Mutagenetix > Incidental Mutation

Incidental Mutation 'R6115:Lmx1b'

485055

Institutional Source

Beutler Lab

Gene Symbol

Lmx1b

Ensembl Gene

ENSMUSG00000038765

Gene Name

LIM homeobox transcription factor 1 beta

Synonyms

GENA 191, LMX1.2, Icst

MMRRC Submission

044264-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.908) question?

Stock #

R6115 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

33450977-33530620 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 33459118 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 145 (D145G)

Ref Sequence

ENSEMBL: ENSMUSP00000043616 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000041730]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000041730
AA Change: D145G

PolyPhen 2 Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000043616
Gene: ENSMUSG00000038765
AA Change: D145G

Domain	Start	End	E-Value	Type
LIM	32	83	4.48e-17	SMART
LIM	91	145	5.51e-17	SMART
low complexity region	151	172	N/A	INTRINSIC
HOX	196	258	1.51e-21	SMART
low complexity region	259	272	N/A	INTRINSIC
low complexity region	328	340	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137559

SMART Domains

Protein: ENSMUSP00000115288
Gene: ENSMUSG00000038765

Domain	Start	End	E-Value	Type
LIM	9	63	5.51e-17	SMART
low complexity region	69	90	N/A	INTRINSIC
low complexity region	95	118	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000176067
AA Change: D134G

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

SMART Domains

Protein: ENSMUSP00000134944
Gene: ENSMUSG00000038765
AA Change: D134G

Domain	Start	End	E-Value	Type
LIM	1	38	2.23e-3	SMART
LIM	46	100	5.51e-17	SMART
low complexity region	106	127	N/A	INTRINSIC
HOX	151	213	1.51e-21	SMART
low complexity region	214	227	N/A	INTRINSIC
low complexity region	290	302	N/A	INTRINSIC

Meta Mutation Damage Score

0.6996

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.5%
20x: 95.9%

Validation Efficiency

98% (51/52)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of LIM-homeodomain family of proteins containing two N-terminal zinc-binding LIM domains, 1 homeodomain, and a C-terminal glutamine-rich domain. It functions as a transcription factor, and is essential for the normal development of dorsal limb structures, the glomerular basement membrane, the anterior segment of the eye, and dopaminergic and serotonergic neurons. Mutations in this gene are associated with nail-patella syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit various skeletal, kidney, and eye defects. Pups also fail to suckle. Heterozygous mice with a homeodomain V265D mutation exhibit a variety of eye defects. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610040J01Rik	C	G	5: 64,055,317 (GRCm39)	Q18E	probably damaging	Het
Acsf3	T	A	8: 123,517,411 (GRCm39)	H402Q	probably damaging	Het
Adam34	T	G	8: 44,105,098 (GRCm39)	Q182H	probably benign	Het
Alx1	G	A	10: 102,864,304 (GRCm39)	P55L	possibly damaging	Het
Arhgef38	A	T	3: 132,838,374 (GRCm39)		probably null	Het
Ccdc102a	T	C	8: 95,629,999 (GRCm39)	N514S	probably benign	Het
Corin	T	A	5: 72,518,072 (GRCm39)	T317S	probably damaging	Het
Ctnna2	A	G	6: 77,613,822 (GRCm39)	V256A	probably benign	Het
Dhx29	A	T	13: 113,089,335 (GRCm39)		probably null	Het
Dnah2	C	A	11: 69,337,475 (GRCm39)	D3209Y	probably damaging	Het
Dnhd1	A	G	7: 105,363,194 (GRCm39)	T3919A	probably benign	Het
F7	T	A	8: 13,083,958 (GRCm39)	N214K	probably benign	Het
Fam3b	T	G	16: 97,276,568 (GRCm39)	Q177H	possibly damaging	Het
Fign	T	C	2: 63,809,654 (GRCm39)	I539V	probably benign	Het
Hc	T	G	2: 34,903,050 (GRCm39)	D1067A	probably damaging	Het
Herc6	A	G	6: 57,560,191 (GRCm39)	D77G	probably benign	Het
Hmg20a	A	T	9: 56,397,116 (GRCm39)	E305D	possibly damaging	Het
Il16	G	A	7: 83,301,775 (GRCm39)	Q116*	probably null	Het
Kif13a	T	A	13: 46,954,789 (GRCm39)	I648F	probably damaging	Het
Lactb	G	T	9: 66,874,969 (GRCm39)	N374K	possibly damaging	Het
Lrfn4	T	C	19: 4,663,937 (GRCm39)	D199G	probably damaging	Het
Lrrc49	A	T	9: 60,522,444 (GRCm39)	V307E	possibly damaging	Het
Magi1	A	C	6: 93,685,051 (GRCm39)	S776A	possibly damaging	Het
Mthfsl	T	A	9: 88,570,807 (GRCm39)	*147L	probably null	Het
Nsmce4a	G	T	7: 130,148,722 (GRCm39)	Q95K	probably benign	Het
Or1j15	A	T	2: 36,458,963 (GRCm39)	M118L	probably damaging	Het
Or4k37	A	G	2: 111,159,558 (GRCm39)	T265A	probably benign	Het
Or4k49	A	T	2: 111,494,987 (GRCm39)	K139*	probably null	Het
Or5b24	T	C	19: 12,912,948 (GRCm39)	V282A	possibly damaging	Het
Pcdha7	A	G	18: 37,107,788 (GRCm39)	E271G	probably damaging	Het
Pcdhga8	T	A	18: 37,860,596 (GRCm39)	F551I	possibly damaging	Het
Prpf31	T	C	7: 3,642,705 (GRCm39)		probably null	Het
Qrfpr	C	T	3: 36,236,742 (GRCm39)	V220I	possibly damaging	Het
Rnf170	T	C	8: 26,615,994 (GRCm39)	F95S	possibly damaging	Het
Scn9a	T	A	2: 66,393,973 (GRCm39)	Y200F	possibly damaging	Het
Sfpq	A	T	4: 126,915,141 (GRCm39)		probably null	Het
Slc9c1	A	T	16: 45,376,132 (GRCm39)	Y406F	probably damaging	Het
Stk32c	G	T	7: 138,700,628 (GRCm39)	Y200*	probably null	Het
Svil	A	G	18: 5,108,675 (GRCm39)	R1938G	probably damaging	Het
Sycp2	G	C	2: 177,990,038 (GRCm39)	R1403G	probably benign	Het
Tm9sf4	T	C	2: 153,024,409 (GRCm39)		probably null	Het
Tmc3	A	T	7: 83,264,170 (GRCm39)	M633L	possibly damaging	Het
Tmem163	T	C	1: 127,605,185 (GRCm39)	D61G	possibly damaging	Het
Unc5b	C	A	10: 60,613,325 (GRCm39)	A304S	probably benign	Het
Vmn2r106	G	A	17: 20,488,638 (GRCm39)	P587L	probably benign	Het
Vmn2r18	A	T	5: 151,508,462 (GRCm39)	S221T	possibly damaging	Het
Vmn2r85	T	G	10: 130,258,672 (GRCm39)	Y461S	probably damaging	Het
Yod1	T	C	1: 130,646,800 (GRCm39)	F226L	possibly damaging	Het
Zbtb4	T	C	11: 69,667,148 (GRCm39)	I151T	probably damaging	Het
Zfp110	A	T	7: 12,583,701 (GRCm39)	Q783L	probably damaging	Het

Other mutations in Lmx1b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01539:Lmx1b	APN	2	33,529,510 (GRCm39)	missense	possibly damaging	0.95
IGL01583:Lmx1b	APN	2	33,459,071 (GRCm39)	missense	probably benign	0.04
IGL02885:Lmx1b	APN	2	33,457,216 (GRCm39)	missense	probably benign	0.10
R1926:Lmx1b	UTSW	2	33,454,674 (GRCm39)	missense	probably damaging	1.00
R3056:Lmx1b	UTSW	2	33,457,297 (GRCm39)	nonsense	probably null
R3522:Lmx1b	UTSW	2	33,529,543 (GRCm39)	missense	probably benign	0.01
R3957:Lmx1b	UTSW	2	33,459,106 (GRCm39)	missense	probably damaging	0.99
R4888:Lmx1b	UTSW	2	33,454,802 (GRCm39)	missense	probably benign	0.01
R8254:Lmx1b	UTSW	2	33,455,126 (GRCm39)	missense
R8787:Lmx1b	UTSW	2	33,529,522 (GRCm39)	missense
RF032:Lmx1b	UTSW	2	33,530,501 (GRCm39)	nonsense	probably null
RF035:Lmx1b	UTSW	2	33,530,501 (GRCm39)	nonsense	probably null
RF038:Lmx1b	UTSW	2	33,530,521 (GRCm39)	start codon destroyed	probably null
RF043:Lmx1b	UTSW	2	33,530,521 (GRCm39)	start codon destroyed	probably null

Predicted Primers

PCR Primer
(F):5'- TGACACCTTGATGCTGGCTG -3'
(R):5'- TAGTGGCTTCCATCCTGAGCAG -3'

Sequencing Primer
(F):5'- TGGCCATGCACGGACATG -3'
(R):5'- GGTAGAGCTGACCACCCAAG -3'

Posted On

2017-08-16