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

GENA 191, LMX1.2, Icst

Accession Numbers

Essential gene?

Probably essential (E-score: 0.906) question?

Stock #

R3522 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

33450977-33530620 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 33529543 bp (GRCm39)

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
Ankrd35	A	G	3: 96,592,378 (GRCm39)	E888G	probably damaging	Het
Arhgef10	T	C	8: 15,004,918 (GRCm39)	F150S	probably damaging	Het
Atp10d	G	T	5: 72,396,500 (GRCm39)	R235L	probably benign	Het
Cacna1b	A	G	2: 24,653,055 (GRCm39)	V2A	possibly damaging	Het
Cand1	A	T	10: 119,075,102 (GRCm39)	L15Q	probably benign	Het
Cavin3	C	A	7: 105,130,350 (GRCm39)	G154V	probably benign	Het
Ccdc73	A	T	2: 104,821,830 (GRCm39)	D593V	probably damaging	Het
Cdk5rap2	T	C	4: 70,168,647 (GRCm39)	K161E	probably damaging	Het
Chil4	A	T	3: 106,111,056 (GRCm39)	N279K	probably benign	Het
Chst13	T	G	6: 90,295,245 (GRCm39)	D56A	probably damaging	Het
Cnn1	C	A	9: 22,010,664 (GRCm39)	H5N	probably benign	Het
Cpsf4l	T	A	11: 113,593,319 (GRCm39)	K88N	probably damaging	Het
Ctnnbl1	G	T	2: 157,713,113 (GRCm39)		probably null	Het
Dnah7a	A	C	1: 53,657,275 (GRCm39)	F834V	probably damaging	Het
Fbxo41	A	G	6: 85,461,163 (GRCm39)	S182P	probably benign	Het
Fkbp5	T	C	17: 28,634,970 (GRCm39)	T180A	probably benign	Het
Flg2	T	A	3: 93,127,334 (GRCm39)	I2082N	unknown	Het
Gm4968	A	G	6: 127,210,725 (GRCm39)		noncoding transcript	Het
Gpc5	T	A	14: 116,761,747 (GRCm39)	H612Q	probably benign	Het
Gsg1	A	T	6: 135,218,251 (GRCm39)	V212D	probably damaging	Het
Hipk1	A	G	3: 103,651,430 (GRCm39)	V1111A	probably damaging	Het
Hormad1	A	T	3: 95,483,596 (GRCm39)	Q136L	probably benign	Het
Ifi35	T	A	11: 101,348,511 (GRCm39)	S147R	probably benign	Het
Iqca1l	A	G	5: 24,754,624 (GRCm39)		probably null	Het
Iqgap3	C	T	3: 87,998,089 (GRCm39)	A282V	probably null	Het
Jmy	T	C	13: 93,590,558 (GRCm39)	D515G	probably damaging	Het
Kctd10	G	A	5: 114,512,984 (GRCm39)	R64C	probably damaging	Het
Kidins220	T	C	12: 25,040,757 (GRCm39)	V121A	probably damaging	Het
Lcn3	G	A	2: 25,656,133 (GRCm39)	V63M	possibly damaging	Het
Lrp1	T	C	10: 127,389,424 (GRCm39)	D3164G	probably damaging	Het
Mdh1b	C	T	1: 63,758,927 (GRCm39)	V222M	probably damaging	Het
Mst1	T	C	9: 107,958,702 (GRCm39)		probably benign	Het
Myo7b	C	A	18: 32,143,132 (GRCm39)	V189F	probably damaging	Het
Ndc1	T	C	4: 107,250,355 (GRCm39)	S533P	probably damaging	Het
Ndrg3	T	C	2: 156,785,947 (GRCm39)	D164G	probably damaging	Het
Nol11	C	T	11: 107,064,454 (GRCm39)	C500Y	possibly damaging	Het
Nsd3	A	G	8: 26,196,642 (GRCm39)	N1208D	probably benign	Het
Nup155	C	T	15: 8,186,162 (GRCm39)		probably benign	Het
Or5ak20	A	T	2: 85,183,347 (GRCm39)	C308S	probably benign	Het
Or6c38	A	G	10: 128,929,711 (GRCm39)	I44T	possibly damaging	Het
Or8b47	A	G	9: 38,435,081 (GRCm39)	T18A	probably damaging	Het
Or8b54	A	T	9: 38,687,016 (GRCm39)	D155V	possibly damaging	Het
Phf3	A	G	1: 30,844,684 (GRCm39)	L1425P	probably damaging	Het
Pla2r1	A	G	2: 60,279,250 (GRCm39)	Y777H	probably damaging	Het
Pld1	A	G	3: 28,085,396 (GRCm39)	E184G	probably damaging	Het
Plxna1	T	C	6: 89,314,335 (GRCm39)		probably null	Het
Ptgfrn	T	C	3: 100,950,718 (GRCm39)	E865G	probably damaging	Het
Ptpn13	G	T	5: 103,737,720 (GRCm39)		probably benign	Het
Pygb	G	T	2: 150,670,473 (GRCm39)	V763F	probably benign	Het
Ros1	A	C	10: 51,967,091 (GRCm39)	Y1705*	probably null	Het
Sec61a2	A	G	2: 5,898,027 (GRCm39)	F5L	probably benign	Het
Skint5	A	G	4: 113,614,102 (GRCm39)		probably null	Het
Sntg2	A	G	12: 30,362,566 (GRCm39)	V60A	probably damaging	Het
Sppl2a	A	G	2: 126,762,242 (GRCm39)	C280R	possibly damaging	Het
Srrm4	A	C	5: 116,584,603 (GRCm39)	M1R	probably null	Het
Sult1c2	T	C	17: 54,279,043 (GRCm39)	E91G	probably damaging	Het
Themis2	C	G	4: 132,512,906 (GRCm39)	R440P	probably damaging	Het
Tmem229a	A	G	6: 24,955,058 (GRCm39)	L232P	probably benign	Het
Trappc1	T	C	11: 69,215,248 (GRCm39)	F43L	probably damaging	Het
Trappc11	A	T	8: 47,951,708 (GRCm39)	Y982N	possibly damaging	Het
Trpv6	A	T	6: 41,604,339 (GRCm39)	M139K	probably damaging	Het
Txnrd3	A	G	6: 89,640,057 (GRCm39)		probably null	Het
Vmn1r184	T	A	7: 25,967,008 (GRCm39)	Y251*	probably null	Het
Vmn1r216	A	G	13: 23,283,544 (GRCm39)	N76D	possibly damaging	Het
Vmn1r71	C	A	7: 10,481,792 (GRCm39)	V233F	probably benign	Het
Vps13a	A	C	19: 16,743,857 (GRCm39)		probably benign	Het
Vwa5b2	A	G	16: 20,420,358 (GRCm39)	S756G	probably damaging	Het
Wdr36	T	A	18: 32,994,538 (GRCm39)		probably null	Het
Wdr86	A	G	5: 24,923,305 (GRCm39)	V129A	probably benign	Het
Zfyve9	A	G	4: 108,576,940 (GRCm39)	L47S	probably benign	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
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
R6115:Lmx1b	UTSW	2	33,459,118 (GRCm39)	missense	probably damaging	0.96
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'- CGGCTGGAAGGAGATGATTC -3'
(R):5'- TTACGGAAAGGAGCGTGCTG -3'

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

Posted On

2015-02-18