Mutagenetix > Incidental Mutation

Incidental Mutation 'R3791:Limd1'

272543

Institutional Source

Beutler Lab

Gene Symbol

Limd1

Ensembl Gene

ENSMUSG00000025239

Gene Name

LIM domains containing 1

Synonyms

D9Ertd192e

Accession Numbers

Essential gene?

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

Stock #

R3791 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

123307771-123350617 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 123309439 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Arginine at position 379 (S379R)

Ref Sequence

ENSEMBL: ENSMUSP00000026269 (fasta)

Gene Model

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

AlphaFold

Q9QXD8

Predicted Effect

possibly damaging
Transcript: ENSMUST00000026269
AA Change: S379R

PolyPhen 2 Score 0.915 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000026269
Gene: ENSMUSG00000025239
AA Change: S379R

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

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.0%
20x: 93.9%

Validation Efficiency

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: 43 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A630073D07Rik	AGGTGGTGGTGGTGGTGGTGGTGG	AGGTGGTGGTGGTGGTGGTGG	6: 132,603,479 (GRCm39)		probably benign	Het
A930009A15Rik	A	T	10: 115,414,194 (GRCm39)		probably benign	Het
Adgrv1	T	C	13: 81,741,221 (GRCm39)	Y81C	probably damaging	Het
Alx3	A	T	3: 107,508,022 (GRCm39)	Y177F	probably damaging	Het
C6	A	G	15: 4,764,717 (GRCm39)	T138A	probably benign	Het
Cacna2d3	T	C	14: 28,905,538 (GRCm39)	M410V	probably benign	Het
Ccn4	A	G	15: 66,791,137 (GRCm39)	Y313C	probably damaging	Het
Celsr3	G	A	9: 108,719,751 (GRCm39)	R2450H	probably benign	Het
Cnrip1	C	T	11: 17,004,845 (GRCm39)		probably benign	Het
Col6a5	A	C	9: 105,741,868 (GRCm39)	D2350E	probably damaging	Het
Cyp4a12b	A	G	4: 115,292,167 (GRCm39)	I407V	probably benign	Het
Gpx4	A	G	10: 79,892,023 (GRCm39)	I245V	probably benign	Het
H2-K2	A	G	17: 34,218,499 (GRCm39)	I139T	probably benign	Het
Hmgcl	A	G	4: 135,687,298 (GRCm39)	K191R	probably benign	Het
Hpdl	A	G	4: 116,677,729 (GRCm39)	V244A	possibly damaging	Het
Hpse	A	G	5: 100,840,104 (GRCm39)	S338P	probably damaging	Het
Ifi203	T	C	1: 173,762,646 (GRCm39)	K162R	possibly damaging	Het
Kit	A	G	5: 75,799,810 (GRCm39)	N514S	probably damaging	Het
Kmt2d	G	A	15: 98,742,030 (GRCm39)		probably benign	Het
Llph	A	G	10: 120,064,060 (GRCm39)	K59E	probably benign	Het
Lrrc7	T	A	3: 157,869,593 (GRCm39)	M709L	probably benign	Het
Muc5ac	A	G	7: 141,352,238 (GRCm39)	S665G	probably benign	Het
Ncapd3	C	T	9: 26,963,931 (GRCm39)	H524Y	probably benign	Het
Nfix	CAAAAA	CAAAA	8: 85,442,876 (GRCm39)		probably null	Het
Or51s1	T	C	7: 102,558,239 (GRCm39)	D269G	probably benign	Het
Phtf2	T	C	5: 20,987,296 (GRCm39)	E400G	probably damaging	Het
Pkd1l3	T	C	8: 110,362,949 (GRCm39)	V1080A	probably damaging	Het
Plch1	A	T	3: 63,606,944 (GRCm39)	H1007Q	probably benign	Het
Prr5	T	C	15: 84,565,417 (GRCm39)	S3P	probably damaging	Het
Qtrt1	G	A	9: 21,330,636 (GRCm39)	D279N	probably damaging	Het
Rundc1	G	A	11: 101,325,027 (GRCm39)	A578T	probably damaging	Het
Shc4	A	T	2: 125,565,251 (GRCm39)	V16E	probably damaging	Het
Sik3	A	T	9: 46,106,120 (GRCm39)	L329F	possibly damaging	Het
Slc36a3	A	G	11: 55,015,982 (GRCm39)	S391P	possibly damaging	Het
Smad1	C	A	8: 80,066,399 (GRCm39)	R426L	probably damaging	Het
Tent4b	G	A	8: 88,969,957 (GRCm39)	E210K	probably damaging	Het
Thrap3	A	T	4: 126,061,293 (GRCm39)	N820K	possibly damaging	Het
Tnrc6b	T	C	15: 80,807,841 (GRCm39)	S1598P	probably damaging	Het
Ttn	T	C	2: 76,545,168 (GRCm39)	I32645V	probably damaging	Het
Zfp266	A	C	9: 20,410,777 (GRCm39)	Y467D	probably damaging	Het
Zfp526	T	A	7: 24,925,628 (GRCm39)	M629K	probably damaging	Het
Zfp788	A	T	7: 41,299,152 (GRCm39)	H596L	probably damaging	Het
Zhx3	A	G	2: 160,622,368 (GRCm39)	W600R	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
R2009:Limd1	UTSW	9	123,308,564 (GRCm39)	missense	probably benign
R2299:Limd1	UTSW	9	123,345,942 (GRCm39)	nonsense	probably null
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'- GATATGAGGCTTCAGGCAGG -3'
(R):5'- GTGAGGGCTTCCAACTTCAATTC -3'

Sequencing Primer
(F):5'- TTCAGGCAGGGTCTTCAAAC -3'
(R):5'- CAACTTCAATTCCGCAGTGG -3'

Posted On

2015-03-25