Mutagenetix > Incidental Mutation

Incidental Mutation 'R9269:Lmx1a'

702718

Institutional Source

Beutler Lab

Gene Symbol

Lmx1a

Ensembl Gene

ENSMUSG00000026686

Gene Name

LIM homeobox transcription factor 1 alpha

Synonyms

shaker short-tail, Lmx1.1

MMRRC Submission

Accession Numbers

Essential gene?

Probably essential (E-score: 0.881) question?

Stock #

R9269 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

167689237-167848741 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 167830625 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Glutamine at position 192 (H192Q)

Ref Sequence

ENSEMBL: ENSMUSP00000028003 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028003] [ENSMUST00000111377]

AlphaFold

Q9JKU8

Predicted Effect

probably benign
Transcript: ENSMUST00000028003
AA Change: H192Q

PolyPhen 2 Score 0.032 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000028003
Gene: ENSMUSG00000026686
AA Change: H192Q

Domain	Start	End	E-Value	Type
LIM	34	85	2.87e-15	SMART
LIM	93	147	3.39e-17	SMART
HOX	195	257	2.62e-21	SMART
low complexity region	337	350	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000111377
AA Change: H192Q

PolyPhen 2 Score 0.032 (Sensitivity: 0.95; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000107008
Gene: ENSMUSG00000026686
AA Change: H192Q

Domain	Start	End	E-Value	Type
LIM	34	85	2.87e-15	SMART
LIM	93	147	3.39e-17	SMART
HOX	195	257	2.62e-21	SMART
low complexity region	337	350	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.6%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a homeodomain and LIM-domain containing protein. The encoded protein is a transcription factor that acts as a positive regulator of insulin gene transcription. This gene also plays a role in the development of dopamine producing neurons during embryogenesis. Mutations in this gene are associated with an increased risk of developing Parkinson's disease. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]
PHENOTYPE: Mutations in the dreher locus produce neurological and skeletal abnormalities, inner ear defects, and belly spotting. Deafness and hypoplasia of Mullerian duct derivatives are also reported for some alleles. Homozygous null mice have fewer dopaminergic neurons. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2410089E03Rik	A	C	15: 8,219,016	Q1683P	probably damaging	Het
A2m	T	C	6: 121,660,906	S845P	probably benign	Het
Actn1	T	A	12: 80,172,971	N709Y	probably benign	Het
Alox5ap	A	G	5: 149,279,196	Y64C	probably damaging	Het
Anapc4	T	A	5: 52,861,278	S521T	possibly damaging	Het
Ap3b1	C	A	13: 94,404,062	P164Q	probably damaging	Het
Arhgef26	A	G	3: 62,340,499	N335D	probably damaging	Het
Arrdc2	G	A	8: 70,836,329	A354V	probably benign	Het
Atg2b	A	G	12: 105,652,100	S898P	probably damaging	Het
Atxn1	T	A	13: 45,557,204	T751S	probably benign	Het
Begain	T	A	12: 109,033,193	R551W	possibly damaging	Het
Borcs8	C	A	8: 70,141,871	D15E	probably benign	Het
Btbd16	C	T	7: 130,815,786	R344C	probably damaging	Het
Card11	A	T	5: 140,906,761	M183K	probably damaging	Het
Cldn3	T	C	5: 134,986,725	L94P	probably damaging	Het
Clvs2	A	T	10: 33,543,426	Y211N	probably damaging	Het
Col15a1	G	C	4: 47,288,200		probably benign	Het
Cop1	C	T	1: 159,288,983	P409L	probably benign	Het
Crhbp	C	A	13: 95,436,516	A241S	probably benign	Het
Cyfip1	C	A	7: 55,907,431	S794*	probably null	Het
D17Wsu92e	A	C	17: 27,786,075	Y169*	probably null	Het
Dlg5	T	A	14: 24,192,813	H172L	probably damaging	Het
Doc2a	T	A	7: 126,850,987	I199N	probably benign	Het
Dock3	T	C	9: 106,941,323	T1191A	probably benign	Het
Efcab8	G	C	2: 153,804,941	V397L	unknown	Het
Fcgr1	C	T	3: 96,285,838	R281H	probably benign	Het
Fndc10	T	C	4: 155,694,748	V83A	possibly damaging	Het
Galnt2	T	A	8: 124,338,463	I444K	probably benign	Het
Gcnt3	T	C	9: 70,034,008	Y426C	probably damaging	Het
Gm5580	C	T	6: 116,552,356	T398I	probably damaging	Het
Gtpbp1	C	T	15: 79,717,654	R533C	probably damaging	Het
Hid1	T	C	11: 115,361,676	E60G	probably damaging	Het
Ighv1-81	A	T	12: 115,920,541	L30Q	possibly damaging	Het
Ighv5-8	TATATATATATATATATATATA	TATATATATATATATATATATATA	12: 113,654,945		probably null	Het
Klf10	A	G	15: 38,297,758	L44P	probably damaging	Het
Lamc3	T	C	2: 31,923,005	V1001A	probably benign	Het
Lamc3	C	A	2: 31,928,896	S1211*	probably null	Het
Nkx2-4	T	C	2: 147,084,264	H226R	possibly damaging	Het
Olfr1046	T	C	2: 86,216,903	H269R	probably damaging	Het
Olfr1179	G	A	2: 88,402,242	R231C	probably benign	Het
Olfr1240	T	A	2: 89,439,932	M116L	probably damaging	Het
Olfr1281	T	C	2: 111,328,952	F178L	probably damaging	Het
Olfr1453	T	C	19: 13,027,630	H233R	probably benign	Het
Olfr1468-ps1	A	T	19: 13,375,640	N226I	unknown	Het
Olfr472	T	A	7: 107,903,320	I201N	possibly damaging	Het
Olfr715	T	C	7: 107,128,626	I256V	probably benign	Het
Olfr869	T	C	9: 20,137,461	M115T	probably damaging	Het
Orai3	G	T	7: 127,774,022	A232S	probably benign	Het
Pak1ip1	G	A	13: 41,009,251	G177R	probably benign	Het
Pcp4l1	T	C	1: 171,174,406	R62G	possibly damaging	Het
Phox2b	T	A	5: 67,098,721	Q74L	probably benign	Het
Pi4kb	A	G	3: 94,984,486	Y159C	probably damaging	Het
Pkd1l3	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	8: 109,624,195		probably benign	Het
Plxna1	T	C	6: 89,329,559	R1430G	probably null	Het
Plxna4	T	C	6: 32,178,380	H1543R	probably benign	Het
Prcc	A	T	3: 87,869,731	F312Y	probably damaging	Het
Ranbp6	A	G	19: 29,809,988	L988P	probably damaging	Het
Rbm27	A	G	18: 42,327,507	T840A	probably benign	Het
Rchy1	G	T	5: 91,957,972	T39N	probably benign	Het
Rmi1	C	T	13: 58,409,026	T363I	probably benign	Het
Rnpc3	A	C	3: 113,611,246	I420S	probably damaging	Het
Rsph4a	T	A	10: 33,909,398	V435E	probably benign	Het
Rwdd1	T	C	10: 34,012,099	T38A	probably damaging	Het
S100a13	G	T	3: 90,515,863	D54Y	unknown	Het
Sel1l3	T	C	5: 53,154,286	Y619C	probably damaging	Het
Sf3b3	T	C	8: 110,812,026	T1121A	probably damaging	Het
Sgk3	T	C	1: 9,872,309	V102A	probably benign	Het
Sh2b1	T	C	7: 126,469,182	T486A	probably damaging	Het
Slc22a5	C	T	11: 53,876,155	R169H	probably damaging	Het
Slc4a5	T	C	6: 83,289,241	V889A	possibly damaging	Het
Spast	C	A	17: 74,339,074	S13*	probably null	Het
Srek1	T	C	13: 103,753,146		probably null	Het
Sugp1	G	T	8: 70,056,570	E164D	probably benign	Het
Synpo2	T	C	3: 123,117,324	D224G	probably benign	Het
Tanc1	A	G	2: 59,800,088	D804G	probably damaging	Het
Tep1	C	T	14: 50,844,309	C1228Y	probably damaging	Het
Tes	T	A	6: 17,100,342	C325S	probably benign	Het
Themis	T	C	10: 28,863,394	V620A	probably benign	Het
Trim17	T	C	11: 58,971,431	S430P	probably damaging	Het
Tubgcp5	T	C	7: 55,795,945	I65T	possibly damaging	Het
Unc13b	T	C	4: 43,171,955	S928P	unknown	Het
Vat1l	C	T	8: 114,289,432	A354V	probably damaging	Het
Vmn1r170	T	A	7: 23,606,838	S222T	probably benign	Het
Vmn2r112	A	T	17: 22,601,232	M29L	probably benign	Het
Vmn2r72	T	C	7: 85,751,203	I213V	probably benign	Het
Wdr89	T	A	12: 75,632,790	Q230L	possibly damaging	Het
Zfp386	A	G	12: 116,059,663	T334A	probably benign	Het
Zfp442	T	A	2: 150,409,367	H205L	probably benign	Het
Zfyve26	A	T	12: 79,276,302	I890N	possibly damaging	Het
Zic1	T	C	9: 91,364,320	E233G	probably damaging	Het

Other mutations in Lmx1a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02624:Lmx1a	APN	1	167844623	splice site	probably benign
IGL02629:Lmx1a	APN	1	167844623	splice site	probably benign
IGL02637:Lmx1a	APN	1	167844623	splice site	probably benign
IGL02642:Lmx1a	APN	1	167844623	splice site	probably benign
IGL02811:Lmx1a	APN	1	167791374	missense	probably benign	0.06
scooby	UTSW	1	167830687	missense	possibly damaging	0.47
R0320:Lmx1a	UTSW	1	167791404	nonsense	probably null
R1217:Lmx1a	UTSW	1	167791399	missense	probably damaging	1.00
R2897:Lmx1a	UTSW	1	167830540	splice site	probably benign
R4211:Lmx1a	UTSW	1	167832859	missense	probably damaging	0.96
R4976:Lmx1a	UTSW	1	167791554	missense	possibly damaging	0.73
R5125:Lmx1a	UTSW	1	167830687	missense	possibly damaging	0.47
R6858:Lmx1a	UTSW	1	167832881	missense	probably damaging	1.00
R7099:Lmx1a	UTSW	1	167830546	missense	probably damaging	1.00
R7177:Lmx1a	UTSW	1	167846678	missense	probably benign
R7380:Lmx1a	UTSW	1	167692040	missense	probably damaging	1.00
R7831:Lmx1a	UTSW	1	167840952	missense	probably benign	0.06
R8329:Lmx1a	UTSW	1	167689803	missense	probably benign	0.00
Z1176:Lmx1a	UTSW	1	167691999	missense	possibly damaging	0.86

Predicted Primers

PCR Primer
(F):5'- CCATCTGGGGAATATGGCATC -3'
(R):5'- CTGAGCAGCATTCCCTATCAC -3'

Sequencing Primer
(F):5'- GGAATATGGCATCCCAGAGCTTATC -3'
(R):5'- GAGCAGCATTCCCTATCACTCAGAC -3'

Posted On

2022-03-25