Mutagenetix > Incidental Mutation

Incidental Mutation 'R7380:Lmx1a'

572607

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

045462-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.882) question?

Stock #

R7380 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

167516806-167676310 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 167519609 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 46 (F46L)

Ref Sequence

ENSEMBL: ENSMUSP00000028003 (fasta)

Gene Model

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

AlphaFold

Q9JKU8

Predicted Effect

probably damaging
Transcript: ENSMUST00000028003
AA Change: F46L

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000028003
Gene: ENSMUSG00000026686
AA Change: F46L

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 damaging
Transcript: ENSMUST00000111377
AA Change: F46L

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000107008
Gene: ENSMUSG00000026686
AA Change: F46L

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: 98.8%

Validation Efficiency

98% (79/81)

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: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700030J22Rik	T	C	8: 117,700,376 (GRCm39)	T9A	probably benign	Het
Abcc5	A	T	16: 20,215,784 (GRCm39)	S414R	possibly damaging	Het
Acads	C	A	5: 115,249,057 (GRCm39)	Q365H	probably damaging	Het
Ankib1	G	T	5: 3,772,576 (GRCm39)	Q487K	probably benign	Het
BC034090	T	G	1: 155,108,229 (GRCm39)	S11R	probably damaging	Het
Car12	A	G	9: 66,654,945 (GRCm39)	N125S	probably benign	Het
Casq1	A	G	1: 172,044,416 (GRCm39)	V137A	probably benign	Het
Cfap54	C	A	10: 92,883,840 (GRCm39)	V305F	probably damaging	Het
Clstn3	T	C	6: 124,433,948 (GRCm39)	E404G	probably benign	Het
Copg1	T	G	6: 87,870,824 (GRCm39)	L209R	probably damaging	Het
Cpb2	A	T	14: 75,493,449 (GRCm39)	Q42L	possibly damaging	Het
Cpd	G	A	11: 76,693,151 (GRCm39)	Q712*	probably null	Het
Csmd3	T	A	15: 47,450,361 (GRCm39)	Y2690F		Het
Dchs1	G	T	7: 105,407,835 (GRCm39)	T1999K	probably benign	Het
Ddx10	T	A	9: 53,151,786 (GRCm39)	T80S	probably damaging	Het
Dmtn	G	A	14: 70,854,768 (GRCm39)	T69I	probably damaging	Het
Dnah5	T	A	15: 28,370,524 (GRCm39)	H2821Q	probably damaging	Het
Fam162b	T	A	10: 51,466,572 (GRCm39)		probably benign	Het
Fam193b	A	C	13: 55,690,612 (GRCm39)	S717A	probably benign	Het
Far2	T	C	6: 148,082,493 (GRCm39)	F500L	unknown	Het
Focad	T	A	4: 88,192,435 (GRCm39)	V588D	unknown	Het
Gm12728	T	C	4: 105,651,593 (GRCm39)	F68L	probably damaging	Het
Gm1527	T	A	3: 28,974,621 (GRCm39)	M478K	probably benign	Het
Gm57858	T	A	3: 36,080,070 (GRCm39)	D229V	possibly damaging	Het
Gpd2	A	T	2: 57,230,171 (GRCm39)	I308F	probably damaging	Het
Igf2bp3	T	C	6: 49,085,933 (GRCm39)	T249A	probably benign	Het
Igfn1	C	A	1: 135,889,746 (GRCm39)	V2434F	probably damaging	Het
Inhca	G	A	9: 103,156,680 (GRCm39)	Q127*	probably null	Het
Kdm5a	C	A	6: 120,382,879 (GRCm39)	Q737K	probably benign	Het
Khdrbs2	T	C	1: 32,372,685 (GRCm39)	S120P	unknown	Het
Lrba	C	G	3: 86,232,381 (GRCm39)	T776R	probably damaging	Het
Lrrc8c	A	G	5: 105,755,701 (GRCm39)	N492S	possibly damaging	Het
Mapk3	A	T	7: 126,363,967 (GRCm39)	I365F		Het
Mcee	A	G	7: 64,061,657 (GRCm39)	I153M	possibly damaging	Het
Mllt3	T	C	4: 87,710,180 (GRCm39)	D415G	possibly damaging	Het
Muc4	A	T	16: 32,575,740 (GRCm39)	T1747S	unknown	Het
Myh14	A	T	7: 44,310,466 (GRCm39)	V139E	probably damaging	Het
Myo10	A	T	15: 25,779,706 (GRCm39)	I772L	probably benign	Het
Naa15	T	G	3: 51,367,268 (GRCm39)		probably null	Het
Nbeal1	T	A	1: 60,283,969 (GRCm39)	I841N	probably damaging	Het
Nf1	C	T	11: 79,437,102 (GRCm39)	T2006I	probably damaging	Het
Npr2	T	A	4: 43,641,254 (GRCm39)	W427R	probably damaging	Het
Nr1h3	A	T	2: 91,020,540 (GRCm39)	F324L	possibly damaging	Het
Obscn	T	C	11: 58,947,740 (GRCm39)	K4430E		Het
Or1e1d-ps1	T	A	11: 73,819,013 (GRCm39)	Y61N	possibly damaging	Het
Or5ac21	A	G	16: 59,124,391 (GRCm39)	R292G	probably damaging	Het
Or6c2	A	T	10: 129,362,530 (GRCm39)	T145S	probably benign	Het
Or6d13	T	C	6: 116,517,894 (GRCm39)	L160P	probably benign	Het
Osgin1	T	A	8: 120,172,170 (GRCm39)	H321Q	probably benign	Het
P4ha1	A	G	10: 59,186,273 (GRCm39)	I251V	probably benign	Het
Padi2	G	A	4: 140,644,997 (GRCm39)	W77*	probably null	Het
Pkd1	T	A	17: 24,800,616 (GRCm39)	I3086N	probably damaging	Het
Plk3	T	C	4: 116,988,350 (GRCm39)	N360S	probably benign	Het
Prr14	A	T	7: 127,075,614 (GRCm39)	S541C	probably null	Het
Ptch2	C	A	4: 116,971,843 (GRCm39)	Q1122K	possibly damaging	Het
Rab3gap1	T	C	1: 127,865,727 (GRCm39)	V764A	possibly damaging	Het
Rad50	T	C	11: 53,586,223 (GRCm39)	I258V	probably benign	Het
Rapgef3	G	T	15: 97,664,672 (GRCm39)	R64S	probably benign	Het
Rbm44	A	G	1: 91,079,938 (GRCm39)	N42S	possibly damaging	Het
Ring1	T	C	17: 34,240,694 (GRCm39)	Y361C	probably damaging	Het
Robo3	T	C	9: 37,329,852 (GRCm39)	T1155A	probably damaging	Het
Rsf1	GGCGG	GGCGGTGGCCGCGG	7: 97,229,122 (GRCm39)		probably benign	Het
Ryr3	T	C	2: 112,470,502 (GRCm39)	T4682A	probably damaging	Het
Scart1	A	T	7: 139,804,790 (GRCm39)	N598Y	possibly damaging	Het
Sema7a	T	C	9: 57,868,847 (GRCm39)	V653A	unknown	Het
Slc16a13	T	C	11: 70,110,105 (GRCm39)	Y132C	probably damaging	Het
Slc24a1	A	G	9: 64,855,815 (GRCm39)	V364A	unknown	Het
Slc8a2	C	T	7: 15,868,278 (GRCm39)	A170V	probably damaging	Het
Slfn8	C	T	11: 82,894,566 (GRCm39)	R691Q	not run	Het
Snx2	T	C	18: 53,327,640 (GRCm39)	V122A	probably benign	Het
Sstr1	A	T	12: 58,260,066 (GRCm39)	M230L	probably benign	Het
Themis2	C	T	4: 132,513,528 (GRCm39)	V233I	possibly damaging	Het
Tmem106b	T	C	6: 13,078,167 (GRCm39)	S121P	probably damaging	Het
Tmem63c	A	G	12: 87,124,722 (GRCm39)	I529V	probably benign	Het
Tmem94	T	C	11: 115,686,971 (GRCm39)		probably null	Het
Trmt10c	A	T	16: 55,854,619 (GRCm39)	W339R	probably damaging	Het
Ugt2b1	A	T	5: 87,065,578 (GRCm39)	F487Y	not run	Het
Vmn2r91	T	A	17: 18,356,838 (GRCm39)	L835*	probably null	Het
Vps52	C	A	17: 34,177,283 (GRCm39)	N108K	possibly damaging	Het
Wdpcp	T	A	11: 21,661,585 (GRCm39)	C286S	possibly damaging	Het
Zfp959	T	A	17: 56,205,551 (GRCm39)	H529Q	possibly damaging	Het

Other mutations in Lmx1a

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02624:Lmx1a	APN	1	167,672,192 (GRCm39)	splice site	probably benign
IGL02629:Lmx1a	APN	1	167,672,192 (GRCm39)	splice site	probably benign
IGL02637:Lmx1a	APN	1	167,672,192 (GRCm39)	splice site	probably benign
IGL02642:Lmx1a	APN	1	167,672,192 (GRCm39)	splice site	probably benign
IGL02811:Lmx1a	APN	1	167,618,943 (GRCm39)	missense	probably benign	0.06
scooby	UTSW	1	167,658,256 (GRCm39)	missense	possibly damaging	0.47
R0320:Lmx1a	UTSW	1	167,618,973 (GRCm39)	nonsense	probably null
R1217:Lmx1a	UTSW	1	167,618,968 (GRCm39)	missense	probably damaging	1.00
R2897:Lmx1a	UTSW	1	167,658,109 (GRCm39)	splice site	probably benign
R4211:Lmx1a	UTSW	1	167,660,428 (GRCm39)	missense	probably damaging	0.96
R4976:Lmx1a	UTSW	1	167,619,123 (GRCm39)	missense	possibly damaging	0.73
R5125:Lmx1a	UTSW	1	167,658,256 (GRCm39)	missense	possibly damaging	0.47
R6858:Lmx1a	UTSW	1	167,660,450 (GRCm39)	missense	probably damaging	1.00
R7099:Lmx1a	UTSW	1	167,658,115 (GRCm39)	missense	probably damaging	1.00
R7177:Lmx1a	UTSW	1	167,674,247 (GRCm39)	missense	probably benign
R7831:Lmx1a	UTSW	1	167,668,521 (GRCm39)	missense	probably benign	0.06
R8329:Lmx1a	UTSW	1	167,517,372 (GRCm39)	missense	probably benign	0.00
R9269:Lmx1a	UTSW	1	167,658,194 (GRCm39)	missense	probably benign	0.03
Z1176:Lmx1a	UTSW	1	167,519,568 (GRCm39)	missense	possibly damaging	0.86

Predicted Primers

PCR Primer
(F):5'- CGTCATCGTCACTTGGTTTG -3'
(R):5'- TTACTGGCCTTTCCTGCGAG -3'

Sequencing Primer
(F):5'- CACTTGGTTTGATTTTTCGGAATATC -3'
(R):5'- TGCGAGTGCCTCCTCGAAG -3'

Posted On

2019-09-13