Mutagenetix > Incidental Mutation

Incidental Mutation 'R3522:Lmx1b'

267508

Institutional Source

Beutler Lab

Gene Symbol

Lmx1b

Ensembl Gene

ENSMUSG00000038765

Gene Name

LIM homeobox transcription factor 1 beta

Synonyms

Icst, LMX1.2, GENA 191

Accession Numbers

Essential gene?

Probably essential (E-score: 0.926) question?

Stock #

R3522 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

33560965-33640511 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 33639531 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Phenylalanine at position 72 (Y72F)

Ref Sequence

ENSEMBL: ENSMUSP00000043616 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000041730
AA Change: Y72F

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)

SMART Domains

Protein: ENSMUSP00000043616
Gene: ENSMUSG00000038765
AA Change: Y72F

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: ENSMUST00000147294

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152118

Predicted Effect

unknown
Transcript: ENSMUST00000176067
AA Change: Y61F

SMART Domains

Protein: ENSMUSP00000134944
Gene: ENSMUSG00000038765
AA Change: Y61F

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

0.0929

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 97.2%
20x: 94.8%

Validation Efficiency

100% (72/72)

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4931409K22Rik	A	G	5: 24,549,626		probably null	Het
Ankrd35	A	G	3: 96,685,062	E888G	probably damaging	Het
Arhgef10	T	C	8: 14,954,918	F150S	probably damaging	Het
Atp10d	G	T	5: 72,239,157	R235L	probably benign	Het
Cacna1b	A	G	2: 24,763,043	V2A	possibly damaging	Het
Cand1	A	T	10: 119,239,197	L15Q	probably benign	Het
Cavin3	C	A	7: 105,481,143	G154V	probably benign	Het
Ccdc73	A	T	2: 104,991,485	D593V	probably damaging	Het
Cdk5rap2	T	C	4: 70,250,410	K161E	probably damaging	Het
Chil4	A	T	3: 106,203,740	N279K	probably benign	Het
Chst13	T	G	6: 90,318,263	D56A	probably damaging	Het
Cnn1	C	A	9: 22,099,368	H5N	probably benign	Het
Cpsf4l	T	A	11: 113,702,493	K88N	probably damaging	Het
Ctnnbl1	G	T	2: 157,871,193		probably null	Het
Dnah7a	A	C	1: 53,618,116	F834V	probably damaging	Het
Fbxo41	A	G	6: 85,484,181	S182P	probably benign	Het
Fkbp5	T	C	17: 28,415,996	T180A	probably benign	Het
Flg2	T	A	3: 93,220,027	I2082N	unknown	Het
Gm4968	A	G	6: 127,233,762		noncoding transcript	Het
Gpc5	T	A	14: 116,524,335	H612Q	probably benign	Het
Gsg1	A	T	6: 135,241,253	V212D	probably damaging	Het
Hipk1	A	G	3: 103,744,114	V1111A	probably damaging	Het
Hormad1	A	T	3: 95,576,285	Q136L	probably benign	Het
Ifi35	T	A	11: 101,457,685	S147R	probably benign	Het
Iqgap3	C	T	3: 88,090,782	A282V	probably null	Het
Jmy	T	C	13: 93,454,050	D515G	probably damaging	Het
Kctd10	G	A	5: 114,374,923	R64C	probably damaging	Het
Kidins220	T	C	12: 24,990,758	V121A	probably damaging	Het
Lcn3	G	A	2: 25,766,121	V63M	possibly damaging	Het
Lrp1	T	C	10: 127,553,555	D3164G	probably damaging	Het
Mdh1b	C	T	1: 63,719,768	V222M	probably damaging	Het
Mst1	T	C	9: 108,081,503		probably benign	Het
Myo7b	C	A	18: 32,010,079	V189F	probably damaging	Het
Ndc1	T	C	4: 107,393,158	S533P	probably damaging	Het
Ndrg3	T	C	2: 156,944,027	D164G	probably damaging	Het
Nol11	C	T	11: 107,173,628	C500Y	possibly damaging	Het
Nsd3	A	G	8: 25,706,614	N1208D	probably benign	Het
Nup155	C	T	15: 8,156,678		probably benign	Het
Olfr768	A	G	10: 129,093,842	I44T	possibly damaging	Het
Olfr911-ps1	A	G	9: 38,523,785	T18A	probably damaging	Het
Olfr921	A	T	9: 38,775,720	D155V	possibly damaging	Het
Olfr988	A	T	2: 85,353,003	C308S	probably benign	Het
Phf3	A	G	1: 30,805,603	L1425P	probably damaging	Het
Pla2r1	A	G	2: 60,448,906	Y777H	probably damaging	Het
Pld1	A	G	3: 28,031,247	E184G	probably damaging	Het
Plxna1	T	C	6: 89,337,353		probably null	Het
Ptgfrn	T	C	3: 101,043,402	E865G	probably damaging	Het
Ptpn13	G	T	5: 103,589,854		probably benign	Het
Pygb	G	T	2: 150,828,553	V763F	probably benign	Het
Ros1	A	C	10: 52,090,995	Y1705*	probably null	Het
Sec61a2	A	G	2: 5,893,216	F5L	probably benign	Het
Skint5	A	G	4: 113,756,905		probably null	Het
Sntg2	A	G	12: 30,312,567	V60A	probably damaging	Het
Sppl2a	A	G	2: 126,920,322	C280R	possibly damaging	Het
Srrm4	A	C	5: 116,446,544	M1R	probably null	Het
Sult1c1	T	C	17: 53,972,015	E91G	probably damaging	Het
Themis2	C	G	4: 132,785,595	R440P	probably damaging	Het
Tmem229a	A	G	6: 24,955,059	L232P	probably benign	Het
Trappc1	T	C	11: 69,324,422	F43L	probably damaging	Het
Trappc11	A	T	8: 47,498,673	Y982N	possibly damaging	Het
Trpv6	A	T	6: 41,627,405	M139K	probably damaging	Het
Txnrd3	A	G	6: 89,663,075		probably null	Het
Vmn1r184	T	A	7: 26,267,583	Y251*	probably null	Het
Vmn1r216	A	G	13: 23,099,374	N76D	possibly damaging	Het
Vmn1r71	C	A	7: 10,747,865	V233F	probably benign	Het
Vps13a	A	C	19: 16,766,493		probably benign	Het
Vwa5b2	A	G	16: 20,601,608	S756G	probably damaging	Het
Wdr36	T	A	18: 32,861,485		probably null	Het
Wdr86	A	G	5: 24,718,307	V129A	probably benign	Het
Zfyve9	A	G	4: 108,719,743	L47S	probably benign	Het

Other mutations in Lmx1b

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01539:Lmx1b	APN	2	33639498	missense	possibly damaging	0.95
IGL01583:Lmx1b	APN	2	33569059	missense	probably benign	0.04
IGL02885:Lmx1b	APN	2	33567204	missense	probably benign	0.10
R1926:Lmx1b	UTSW	2	33564662	missense	probably damaging	1.00
R3056:Lmx1b	UTSW	2	33567285	nonsense	probably null
R3957:Lmx1b	UTSW	2	33569094	missense	probably damaging	0.99
R4888:Lmx1b	UTSW	2	33564790	missense	probably benign	0.01
R6115:Lmx1b	UTSW	2	33569106	missense	probably damaging	0.96
R8254:Lmx1b	UTSW	2	33565114	missense
R8787:Lmx1b	UTSW	2	33639510	missense
RF032:Lmx1b	UTSW	2	33640489	nonsense	probably null
RF035:Lmx1b	UTSW	2	33640489	nonsense	probably null
RF038:Lmx1b	UTSW	2	33640509	start codon destroyed	probably null
RF043:Lmx1b	UTSW	2	33640509	start codon destroyed	probably null

Predicted Primers

PCR Primer
(F):5'- CGGCTGGAAGGAGATGATTC -3'
(R):5'- TTACGGAAAGGAGCGTGCTG -3'

Sequencing Primer
(F):5'- TGGAAGGAGATGATTCGCCCC -3'
(R):5'- AAGGAGCGTGCTGTCTAGG -3'

Posted On

2015-02-18