,705,035 (GRCm39)	S100T	probably damaging	Het
Miga2	T	A	2: 30,271,735 (GRCm39)	L419Q	probably damaging	Het
Ms4a13	A	C	19: 11,168,950 (GRCm39)	I25S		Het
Nnmt	T	C	9: 48,503,367 (GRCm39)	T220A	probably benign	Het
Nrg3	G	A	14: 38,734,052 (GRCm39)	T278I	probably damaging	Het
Nup98	A	G	7: 101,783,895 (GRCm39)	W1146R	probably damaging	Het
Or13a28	T	G	7: 140,217,695 (GRCm39)	L27R		Het
Or5m10	T	C	2: 85,717,920 (GRCm39)	Y259H	probably benign	Het
Pacsin3	T	C	2: 91,091,557 (GRCm39)	F85L	probably benign	Het
Padi4	T	A	4: 140,477,953 (GRCm39)	D465V	probably damaging	Het
Pakap	A	G	4: 57,855,412 (GRCm39)	E247G	probably damaging	Het
Pclo	A	T	5: 14,726,599 (GRCm39)	Y1819F	unknown	Het
Pitpnm1	C	A	19: 4,156,869 (GRCm39)	T464N	probably damaging	Het
Rnf214	T	C	9: 45,809,772 (GRCm39)		probably benign	Het
Rrs1	G	A	1: 9,616,677 (GRCm39)	G310D	probably damaging	Het
Rsf1	CGGCGGCGG	CGGCGGCGGGGGCGGCGG	7: 97,229,130 (GRCm39)		probably benign	Het
Slc35e3	A	G	10: 117,581,688 (GRCm39)		probably null	Het
Slc47a2	T	C	11: 61,227,699 (GRCm39)	I142V	probably benign	Het
Slc8a3	G	A	12: 81,260,852 (GRCm39)	R626C	probably benign	Het
Spart	T	C	3: 55,032,275 (GRCm39)	S370P	probably benign	Het
Spata31e1	G	A	13: 49,940,087 (GRCm39)	S541F	probably damaging	Het
Spmap2	G	T	10: 79,420,571 (GRCm39)	L189I	probably damaging	Het
Tle3	T	A	9: 61,282,821 (GRCm39)	M67K	probably damaging	Het
Tmco1	C	T	1: 167,136,132 (GRCm39)		probably benign	Het
Ubr3	T	A	2: 69,839,489 (GRCm39)	Y1534*	probably null	Het
Usp13	T	C	3: 32,965,812 (GRCm39)		probably null	Het
Vmn2r97	T	C	17: 19,134,585 (GRCm39)	M1T	probably null	Het
Zc3h7a	G	A	16: 10,969,047 (GRCm39)	T438I	probably damaging	Het
Zfhx2	A	G	14: 55,311,803 (GRCm39)	V297A	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
R1612:Limd1	UTSW	9	123,347,219 (GRCm39)	missense	probably damaging	1.00
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
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'- ATGGGCCCAAGTCTTACCTC -3'
(R):5'- TCCAAAGCATCTTACTTACCGAAG -3'

Sequencing Primer
(F):5'- ATTATCCTCGACAGCTGGCAAGG -3'
(R):5'- ACCGAAGTAGTCCGCTTTG -3'

Posted On

2021-11-19